abutils - npm Package Compare versions

Comparing version 0.4.17 to 0.4.18

abutils.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: abutils
-Version: 0.4.17
+Version: 0.4.18
 Summary: Utilities for analysis of adaptive immune receptor repertoire (AIRR) data
@@ -5,0 +5,0 @@ Home-page: https://github.com/briney/abutils

abutils.egg-info/SOURCES.txt

@@ -19,145 +19,2 @@ LICENSE
 abutils.egg-info/top_level.txt
-abutils/bin/cdhit_darwin_amd64
-abutils/bin/cdhit_darwin_arm64
-abutils/bin/cdhit_linux_amd64
-abutils/bin/fastp_darwin
-abutils/bin/fastp_linux
-abutils/bin/fasttree_darwin_amd64
-abutils/bin/fasttree_darwin_arm64
-abutils/bin/fasttree_linux_amd64
-abutils/bin/mafft_darwin
-abutils/bin/mafft_linux
-abutils/bin/mmseqs_darwin_amd64
-abutils/bin/mmseqs_darwin_arm64
-abutils/bin/mmseqs_linux_amd64
-abutils/bin/muscle3_darwin
-abutils/bin/muscle3_linux
-abutils/bin/muscle_darwin_amd64
-abutils/bin/muscle_darwin_arm64
-abutils/bin/muscle_linux_amd64
-abutils/bin/vsearch_darwin_amd64
-abutils/bin/vsearch_darwin_arm64
-abutils/bin/vsearch_linux_amd64
-abutils/bin/mafft_darwin_amd64/in
-abutils/bin/mafft_darwin_amd64/mafft.bat
-abutils/bin/mafft_darwin_amd64/mafftdir/bin/mafft
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/addsingle
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/contrafoldwrap
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/countlen
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/dash_client
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/disttbfast
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/dndblast
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/dndfast7
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/dndpre
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/dvtditr
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/f2cl
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/filter
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/getlag
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/hex2maffttext
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/mafft-distance
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/mafft-homologs.1
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/mafft-profile
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/mafft.1
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/mafftash_premafft.pl
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/maffttext2hex
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/makedirectionlist
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/mccaskillwrap
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/multi2hat3s
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/nodepair
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/pairash
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/pairlocalalign
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/regtable2seq
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/replaceu
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/restoreu
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/score
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/seekquencer_premafft.pl
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/seq2regtable
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/setcore
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/setdirection
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/sextet5
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/splittbfast
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/tbfast
-abutils/bin/mafft_darwin_amd64/mafftdir/libexec/version
-abutils/bin/mafft_darwin_arm64/in
-abutils/bin/mafft_darwin_arm64/mafft.bat
-abutils/bin/mafft_darwin_arm64/mafftdir/bin/mafft
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/addsingle
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/contrafoldwrap
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/countlen
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/dash_client
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/disttbfast
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/dndblast
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/dndfast7
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/dndpre
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/dvtditr
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/f2cl
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/filter
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/getlag
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/hex2maffttext
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/mafft-distance
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/mafft-homologs.1
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/mafft-profile
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/mafft.1
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/mafftash_premafft.pl
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/maffttext2hex
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/makedirectionlist
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/mccaskillwrap
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/multi2hat3s
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/nodepair
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/pairash
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/pairlocalalign
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/regtable2seq
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/replaceu
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/restoreu
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/score
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/seekquencer_premafft.pl
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/seq2regtable
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/setcore
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/setdirection
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/sextet5
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/splittbfast
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/tbfast
-abutils/bin/mafft_darwin_arm64/mafftdir/libexec/version
-abutils/bin/mafft_linux_amd64/mafft.bat
-abutils/bin/mafft_linux_amd64/mafftdir/bin/mafft
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/addsingle
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/contrafoldwrap
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/countlen
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/dash_alignments
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/dash_client
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/dash_sequences.fa
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/disttbfast
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/dndblast
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/dndfast7
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/dndpre
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/dvtditr
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/f2cl
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/filter
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/getlag
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/hat3
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/hex2maffttext
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/mafft-distance
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/mafft-homologs.1
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/mafft-profile
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/mafft.1
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/mafftash_premafft.pl
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/maffttext2hex
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/makedirectionlist
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/mccaskillwrap
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/multi2hat3s
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/nodepair
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/pairash
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/pairlocalalign
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/regtable2seq
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/replaceu
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/restoreu
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/score
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/seekquencer_premafft.pl
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/seq2regtable
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/setcore
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/setdirection
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/sextet5
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/splittbfast
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/tbfast
-abutils/bin/mafft_linux_amd64/mafftdir/libexec/version
 abutils/core/__init__.py
@@ -164,0 +21,0 @@ abutils/core/lineage.py

abutils/__init__.py

@@ -6,3 +6,3 @@ # from .core import *
 
-# from . import bin, cl, io, pl, tl
+from . import bin, cl, io, pl, tl
 from . import cl as color
@@ -37,2 +37,2 @@ from .core import lineage, pair, sequence
 
-BINARY_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), "bin"))
+BINARY_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), "binaries"))

abutils/bin.py

@@ -44,3 +44,3 @@ #!/usr/bin/env python
 
-BIN_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), "bin")
+BIN_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), "binaries")
 SYSTEM = platform.system().lower()
@@ -47,0 +47,0 @@ MACHINE = platform.machine().lower().replace("x86_64", "amd64")

abutils/version.py

@@ -6,2 +6,2 @@ # Store the version here so:
 
-__version__ = "0.4.17"
+__version__ = "0.4.18"

PKG-INFO

 Metadata-Version: 2.1
 Name: abutils
-Version: 0.4.17
+Version: 0.4.18
 Summary: Utilities for analysis of adaptive immune receptor repertoire (AIRR) data
@@ -5,0 +5,0 @@ Home-page: https://github.com/briney/abutils

abutils/bin/mafft_darwin_amd64/mafft.bat

-#! /bin/sh
-
-pushd "`dirname "$0"`" > /dev/null 2>&1; rootdir="$PWD"; popd > /dev/null 2>&1;
-MAFFT_BINARIES="$rootdir/mafftdir/libexec"; export MAFFT_BINARIES;
-
-"$rootdir/mafftdir/bin/mafft" "$@"
-# $1 can have space in file name

abutils/bin/mafft_...4/mafftdir/libexec/mafftash_premafft.pl

-#!/usr/bin/perl
-
-#####################################################################
-# Author:  KM Amada ([e-mail])
-#
-# Ver. Date      Changelog
-#####################################################################
-# 1.0  07.26.13  Initial release
-# 2.0  09.03.13  Added extensive warnings and error messages
-# 3.0  10.28.13  Fix for retrieving large files. Added STDERR logs
-# 3.1  11.08.13  Added LWP failsafe. Made hat3 not a required output
-# 3.2  12.08.14  Removed 5-char restriction for own structure files
-#
-#####################################################################
-
-use strict;
-use Getopt::Long;
-use File::Path qw(make_path remove_tree);
-use LWP::Simple;
-use LWP::UserAgent;
-
-# to prevent error 'Header line too long (limit is 8192)' [v3.1]
-use LWP::Protocol::http;
-push(@LWP::Protocol::http::EXTRA_SOCK_OPTS, MaxLineLength => 0);
-
-
-
-my $BASEURL = "http://sysimm.ifrec.osaka-u.ac.jp/MAFFTash/REST/service.cgi/premafft";
-
-my ( $WORKDIR, $PDBLIST, $OWNLIST, $HAT3FILE, $INSTRFILE );
-
-GetOptions
-(
-    'd=s' => \$WORKDIR,
-    'p=s' => \$PDBLIST,
-    'o=s' => \$OWNLIST,
-    'h=s' => \$HAT3FILE,
-    'i=s' => \$INSTRFILE,
-);
-
-print STDERR "[MAFFTash-premafft]\n";
-
-# set temp directory
-my $TMP = "/tmp/mapremafft$$";
-make_path($TMP) unless -d $TMP;
-
-
-
-######
-# validation
-&help("Required parameter : atleast one of either '-p' or '-o'") unless ( defined $PDBLIST || defined $OWNLIST);
-&help("Required parameter : '-d'") if defined $OWNLIST && ! defined $WORKDIR;
-
-$HAT3FILE = "hat3" unless defined $HAT3FILE;
-$INSTRFILE = "instr" unless defined $INSTRFILE;
-chop $WORKDIR if defined $WORKDIR && $WORKDIR =~ m/\/$/g;
-
-
-######
-# prepare inputs
-print STDERR "Preparing inputs for service request...\n";
-
-my @files = ();
-push(@files, "strweight" => "0.5");
-push(@files, "premafft" => "1");
-
-
-# pdb entries
-if ( defined $PDBLIST )
-{
-    print STDERR "PDB List defined!\n";
-    &bail("Error: Input file $PDBLIST does not exists!") unless -e $PDBLIST;
-    my $listfile = "$TMP/pdblist.inp";
-
-
-    open(INPF,"<$PDBLIST") or &bail("Error: Cannot open file $PDBLIST for reading!");
-    open(OUTF,">$listfile") or &bail("Error: Cannot open temporary file $listfile for writing!");
-
-    while(<INPF>)
-    {
-        chomp;
-        if ( /^(\w{5})$/ )
-        {
-            print OUTF ">PDBID\n$1\n";
-        }
-    }
-
-    close OUTF;
-    close INPF;
-
-    push(@files, "inputfile" => ["$listfile"]);
-}
-
-
-
-# upload own structures
-my %ownids = ();
-
-if ( defined $OWNLIST  )
-{
-    print STDERR "OWN List defined!\n";
-    &bail("Error: Input file $OWNLIST does not exists!") unless -e $OWNLIST;
-
-
-    open(OWNINPF,"<$OWNLIST") or &bail("Error: Cannot open file $OWNLIST for reading!");
-
-    while(<OWNINPF>)
-    {
-        chomp;
-
-        if ( /^(\S+)$/ )
-        {
-            my $fileref = "$WORKDIR/$1.pdb";
-
-            unless (-e $fileref)
-            {
-                close OWNINPF;
-                &bail("Error: File $fileref does not exists!");
-            }
-
-            push(@files, "inputownfile[]" => ["$fileref"]);
-            $ownids{$1} = 1;
-        }
-    }
-
-    close OWNINPF;
-}
-
-
-
-######
-# start rest service
-print STDERR "Sending service request...\n";
-
-my $browser = LWP::UserAgent->new;
-$browser->timeout(0);
-
-
-# post: running a mafftash job
-my $postResponse = $browser->post( $BASEURL, \@files, 'Content_Type' => 'form-data' );
-&bail(sprintf("[%d] %s\n", $postResponse->code, &parseError($postResponse->content))) unless($postResponse->is_success);
-
-
-# get response from post request
-my ($status, $mafftashid) = &parseResponse($postResponse->content);
-
-
-
-my $MAXTRIES = 3;
-my $STIMER = 4;
-my $longtimer = 0;
-
-print STDERR "Request sent! Waiting for response...[$mafftashid]\n";
-
-
-# wait for results until it becomes available
-while(1)
-{
-    $longtimer = $longtimer <= ($STIMER*3) ? $longtimer+$STIMER : $STIMER;
-    sleep $longtimer;
-
-
-    # get: get results for mafftash job
-    my $getResponse = $browser->get("$BASEURL/$mafftashid");
-
-    if ( $getResponse->is_success )
-    {
-
-        # get response from get request
-        ($status, $mafftashid) = &parseResponse($getResponse->content);
-        next unless ( $status eq "done" );
-
-
-        # if job is finished and ready
-        print STDERR "Results found!\n";
-        my $csfile = "$TMP/checksum.tar.gz";
-        my $try1 = 1;
-
-
-        while(1)
-        {
-            print STDERR "Fetching Results... [Trial $try1]\n";
-
-            if ( is_success(getstore("$BASEURL/getmdlist/$mafftashid", $csfile)) && -e $csfile && -s $csfile )
-            {
-                # get response from get request
-                my $checklist = &extractchecksum($csfile);
-                &bail("Error retrieving list of compressed files!") unless ( scalar %$checklist > 0 );
-
-
-                foreach my $id ( keys %$checklist )
-                {
-                    my $checkfile = "$TMP/$id";
-                    my $checkid = $checklist->{$id};
-                    my $try2 = 1;
-
-                    while(1)
-                    {
-                        unlink $checkfile if -e $checkfile;
-
-                        if ( is_success(getstore("$BASEURL/get/$mafftashid/$id", $checkfile)) && -e $checkfile && -s $checkfile )
-                        {
-                            my $hashid = &getchecksum($checkfile);
-                            #print STDERR "[hashid]$hashid [checkid]$checkid\n";
-
-                            if ($hashid ne "" && $hashid ne $checkid )
-                            {
-                                unlink $checkfile if -e $checkfile;
-                                &bail("Error retrieving compressed file from server! [Checksum Failed]") if $try2 >= $MAXTRIES;
-                                $try2++;
-                                sleep $STIMER;
-                            }
-                            else
-                            {
-                                last;
-                            }
-                        }
-                        else
-                        {
-                            &bail("Error retrieving compressed file from server!") if $try2 >= $MAXTRIES;
-                            $try2++;
-                            sleep $STIMER;
-                        }
-                    }
-                }
-
-                last;
-            }
-            else
-            {
-                &bail("Error retrieving list of compressed files from server!") if $try1 >= $MAXTRIES;
-                $try1++;
-                sleep $STIMER;
-            }
-        }
-
-        last;
-
-    }
-    else
-    {
-        &bail(sprintf("[%d] %s\n", $getResponse->code, &parseError($getResponse->content)));
-    }
-
-}
-
-
-# make sure outputs were generated
-# decompress
-print STDERR "Assembling final results...\n";
-
-&backticks("cat $TMP/archive.tar.gz* | tar -zxf - -C $TMP/");
-&backticks("mv -f $TMP/instr $INSTRFILE") if -e "$TMP/instr";
-&backticks("mv -f $TMP/hat3 $HAT3FILE") if -e "$TMP/hat3";
-
-# sometimes no hat3 file is generated [v3.1]
-#&bail("Error: Output file $HAT3FILE not found!") unless -e $HAT3FILE;
-&bail("Error: Output file $INSTRFILE not found!") unless -e $INSTRFILE;
-
-
-# warn if some ownids were ommitted
-if ( scalar keys(%ownids) > 0 )
-{
-    my %instrids = ();
-
-    open(INSTRF,"<$INSTRFILE") or &bail("Error: Cannot open file $INSTRFILE for reading!");
-
-    while(<INSTRF>)
-    {
-        chomp;
-
-        if ( /^>\d+_(\S+)$/ )
-        {
-            $instrids{$1} = 1;
-        }
-    }
-
-    close INSTRF;
-
-    foreach my $id ( keys %ownids )
-    {
-        warn "Warning: Own structure $id was excluded from instr/hat3.\n" unless $instrids{$id};
-    }
-
-}
-
-
-
-&cleanup();
-
-
-
-####################
-####################
-
-
-
-sub parseResponse
-{
-    my $response = shift;
-
-    #"status":"wait","mafftashid":"Ma8211432R"
-
-    my $status = "";
-    my $mafftashid = "";
-
-    if ( $response =~ /^([^\s:]+):([^\s:]+)$/ )
-    {
-        $mafftashid = $1;
-        $status = $2;
-    }
-
-    return ($status, $mafftashid);
-
-}
-
-
-sub extractchecksum
-{
-    my $infile = shift;
-    my %dataset = ();
-
-    open CSUM, "tar -zxf $infile -O|" or return \%dataset;
-
-    while(<CSUM>)
-    {
-        chomp;
-        if ( /^(\S+)\s+(\S+)$/ )
-        {
-            $dataset{$2} = $1;
-        }
-
-    }
-
-    close CSUM;
-
-    return \%dataset;
-
-}
-
-
-sub parseError
-{
-    my $response = shift;
-
-    #"error":"Invalid number of inputs found."
-    my $errorstr = ( $response =~ /\"error\"\s*:\s*\"([^\"]+)\"/ ) ? $1 : "";
-    return $errorstr;
-}
-
-
-sub getchecksum
-{
-    my $infile = shift;
-
-    # md5 binary check
-    my $MD5BIN = "";
-
-    if ( -x "/usr/bin/md5sum" )
-    {
-        $MD5BIN = "/usr/bin/md5sum";
-    }
-    elsif ( -x "/sbin/md5" )
-    {
-        $MD5BIN = "/sbin/md5 -q";
-    }
-
-    return "" if $MD5BIN eq "";
-
-
-    my $checksum = "";
-    open MD5EXE, "$MD5BIN $infile|" or return "";
-
-    while(<MD5EXE>)
-    {
-        if (/^(\S+)\s+(\S+)$/)
-        {
-            $checksum = $1;
-            last;
-        }
-        elsif (/^(\S+)$/)
-        {
-            $checksum = $1;
-            last;
-        }
-    }
-
-    close MD5EXE;
-
-    return $checksum;
-
-}
-
-
-sub backticks
-{
-    my $command = shift;
-
-    `$command`;
-    return ($? == -1) ? 0 : 1;
-}
-
-
-sub bail
-{
-    my $str = shift;
-    print STDERR "$str\n" if defined $str;
-
-    &cleanup();
-    exit(1);
-}
-
-
-sub cleanup
-{
-    return if ($TMP eq "" || !-d $TMP);
-
-    opendir(MAINDIR, $TMP);
-    my @files = readdir(MAINDIR);
-    closedir(MAINDIR);
-
-    foreach my $file (@files)
-    {
-        unlink "$TMP/$file" if -e "$TMP/$file";
-    }
-
-    remove_tree($TMP);
-
-}
-
-
-sub help
-{
-    my $str = shift;
-
-    print <<'HELPME';
-
-USAGE
-  ./mafftash_premafft.pl -p [FILE]
-  ./mafftash_premafft.pl -o [FILE] -d [DIRECTORY]
-  ./mafftash_premafft.pl -p [FILE] -o [FILE] -d [DIRECTORY]
-
-
-PARAMETERS
-  -p [FILE]
-     FILE contains a list of PDBIDs (one entry per line); make sure that the PDBIDs are in the standard 5-character pdbid+chain naming format
-
-  -o [FILE] -d [DIRECTORY]
-     FILE contains a list of IDs from your own structure/pdb files (one entry per line)
-     for each ID in the list make sure that a corresponding structure file (same ID with .pdb extension) is stored in DIRECTORY
-
-  -h [HATFILE]
-     save the output hat3 file in HATFILE; if not set, the output is written to a file named 'hat3' in your current directory
-
-  -i [INSTRFILE]
-     save the output instr file in INSTRFILE; if not set, the output is written to a file named 'instr' in your current directory
-
-HELPME
-
-    &bail($str);
-}
-
-
-

abutils/bin/mafft_...afftdir/libexec/seekquencer_premafft.pl

-#!/usr/bin/perl
-
-####################################################################################
-# Author:  KM Amada ([e-mail])
-#
-# Ver. Date      Changelog
-####################################################################################
-# 1.0  11.01.13  Initial release
-#
-# **Skipped version 2 to standardise version numbers to seekquencer.pl script**
-#
-# 3.0  04.24.14  Added split option -mod <mafftash-split> for output
-#                Uses seekquencer_v3 backend
-#
-# 4.0  05.12.14  Added new options: -run <thread|normal> -trd <count> -noin
-#                Sets -seqa fast in seekquencer.pl
-#                Uses seekquencer_v4 backend
-#
-# 4.1  05.19.14  Added a check on running REST requests before proceeding
-#                to avoid server load problems
-#
-# 4.2  05.27.14  Seq limit processing done in seekquencer.pl script
-#                to avoid server load problems
-#
-# 4.3  07.22.14  Added new option: -seqd <uniref100|uniref90|uniref70|uniprot>
-#                Blast limit changed from factor of 10 to -blim option
-#                Timing on sleep changed; added srand() for making seed
-#                Moved the job limit processing to server side
-#
-# 4.4  08.05.14  Modified to work in multiple OS
-#
-#
-####################################################################################
-
-use strict;
-use Getopt::Long;
-use File::Path qw(make_path remove_tree);
-use Cwd;
-use LWP::Simple;
-use LWP::UserAgent;
-
-# to prevent error: Header line too long (limit is 8192)
-use LWP::Protocol::http;
-push(@LWP::Protocol::http::EXTRA_SOCK_OPTS, MaxLineLength => 0);
-
-
-
-my $BASEURL = "http://sysimm.ifrec.osaka-u.ac.jp/seekquencer/REST/service.cgi/premafft";
-my ( $INPUTFILE, $IDLISTFILE, $SEQFASTAFILE, $OUTPUTFILE, $SEQFLAG, $STRFLAG, $EVALFLAG, $NOINFLAG );
-my $OUTTYPE = "mafftash";
-
-my $SEQDATABASE = "uniref100";
-my $SEQLIMIT = 100;
-my $SEQBLASTLIMIT = 100;
-
-my $RUNMODE = "normal";    # thread|normal
-my $THREADCOUNT = 3;
-
-
-GetOptions
-(
-    'inp=s'  => \$INPUTFILE,
-    'idf=s'  => \$IDLISTFILE,
-    'seqf=s' => \$SEQFASTAFILE,
-    'out=s'  => \$OUTPUTFILE,
-    'str'    => \$STRFLAG,
-    'seq'    => \$SEQFLAG,
-    'seqd=s' => \$SEQDATABASE,
-    'lim=i'  => \$SEQLIMIT,
-    'blim=i' => \$SEQBLASTLIMIT,
-    'pre'    => \$EVALFLAG,
-    'noin'   => \$NOINFLAG,
-    'mod=s'  => \$OUTTYPE,
-    'run=s'  => \$RUNMODE,
-    'trd=i'  => \$THREADCOUNT,
-
-
-);
-
-my $ISWINDOWS = ( $^O =~ /^MSWin/ ) ? 1 : 0;
-print STDERR "[Seekquencer-premafft 4.4 on $^O]\n";
-
-
-# set temp directory
-my $CWD = getcwd;
-my $TMP = "$CWD/seekpremafft$$";
-make_path($TMP) unless -d $TMP;
-
-
-
-######
-# validation
-help("Required parameter: define input as '-inp' or '-idf' or '-seqf'") if ( !defined $INPUTFILE && !defined $IDLISTFILE && !defined $SEQFASTAFILE );
-help("'-inp' is already defined") if ( defined $INPUTFILE && (defined $IDLISTFILE || defined $SEQFASTAFILE) );
-help("Input file $INPUTFILE does not exist (or filesize is 0)") if ( defined $INPUTFILE && (! -e $INPUTFILE || !-s $INPUTFILE) );
-help("Input file $IDLISTFILE does not exist (or filesize is 0)") if ( defined $IDLISTFILE && (! -e $IDLISTFILE || !-s $IDLISTFILE) );
-help("Input file $SEQFASTAFILE does not exist (or filesize is 0)") if ( defined $SEQFASTAFILE && (! -e $SEQFASTAFILE || !-s $SEQFASTAFILE) );
-help("Required parameter: output file '-out'") unless ( defined $OUTPUTFILE );
-help("Set either '-str' or '-seq' or dont set any at all") if ( defined $STRFLAG && defined $SEQFLAG );
-
-help("Invalid value for '-seqd <uniref100|uniref90|uniref70|uniprot>'") if ( $SEQDATABASE ne "uniref100" && $SEQDATABASE ne "uniref90" && $SEQDATABASE ne "uniref70" && $SEQDATABASE ne "uniprot");
-help("Invalid value for '-mod <fasta|mafftash|mafftash-split>'") if ( $OUTTYPE ne "fasta" && $OUTTYPE ne "mafftash" && $OUTTYPE ne "mafftash-split" );
-help("Invalid value for '-run <thread|normal>'") if ( $RUNMODE ne "thread" && $RUNMODE ne "normal" );
-help("Invalid value for '-trd <count>'; count should be between 1 and 5 (inclusive)") if ( $RUNMODE eq "thread" && ($THREADCOUNT <= 0 || $THREADCOUNT > 5) );
-
-
-######
-# check existing requests
-print STDERR "Checking server status...\n";
-
-# generate seed
-srand($$);
-
-# sleep a bit to give time for lsf response
-sleep(int(rand(6))+1);
-
-
-my $browser = LWP::UserAgent->new;
-$browser->timeout(0);
-
-# get: check if you can send a new request this time
-my $jobsResponse = $browser->get("$BASEURL/isAllowed");
-
-if ( $jobsResponse->is_success )
-{
-    my $status = parseJobQueryResponse($jobsResponse->content);
-    bail("Max jobs reached. The server cannot process your request right now; try again later.", 0) unless $status > 0;
-}
-else
-{
-    bail(sprintf("[%d] %s\n", $jobsResponse->code, parseError($jobsResponse->content)));
-}
-
-
-######
-# make a temporary input if lists were provided
-unless ( defined $INPUTFILE )
-{
-    $INPUTFILE = "$TMP/input.homemade";
-    open INPF, ">$INPUTFILE" or bail("Error writing to input file.");
-
-    if ( defined $IDLISTFILE )
-    {
-        open IDLIST, "<$IDLISTFILE" or bail("Error reading input file.");
-        while( <IDLIST> )
-    	{
-        	chomp;
-        	if ( /(\w{5})/ )
-        	{
-        	    print INPF ">PDBID\n$1\n";
-        	}
-        }
-        close IDLIST;
-    }
-
-
-    if ( defined $SEQFASTAFILE )
-    {
-        open FASTA, "<$SEQFASTAFILE" or bail("Error reading input file.");
-        while( <FASTA> )
-    	{
-        	chomp;
-            print INPF "$_\n";
-        }
-        close FASTA;
-    }
-
-    close INPF;
-}
-
-
-######
-# prepare parameters
-print STDERR "Preparing parameters for service request...\n";
-
-my @parameters = ();
-push(@parameters, "fileinput" => ["$INPUTFILE"]);
-push(@parameters, "out_type" => $OUTTYPE);
-
-push(@parameters, "rest_flag" => "1");
-push(@parameters, "cls_flag" => "1");
-push(@parameters, "pre_flag" => "1") if defined $EVALFLAG;
-push(@parameters, "noin_flag" => "1") if defined $NOINFLAG;
-
-push(@parameters, "run_mode" => $RUNMODE);
-push(@parameters, "thread_count" => $THREADCOUNT) if $RUNMODE eq "thread";
-
-
-if ( defined $STRFLAG )
-{
-    push(@parameters, "str_flag" => "1");
-    push(@parameters, "ash_flag" => "1");
-}
-elsif ( defined $SEQFLAG )
-{
-    push(@parameters, "seq_flag" => "1");
-    push(@parameters, "seq_algorithm" => "fast");
-    push(@parameters, "seq_database" => $SEQDATABASE);
-    push(@parameters, "seq_blastlimit" => $SEQBLASTLIMIT);
-    push(@parameters, "seq_outputlimit" => $SEQLIMIT);
-}
-else
-{
-    push(@parameters, "str_flag" => "1");
-    push(@parameters, "ash_flag" => "1");
-    push(@parameters, "seq_flag" => "1");
-    push(@parameters, "seq_algorithm" => "fast");
-    push(@parameters, "seq_database" => $SEQDATABASE);
-    push(@parameters, "seq_blastlimit" => $SEQBLASTLIMIT);
-    push(@parameters, "seq_outputlimit" => $SEQLIMIT);
-}
-
-
-
-######
-# start rest service
-print STDERR "Sending service request...\n";
-
-# post: running a mafftash job
-my $postResponse = $browser->post( $BASEURL, \@parameters, 'Content_Type' => 'form-data' );
-bail(sprintf("[%d] %s\n", $postResponse->code, parseError($postResponse->content))) unless($postResponse->is_success);
-
-
-# get response from post request
-my ($status, $seekid) = parseResponse($postResponse->content);
-
-my $MAXTRIES = 3;
-my $STIMER = 5;
-my $timer = 0;
-
-print STDERR "Request sent! Waiting for response...[$seekid]\n";
-
-my $checklist = {};
-
-# wait for results until it becomes available
-while(1)
-{
-    # sleeps for 5+random, 10+random, 15+random, 20+random, 25+random, 30+random ,,, 60+random, 60+random,,,
-    $timer = $timer >= 60 ? 60 : $timer+$STIMER;
-    sleep($timer+int(rand(4)));
-
-    # get: get results for mafftash job
-    my $getResponse = $browser->get("$BASEURL/$seekid");
-
-    if ( $getResponse->is_success )
-    {
-
-        # get response from get request
-        ($status, $seekid) = parseResponse($getResponse->content);
-        next unless ( $status eq "done" );
-
-
-        # if job is finished and ready
-        print STDERR "Results found!\n";
-        my $csfile = "$TMP/checksum";
-        my $try1 = 1;
-
-
-        while(1)
-        {
-            print STDERR "Fetching Results... [Trial $try1]\n";
-
-            if ( is_success(getstore("$BASEURL/get/$seekid/checksum", $csfile)) && -e $csfile && -s $csfile )
-            {
-                # get response from get request
-                $checklist = extractchecksum($csfile);
-                bail("Error retrieving list of compressed files!") unless ( scalar %$checklist > 0 );
-
-
-                foreach my $id ( sort keys %$checklist )
-                {
-                    sleep 1;
-                    my $checkfile = "$TMP/$id";
-                    my $checkid = $checklist->{$id};
-                    my $try2 = 1;
-
-                    while(1)
-                    {
-                        unlink $checkfile if -e $checkfile;
-
-                        if ( is_success(getstore("$BASEURL/get/$seekid/$id", $checkfile)) && -e $checkfile && -s $checkfile )
-                        {
-                            last if $ISWINDOWS;
-
-                            my $hashid = getchecksum($checkfile);
-                            #print STDERR "[hashid]$hashid [checkid]$checkid\n";
-
-                            if ($hashid ne "" && $hashid ne $checkid )
-                            {
-                                #unlink $checkfile if -e $checkfile;
-                                bail("Error retrieving compressed file from server! [Checksum Failed]") if $try2 >= $MAXTRIES;
-                                $try2++;
-                                sleep $STIMER;
-                            }
-                            else
-                            {
-                                last;
-                            }
-                        }
-                        else
-                        {
-                            bail("Error retrieving compressed file from server!") if $try2 >= $MAXTRIES;
-                            $try2++;
-                            sleep $STIMER;
-                        }
-                    }
-                }
-
-                last;
-            }
-            else
-            {
-                bail("Error retrieving list of compressed files from server!") if $try1 >= $MAXTRIES;
-                $try1++;
-                sleep $STIMER;
-            }
-        }
-
-        last;
-
-    }
-    else
-    {
-        bail(sprintf("[%d] %s\n", $getResponse->code, parseError($getResponse->content)));
-    }
-
-}
-
-
-# make sure outputs were generated
-# decompress
-print STDERR "Assembling final results...\n";
-
-foreach my $id ( sort keys %$checklist )
-{
-    if ( $id =~ /^$seekid\.out(\.str|\.seq)?/  )
-    {
-        bail("Error: Output file corrupted!") unless -e "$TMP/$id";
-        appendToFile("$TMP/$id","$OUTPUTFILE".$1);
-    }
-}
-
-cleanup();
-
-
-
-####################
-####################
-
-
-sub parseResponse
-{
-    my $response = shift;
-    my $status = "";
-    my $seekid = "";
-
-    if ( $response =~ /^([^\s:]+):([^\s:]+)$/ )
-    {
-        $seekid = $1;
-        $status = $2;
-    }
-
-    return ($status, $seekid);
-}
-
-
-sub parseJobQueryResponse
-{
-    my $response = shift;
-    my $jobs = 100;
-
-    if ( $response =~ /^(\d+)$/ )
-    {
-        $jobs = $1;
-    }
-
-    return $jobs;
-}
-
-
-sub extractchecksum
-{
-    my $infile = shift;
-    my %dataset = ();
-
-    #open CSUM, "tar -zxf $infile -O|" or return \%dataset;
-    open CSUM, "<$infile" or return \%dataset;
-
-    while(<CSUM>)
-    {
-        chomp;
-        if ( /^(\S+)\s+(\S+)$/ )
-        {
-            $dataset{$2} = $1;
-        }
-    }
-
-    close CSUM;
-
-    return \%dataset;
-}
-
-
-sub parseError
-{
-    my $response = shift;
-
-    #"error":"Invalid number of inputs found."
-    my $errorstr = ( $response =~ /\"error\"\s*:\s*\"([^\"]+)\"/ ) ? $1 : $response;
-    return $errorstr;
-}
-
-
-sub getchecksum
-{
-    my $infile = shift;
-
-    # md5 binary check
-    my $MD5BIN = "";
-
-    if ( -x "/usr/bin/md5sum" )
-    {
-        $MD5BIN = "/usr/bin/md5sum";
-    }
-    elsif ( -x "/sbin/md5" )
-    {
-        $MD5BIN = "/sbin/md5 -q";
-    }
-
-    return "" if $MD5BIN eq "";
-
-
-    my $checksum = "";
-    open MD5EXE, "$MD5BIN $infile|" or return "";
-
-    while(<MD5EXE>)
-    {
-        if (/^(\S+)\s+(\S+)$/)
-        {
-            $checksum = $1;
-            last;
-        }
-        elsif (/^(\S+)$/)
-        {
-            $checksum = $1;
-            last;
-        }
-    }
-
-    close MD5EXE;
-
-    return $checksum;
-
-}
-
-
-sub backticks
-{
-    my $command = shift;
-
-    `$command`;
-    return ($? == -1) ? 0 : 1;
-}
-
-
-sub bail
-{
-    my $str = shift;
-    my $status = shift;
-
-    #0 for success and 1 for error
-    $status = 1 unless defined;
-
-    print STDERR "$str\n" if defined $str;
-
-    cleanup();
-
-    exit($status);
-}
-
-
-sub cleanup
-{
-    return if ($TMP eq "" || !-d $TMP);
-
-    opendir(MAINDIR, $TMP);
-    my @files = readdir(MAINDIR);
-    closedir(MAINDIR);
-
-    foreach my $file (@files)
-    {
-        unlink "$TMP/$file" if -e "$TMP/$file";
-    }
-
-    remove_tree($TMP);
-
-}
-
-
-sub appendToFile
-{
-    my $inpfile = shift;
-    my $outfile = shift;
-
-    open INPF, "<$inpfile" or bail("Server Error: Error in reading file.");
-    open OUTF, ">>$outfile" or bail("Server Error: Error in writing to file.");
-
-    while(<INPF>)
-    {
-        print OUTF $_;
-    }
-
-    close OUTF;
-    close INPF;
-}
-
-
-
-sub help
-{
-    my $str = shift;
-
-    print <<'HELPME';
-
-USAGE
-  ./seekquencer_premafft.pl -inp <INFILE> -out <OUTFILE> [-str|-seq]
-  ./seekquencer_premafft.pl -idf <LISTFILE> -seqf <SEQFASTA> -out <OUTFILE> [-str|-seq]
-
-
-PARAMETERS
-  -inp <INFILE>
-     INFILE is a FASTA-formatted file
-     PDB entries are written as:
-        >PDBID
-        [5-character pdbid+chain]
-
-     While sequence entries are written as:
-        >[id]
-        [sequence]
-
-  -idf <LISTFILE>
-     IDLISTFILE is a file containing a list of pdbids
-     pdbids should be a 5-character pdbid + chain
-
-  -seqf <SEQFASTA>
-     SEQFASTA is a fasta file
-     entries are written as:
-        >[id]
-        [sequence]
-
-  -out <OUTFILE>
-     Results are writen to a file named OUTFILE
-
-  -str
-     Only structures will be collected by Seekquencer
-     If neither -str nor -seq is set, both structures and sequences will be collected by Seekquencer
-
-  -seq
-     Only sequences will be collected by Seekquencer
-     If neither -str nor -seq is set, both structures and sequences will be collected by Seekquencer
-
-
-OPTIONAL PARAMETERS:
-  -seqd <uniref100|uniref90|uniref70|uniprot>
-     Search Database for sequence homologs. Default value: uniref100
-
-  -lim <count>
-     this sets the maximum number of sequence homologs collected. Default value: 100
-
-  -blim <count>
-     this sets the -b and -v value when running blastall. Default value: 100
-
-  -pre
-     When -str is set, this will compare all structures against all using pdp-ash
-     This would ensure that all structures collected are matching
-     All structures that do not match will be removed
-
-  -noin
-     When set, inputs will not be included in the output
-
-  -mod <mafftash|mafftash-split|fasta>
-     Defines the output format
-     mafftash (default) will print a mafftash-formatted fasta file
-     mafftash-split will make 2 files separating the structures (OUTFILE.str) from sequences (OUTFILE.seq)
-     fasta will print a regular fasta file
-
-  -run <thread|normal>
-    thread will run simultaneous jobs during blast queries (faster but takes more nodes)
-    normal will run sequential blast queries (slower but takes less nodes)
-    Default value: normal
-
-  -trd <count>
-    if -run <thread> is defined, this sets the number of parallel jobs to run. Default value: 3
-
-
-HELPME
-
-    bail($str);
-}
-

abutils/bin/mafft_darwin_arm64/mafft.bat

-#! /bin/sh
-
-pushd "`dirname "$0"`" > /dev/null 2>&1; rootdir="$PWD"; popd > /dev/null 2>&1;
-MAFFT_BINARIES="$rootdir/mafftdir/libexec"; export MAFFT_BINARIES;
-
-"$rootdir/mafftdir/bin/mafft" "$@"
-# $1 can have space in file name

abutils/bin/mafft_...4/mafftdir/libexec/mafftash_premafft.pl

-#!/usr/bin/perl
-
-#####################################################################
-# Author:  KM Amada ([e-mail])
-#
-# Ver. Date      Changelog
-#####################################################################
-# 1.0  07.26.13  Initial release
-# 2.0  09.03.13  Added extensive warnings and error messages
-# 3.0  10.28.13  Fix for retrieving large files. Added STDERR logs
-# 3.1  11.08.13  Added LWP failsafe. Made hat3 not a required output
-# 3.2  12.08.14  Removed 5-char restriction for own structure files
-#
-#####################################################################
-
-use strict;
-use Getopt::Long;
-use File::Path qw(make_path remove_tree);
-use LWP::Simple;
-use LWP::UserAgent;
-
-# to prevent error 'Header line too long (limit is 8192)' [v3.1]
-use LWP::Protocol::http;
-push(@LWP::Protocol::http::EXTRA_SOCK_OPTS, MaxLineLength => 0);
-
-
-
-my $BASEURL = "http://sysimm.ifrec.osaka-u.ac.jp/MAFFTash/REST/service.cgi/premafft";
-
-my ( $WORKDIR, $PDBLIST, $OWNLIST, $HAT3FILE, $INSTRFILE );
-
-GetOptions
-(
-    'd=s' => \$WORKDIR,
-    'p=s' => \$PDBLIST,
-    'o=s' => \$OWNLIST,
-    'h=s' => \$HAT3FILE,
-    'i=s' => \$INSTRFILE,
-);
-
-print STDERR "[MAFFTash-premafft]\n";
-
-# set temp directory
-my $TMP = "/tmp/mapremafft$$";
-make_path($TMP) unless -d $TMP;
-
-
-
-######
-# validation
-&help("Required parameter : atleast one of either '-p' or '-o'") unless ( defined $PDBLIST || defined $OWNLIST);
-&help("Required parameter : '-d'") if defined $OWNLIST && ! defined $WORKDIR;
-
-$HAT3FILE = "hat3" unless defined $HAT3FILE;
-$INSTRFILE = "instr" unless defined $INSTRFILE;
-chop $WORKDIR if defined $WORKDIR && $WORKDIR =~ m/\/$/g;
-
-
-######
-# prepare inputs
-print STDERR "Preparing inputs for service request...\n";
-
-my @files = ();
-push(@files, "strweight" => "0.5");
-push(@files, "premafft" => "1");
-
-
-# pdb entries
-if ( defined $PDBLIST )
-{
-    print STDERR "PDB List defined!\n";
-    &bail("Error: Input file $PDBLIST does not exists!") unless -e $PDBLIST;
-    my $listfile = "$TMP/pdblist.inp";
-
-
-    open(INPF,"<$PDBLIST") or &bail("Error: Cannot open file $PDBLIST for reading!");
-    open(OUTF,">$listfile") or &bail("Error: Cannot open temporary file $listfile for writing!");
-
-    while(<INPF>)
-    {
-        chomp;
-        if ( /^(\w{5})$/ )
-        {
-            print OUTF ">PDBID\n$1\n";
-        }
-    }
-
-    close OUTF;
-    close INPF;
-
-    push(@files, "inputfile" => ["$listfile"]);
-}
-
-
-
-# upload own structures
-my %ownids = ();
-
-if ( defined $OWNLIST  )
-{
-    print STDERR "OWN List defined!\n";
-    &bail("Error: Input file $OWNLIST does not exists!") unless -e $OWNLIST;
-
-
-    open(OWNINPF,"<$OWNLIST") or &bail("Error: Cannot open file $OWNLIST for reading!");
-
-    while(<OWNINPF>)
-    {
-        chomp;
-
-        if ( /^(\S+)$/ )
-        {
-            my $fileref = "$WORKDIR/$1.pdb";
-
-            unless (-e $fileref)
-            {
-                close OWNINPF;
-                &bail("Error: File $fileref does not exists!");
-            }
-
-            push(@files, "inputownfile[]" => ["$fileref"]);
-            $ownids{$1} = 1;
-        }
-    }
-
-    close OWNINPF;
-}
-
-
-
-######
-# start rest service
-print STDERR "Sending service request...\n";
-
-my $browser = LWP::UserAgent->new;
-$browser->timeout(0);
-
-
-# post: running a mafftash job
-my $postResponse = $browser->post( $BASEURL, \@files, 'Content_Type' => 'form-data' );
-&bail(sprintf("[%d] %s\n", $postResponse->code, &parseError($postResponse->content))) unless($postResponse->is_success);
-
-
-# get response from post request
-my ($status, $mafftashid) = &parseResponse($postResponse->content);
-
-
-
-my $MAXTRIES = 3;
-my $STIMER = 4;
-my $longtimer = 0;
-
-print STDERR "Request sent! Waiting for response...[$mafftashid]\n";
-
-
-# wait for results until it becomes available
-while(1)
-{
-    $longtimer = $longtimer <= ($STIMER*3) ? $longtimer+$STIMER : $STIMER;
-    sleep $longtimer;
-
-
-    # get: get results for mafftash job
-    my $getResponse = $browser->get("$BASEURL/$mafftashid");
-
-    if ( $getResponse->is_success )
-    {
-
-        # get response from get request
-        ($status, $mafftashid) = &parseResponse($getResponse->content);
-        next unless ( $status eq "done" );
-
-
-        # if job is finished and ready
-        print STDERR "Results found!\n";
-        my $csfile = "$TMP/checksum.tar.gz";
-        my $try1 = 1;
-
-
-        while(1)
-        {
-            print STDERR "Fetching Results... [Trial $try1]\n";
-
-            if ( is_success(getstore("$BASEURL/getmdlist/$mafftashid", $csfile)) && -e $csfile && -s $csfile )
-            {
-                # get response from get request
-                my $checklist = &extractchecksum($csfile);
-                &bail("Error retrieving list of compressed files!") unless ( scalar %$checklist > 0 );
-
-
-                foreach my $id ( keys %$checklist )
-                {
-                    my $checkfile = "$TMP/$id";
-                    my $checkid = $checklist->{$id};
-                    my $try2 = 1;
-
-                    while(1)
-                    {
-                        unlink $checkfile if -e $checkfile;
-
-                        if ( is_success(getstore("$BASEURL/get/$mafftashid/$id", $checkfile)) && -e $checkfile && -s $checkfile )
-                        {
-                            my $hashid = &getchecksum($checkfile);
-                            #print STDERR "[hashid]$hashid [checkid]$checkid\n";
-
-                            if ($hashid ne "" && $hashid ne $checkid )
-                            {
-                                unlink $checkfile if -e $checkfile;
-                                &bail("Error retrieving compressed file from server! [Checksum Failed]") if $try2 >= $MAXTRIES;
-                                $try2++;
-                                sleep $STIMER;
-                            }
-                            else
-                            {
-                                last;
-                            }
-                        }
-                        else
-                        {
-                            &bail("Error retrieving compressed file from server!") if $try2 >= $MAXTRIES;
-                            $try2++;
-                            sleep $STIMER;
-                        }
-                    }
-                }
-
-                last;
-            }
-            else
-            {
-                &bail("Error retrieving list of compressed files from server!") if $try1 >= $MAXTRIES;
-                $try1++;
-                sleep $STIMER;
-            }
-        }
-
-        last;
-
-    }
-    else
-    {
-        &bail(sprintf("[%d] %s\n", $getResponse->code, &parseError($getResponse->content)));
-    }
-
-}
-
-
-# make sure outputs were generated
-# decompress
-print STDERR "Assembling final results...\n";
-
-&backticks("cat $TMP/archive.tar.gz* | tar -zxf - -C $TMP/");
-&backticks("mv -f $TMP/instr $INSTRFILE") if -e "$TMP/instr";
-&backticks("mv -f $TMP/hat3 $HAT3FILE") if -e "$TMP/hat3";
-
-# sometimes no hat3 file is generated [v3.1]
-#&bail("Error: Output file $HAT3FILE not found!") unless -e $HAT3FILE;
-&bail("Error: Output file $INSTRFILE not found!") unless -e $INSTRFILE;
-
-
-# warn if some ownids were ommitted
-if ( scalar keys(%ownids) > 0 )
-{
-    my %instrids = ();
-
-    open(INSTRF,"<$INSTRFILE") or &bail("Error: Cannot open file $INSTRFILE for reading!");
-
-    while(<INSTRF>)
-    {
-        chomp;
-
-        if ( /^>\d+_(\S+)$/ )
-        {
-            $instrids{$1} = 1;
-        }
-    }
-
-    close INSTRF;
-
-    foreach my $id ( keys %ownids )
-    {
-        warn "Warning: Own structure $id was excluded from instr/hat3.\n" unless $instrids{$id};
-    }
-
-}
-
-
-
-&cleanup();
-
-
-
-####################
-####################
-
-
-
-sub parseResponse
-{
-    my $response = shift;
-
-    #"status":"wait","mafftashid":"Ma8211432R"
-
-    my $status = "";
-    my $mafftashid = "";
-
-    if ( $response =~ /^([^\s:]+):([^\s:]+)$/ )
-    {
-        $mafftashid = $1;
-        $status = $2;
-    }
-
-    return ($status, $mafftashid);
-
-}
-
-
-sub extractchecksum
-{
-    my $infile = shift;
-    my %dataset = ();
-
-    open CSUM, "tar -zxf $infile -O|" or return \%dataset;
-
-    while(<CSUM>)
-    {
-        chomp;
-        if ( /^(\S+)\s+(\S+)$/ )
-        {
-            $dataset{$2} = $1;
-        }
-
-    }
-
-    close CSUM;
-
-    return \%dataset;
-
-}
-
-
-sub parseError
-{
-    my $response = shift;
-
-    #"error":"Invalid number of inputs found."
-    my $errorstr = ( $response =~ /\"error\"\s*:\s*\"([^\"]+)\"/ ) ? $1 : "";
-    return $errorstr;
-}
-
-
-sub getchecksum
-{
-    my $infile = shift;
-
-    # md5 binary check
-    my $MD5BIN = "";
-
-    if ( -x "/usr/bin/md5sum" )
-    {
-        $MD5BIN = "/usr/bin/md5sum";
-    }
-    elsif ( -x "/sbin/md5" )
-    {
-        $MD5BIN = "/sbin/md5 -q";
-    }
-
-    return "" if $MD5BIN eq "";
-
-
-    my $checksum = "";
-    open MD5EXE, "$MD5BIN $infile|" or return "";
-
-    while(<MD5EXE>)
-    {
-        if (/^(\S+)\s+(\S+)$/)
-        {
-            $checksum = $1;
-            last;
-        }
-        elsif (/^(\S+)$/)
-        {
-            $checksum = $1;
-            last;
-        }
-    }
-
-    close MD5EXE;
-
-    return $checksum;
-
-}
-
-
-sub backticks
-{
-    my $command = shift;
-
-    `$command`;
-    return ($? == -1) ? 0 : 1;
-}
-
-
-sub bail
-{
-    my $str = shift;
-    print STDERR "$str\n" if defined $str;
-
-    &cleanup();
-    exit(1);
-}
-
-
-sub cleanup
-{
-    return if ($TMP eq "" || !-d $TMP);
-
-    opendir(MAINDIR, $TMP);
-    my @files = readdir(MAINDIR);
-    closedir(MAINDIR);
-
-    foreach my $file (@files)
-    {
-        unlink "$TMP/$file" if -e "$TMP/$file";
-    }
-
-    remove_tree($TMP);
-
-}
-
-
-sub help
-{
-    my $str = shift;
-
-    print <<'HELPME';
-
-USAGE
-  ./mafftash_premafft.pl -p [FILE]
-  ./mafftash_premafft.pl -o [FILE] -d [DIRECTORY]
-  ./mafftash_premafft.pl -p [FILE] -o [FILE] -d [DIRECTORY]
-
-
-PARAMETERS
-  -p [FILE]
-     FILE contains a list of PDBIDs (one entry per line); make sure that the PDBIDs are in the standard 5-character pdbid+chain naming format
-
-  -o [FILE] -d [DIRECTORY]
-     FILE contains a list of IDs from your own structure/pdb files (one entry per line)
-     for each ID in the list make sure that a corresponding structure file (same ID with .pdb extension) is stored in DIRECTORY
-
-  -h [HATFILE]
-     save the output hat3 file in HATFILE; if not set, the output is written to a file named 'hat3' in your current directory
-
-  -i [INSTRFILE]
-     save the output instr file in INSTRFILE; if not set, the output is written to a file named 'instr' in your current directory
-
-HELPME
-
-    &bail($str);
-}
-
-
-

abutils/bin/mafft_...afftdir/libexec/seekquencer_premafft.pl

-#!/usr/bin/perl
-
-####################################################################################
-# Author:  KM Amada ([e-mail])
-#
-# Ver. Date      Changelog
-####################################################################################
-# 1.0  11.01.13  Initial release
-#
-# **Skipped version 2 to standardise version numbers to seekquencer.pl script**
-#
-# 3.0  04.24.14  Added split option -mod <mafftash-split> for output
-#                Uses seekquencer_v3 backend
-#
-# 4.0  05.12.14  Added new options: -run <thread|normal> -trd <count> -noin
-#                Sets -seqa fast in seekquencer.pl
-#                Uses seekquencer_v4 backend
-#
-# 4.1  05.19.14  Added a check on running REST requests before proceeding
-#                to avoid server load problems
-#
-# 4.2  05.27.14  Seq limit processing done in seekquencer.pl script
-#                to avoid server load problems
-#
-# 4.3  07.22.14  Added new option: -seqd <uniref100|uniref90|uniref70|uniprot>
-#                Blast limit changed from factor of 10 to -blim option
-#                Timing on sleep changed; added srand() for making seed
-#                Moved the job limit processing to server side
-#
-# 4.4  08.05.14  Modified to work in multiple OS
-#
-#
-####################################################################################
-
-use strict;
-use Getopt::Long;
-use File::Path qw(make_path remove_tree);
-use Cwd;
-use LWP::Simple;
-use LWP::UserAgent;
-
-# to prevent error: Header line too long (limit is 8192)
-use LWP::Protocol::http;
-push(@LWP::Protocol::http::EXTRA_SOCK_OPTS, MaxLineLength => 0);
-
-
-
-my $BASEURL = "http://sysimm.ifrec.osaka-u.ac.jp/seekquencer/REST/service.cgi/premafft";
-my ( $INPUTFILE, $IDLISTFILE, $SEQFASTAFILE, $OUTPUTFILE, $SEQFLAG, $STRFLAG, $EVALFLAG, $NOINFLAG );
-my $OUTTYPE = "mafftash";
-
-my $SEQDATABASE = "uniref100";
-my $SEQLIMIT = 100;
-my $SEQBLASTLIMIT = 100;
-
-my $RUNMODE = "normal";    # thread|normal
-my $THREADCOUNT = 3;
-
-
-GetOptions
-(
-    'inp=s'  => \$INPUTFILE,
-    'idf=s'  => \$IDLISTFILE,
-    'seqf=s' => \$SEQFASTAFILE,
-    'out=s'  => \$OUTPUTFILE,
-    'str'    => \$STRFLAG,
-    'seq'    => \$SEQFLAG,
-    'seqd=s' => \$SEQDATABASE,
-    'lim=i'  => \$SEQLIMIT,
-    'blim=i' => \$SEQBLASTLIMIT,
-    'pre'    => \$EVALFLAG,
-    'noin'   => \$NOINFLAG,
-    'mod=s'  => \$OUTTYPE,
-    'run=s'  => \$RUNMODE,
-    'trd=i'  => \$THREADCOUNT,
-
-
-);
-
-my $ISWINDOWS = ( $^O =~ /^MSWin/ ) ? 1 : 0;
-print STDERR "[Seekquencer-premafft 4.4 on $^O]\n";
-
-
-# set temp directory
-my $CWD = getcwd;
-my $TMP = "$CWD/seekpremafft$$";
-make_path($TMP) unless -d $TMP;
-
-
-
-######
-# validation
-help("Required parameter: define input as '-inp' or '-idf' or '-seqf'") if ( !defined $INPUTFILE && !defined $IDLISTFILE && !defined $SEQFASTAFILE );
-help("'-inp' is already defined") if ( defined $INPUTFILE && (defined $IDLISTFILE || defined $SEQFASTAFILE) );
-help("Input file $INPUTFILE does not exist (or filesize is 0)") if ( defined $INPUTFILE && (! -e $INPUTFILE || !-s $INPUTFILE) );
-help("Input file $IDLISTFILE does not exist (or filesize is 0)") if ( defined $IDLISTFILE && (! -e $IDLISTFILE || !-s $IDLISTFILE) );
-help("Input file $SEQFASTAFILE does not exist (or filesize is 0)") if ( defined $SEQFASTAFILE && (! -e $SEQFASTAFILE || !-s $SEQFASTAFILE) );
-help("Required parameter: output file '-out'") unless ( defined $OUTPUTFILE );
-help("Set either '-str' or '-seq' or dont set any at all") if ( defined $STRFLAG && defined $SEQFLAG );
-
-help("Invalid value for '-seqd <uniref100|uniref90|uniref70|uniprot>'") if ( $SEQDATABASE ne "uniref100" && $SEQDATABASE ne "uniref90" && $SEQDATABASE ne "uniref70" && $SEQDATABASE ne "uniprot");
-help("Invalid value for '-mod <fasta|mafftash|mafftash-split>'") if ( $OUTTYPE ne "fasta" && $OUTTYPE ne "mafftash" && $OUTTYPE ne "mafftash-split" );
-help("Invalid value for '-run <thread|normal>'") if ( $RUNMODE ne "thread" && $RUNMODE ne "normal" );
-help("Invalid value for '-trd <count>'; count should be between 1 and 5 (inclusive)") if ( $RUNMODE eq "thread" && ($THREADCOUNT <= 0 || $THREADCOUNT > 5) );
-
-
-######
-# check existing requests
-print STDERR "Checking server status...\n";
-
-# generate seed
-srand($$);
-
-# sleep a bit to give time for lsf response
-sleep(int(rand(6))+1);
-
-
-my $browser = LWP::UserAgent->new;
-$browser->timeout(0);
-
-# get: check if you can send a new request this time
-my $jobsResponse = $browser->get("$BASEURL/isAllowed");
-
-if ( $jobsResponse->is_success )
-{
-    my $status = parseJobQueryResponse($jobsResponse->content);
-    bail("Max jobs reached. The server cannot process your request right now; try again later.", 0) unless $status > 0;
-}
-else
-{
-    bail(sprintf("[%d] %s\n", $jobsResponse->code, parseError($jobsResponse->content)));
-}
-
-
-######
-# make a temporary input if lists were provided
-unless ( defined $INPUTFILE )
-{
-    $INPUTFILE = "$TMP/input.homemade";
-    open INPF, ">$INPUTFILE" or bail("Error writing to input file.");
-
-    if ( defined $IDLISTFILE )
-    {
-        open IDLIST, "<$IDLISTFILE" or bail("Error reading input file.");
-        while( <IDLIST> )
-    	{
-        	chomp;
-        	if ( /(\w{5})/ )
-        	{
-        	    print INPF ">PDBID\n$1\n";
-        	}
-        }
-        close IDLIST;
-    }
-
-
-    if ( defined $SEQFASTAFILE )
-    {
-        open FASTA, "<$SEQFASTAFILE" or bail("Error reading input file.");
-        while( <FASTA> )
-    	{
-        	chomp;
-            print INPF "$_\n";
-        }
-        close FASTA;
-    }
-
-    close INPF;
-}
-
-
-######
-# prepare parameters
-print STDERR "Preparing parameters for service request...\n";
-
-my @parameters = ();
-push(@parameters, "fileinput" => ["$INPUTFILE"]);
-push(@parameters, "out_type" => $OUTTYPE);
-
-push(@parameters, "rest_flag" => "1");
-push(@parameters, "cls_flag" => "1");
-push(@parameters, "pre_flag" => "1") if defined $EVALFLAG;
-push(@parameters, "noin_flag" => "1") if defined $NOINFLAG;
-
-push(@parameters, "run_mode" => $RUNMODE);
-push(@parameters, "thread_count" => $THREADCOUNT) if $RUNMODE eq "thread";
-
-
-if ( defined $STRFLAG )
-{
-    push(@parameters, "str_flag" => "1");
-    push(@parameters, "ash_flag" => "1");
-}
-elsif ( defined $SEQFLAG )
-{
-    push(@parameters, "seq_flag" => "1");
-    push(@parameters, "seq_algorithm" => "fast");
-    push(@parameters, "seq_database" => $SEQDATABASE);
-    push(@parameters, "seq_blastlimit" => $SEQBLASTLIMIT);
-    push(@parameters, "seq_outputlimit" => $SEQLIMIT);
-}
-else
-{
-    push(@parameters, "str_flag" => "1");
-    push(@parameters, "ash_flag" => "1");
-    push(@parameters, "seq_flag" => "1");
-    push(@parameters, "seq_algorithm" => "fast");
-    push(@parameters, "seq_database" => $SEQDATABASE);
-    push(@parameters, "seq_blastlimit" => $SEQBLASTLIMIT);
-    push(@parameters, "seq_outputlimit" => $SEQLIMIT);
-}
-
-
-
-######
-# start rest service
-print STDERR "Sending service request...\n";
-
-# post: running a mafftash job
-my $postResponse = $browser->post( $BASEURL, \@parameters, 'Content_Type' => 'form-data' );
-bail(sprintf("[%d] %s\n", $postResponse->code, parseError($postResponse->content))) unless($postResponse->is_success);
-
-
-# get response from post request
-my ($status, $seekid) = parseResponse($postResponse->content);
-
-my $MAXTRIES = 3;
-my $STIMER = 5;
-my $timer = 0;
-
-print STDERR "Request sent! Waiting for response...[$seekid]\n";
-
-my $checklist = {};
-
-# wait for results until it becomes available
-while(1)
-{
-    # sleeps for 5+random, 10+random, 15+random, 20+random, 25+random, 30+random ,,, 60+random, 60+random,,,
-    $timer = $timer >= 60 ? 60 : $timer+$STIMER;
-    sleep($timer+int(rand(4)));
-
-    # get: get results for mafftash job
-    my $getResponse = $browser->get("$BASEURL/$seekid");
-
-    if ( $getResponse->is_success )
-    {
-
-        # get response from get request
-        ($status, $seekid) = parseResponse($getResponse->content);
-        next unless ( $status eq "done" );
-
-
-        # if job is finished and ready
-        print STDERR "Results found!\n";
-        my $csfile = "$TMP/checksum";
-        my $try1 = 1;
-
-
-        while(1)
-        {
-            print STDERR "Fetching Results... [Trial $try1]\n";
-
-            if ( is_success(getstore("$BASEURL/get/$seekid/checksum", $csfile)) && -e $csfile && -s $csfile )
-            {
-                # get response from get request
-                $checklist = extractchecksum($csfile);
-                bail("Error retrieving list of compressed files!") unless ( scalar %$checklist > 0 );
-
-
-                foreach my $id ( sort keys %$checklist )
-                {
-                    sleep 1;
-                    my $checkfile = "$TMP/$id";
-                    my $checkid = $checklist->{$id};
-                    my $try2 = 1;
-
-                    while(1)
-                    {
-                        unlink $checkfile if -e $checkfile;
-
-                        if ( is_success(getstore("$BASEURL/get/$seekid/$id", $checkfile)) && -e $checkfile && -s $checkfile )
-                        {
-                            last if $ISWINDOWS;
-
-                            my $hashid = getchecksum($checkfile);
-                            #print STDERR "[hashid]$hashid [checkid]$checkid\n";
-
-                            if ($hashid ne "" && $hashid ne $checkid )
-                            {
-                                #unlink $checkfile if -e $checkfile;
-                                bail("Error retrieving compressed file from server! [Checksum Failed]") if $try2 >= $MAXTRIES;
-                                $try2++;
-                                sleep $STIMER;
-                            }
-                            else
-                            {
-                                last;
-                            }
-                        }
-                        else
-                        {
-                            bail("Error retrieving compressed file from server!") if $try2 >= $MAXTRIES;
-                            $try2++;
-                            sleep $STIMER;
-                        }
-                    }
-                }
-
-                last;
-            }
-            else
-            {
-                bail("Error retrieving list of compressed files from server!") if $try1 >= $MAXTRIES;
-                $try1++;
-                sleep $STIMER;
-            }
-        }
-
-        last;
-
-    }
-    else
-    {
-        bail(sprintf("[%d] %s\n", $getResponse->code, parseError($getResponse->content)));
-    }
-
-}
-
-
-# make sure outputs were generated
-# decompress
-print STDERR "Assembling final results...\n";
-
-foreach my $id ( sort keys %$checklist )
-{
-    if ( $id =~ /^$seekid\.out(\.str|\.seq)?/  )
-    {
-        bail("Error: Output file corrupted!") unless -e "$TMP/$id";
-        appendToFile("$TMP/$id","$OUTPUTFILE".$1);
-    }
-}
-
-cleanup();
-
-
-
-####################
-####################
-
-
-sub parseResponse
-{
-    my $response = shift;
-    my $status = "";
-    my $seekid = "";
-
-    if ( $response =~ /^([^\s:]+):([^\s:]+)$/ )
-    {
-        $seekid = $1;
-        $status = $2;
-    }
-
-    return ($status, $seekid);
-}
-
-
-sub parseJobQueryResponse
-{
-    my $response = shift;
-    my $jobs = 100;
-
-    if ( $response =~ /^(\d+)$/ )
-    {
-        $jobs = $1;
-    }
-
-    return $jobs;
-}
-
-
-sub extractchecksum
-{
-    my $infile = shift;
-    my %dataset = ();
-
-    #open CSUM, "tar -zxf $infile -O|" or return \%dataset;
-    open CSUM, "<$infile" or return \%dataset;
-
-    while(<CSUM>)
-    {
-        chomp;
-        if ( /^(\S+)\s+(\S+)$/ )
-        {
-            $dataset{$2} = $1;
-        }
-    }
-
-    close CSUM;
-
-    return \%dataset;
-}
-
-
-sub parseError
-{
-    my $response = shift;
-
-    #"error":"Invalid number of inputs found."
-    my $errorstr = ( $response =~ /\"error\"\s*:\s*\"([^\"]+)\"/ ) ? $1 : $response;
-    return $errorstr;
-}
-
-
-sub getchecksum
-{
-    my $infile = shift;
-
-    # md5 binary check
-    my $MD5BIN = "";
-
-    if ( -x "/usr/bin/md5sum" )
-    {
-        $MD5BIN = "/usr/bin/md5sum";
-    }
-    elsif ( -x "/sbin/md5" )
-    {
-        $MD5BIN = "/sbin/md5 -q";
-    }
-
-    return "" if $MD5BIN eq "";
-
-
-    my $checksum = "";
-    open MD5EXE, "$MD5BIN $infile|" or return "";
-
-    while(<MD5EXE>)
-    {
-        if (/^(\S+)\s+(\S+)$/)
-        {
-            $checksum = $1;
-            last;
-        }
-        elsif (/^(\S+)$/)
-        {
-            $checksum = $1;
-            last;
-        }
-    }
-
-    close MD5EXE;
-
-    return $checksum;
-
-}
-
-
-sub backticks
-{
-    my $command = shift;
-
-    `$command`;
-    return ($? == -1) ? 0 : 1;
-}
-
-
-sub bail
-{
-    my $str = shift;
-    my $status = shift;
-
-    #0 for success and 1 for error
-    $status = 1 unless defined;
-
-    print STDERR "$str\n" if defined $str;
-
-    cleanup();
-
-    exit($status);
-}
-
-
-sub cleanup
-{
-    return if ($TMP eq "" || !-d $TMP);
-
-    opendir(MAINDIR, $TMP);
-    my @files = readdir(MAINDIR);
-    closedir(MAINDIR);
-
-    foreach my $file (@files)
-    {
-        unlink "$TMP/$file" if -e "$TMP/$file";
-    }
-
-    remove_tree($TMP);
-
-}
-
-
-sub appendToFile
-{
-    my $inpfile = shift;
-    my $outfile = shift;
-
-    open INPF, "<$inpfile" or bail("Server Error: Error in reading file.");
-    open OUTF, ">>$outfile" or bail("Server Error: Error in writing to file.");
-
-    while(<INPF>)
-    {
-        print OUTF $_;
-    }
-
-    close OUTF;
-    close INPF;
-}
-
-
-
-sub help
-{
-    my $str = shift;
-
-    print <<'HELPME';
-
-USAGE
-  ./seekquencer_premafft.pl -inp <INFILE> -out <OUTFILE> [-str|-seq]
-  ./seekquencer_premafft.pl -idf <LISTFILE> -seqf <SEQFASTA> -out <OUTFILE> [-str|-seq]
-
-
-PARAMETERS
-  -inp <INFILE>
-     INFILE is a FASTA-formatted file
-     PDB entries are written as:
-        >PDBID
-        [5-character pdbid+chain]
-
-     While sequence entries are written as:
-        >[id]
-        [sequence]
-
-  -idf <LISTFILE>
-     IDLISTFILE is a file containing a list of pdbids
-     pdbids should be a 5-character pdbid + chain
-
-  -seqf <SEQFASTA>
-     SEQFASTA is a fasta file
-     entries are written as:
-        >[id]
-        [sequence]
-
-  -out <OUTFILE>
-     Results are writen to a file named OUTFILE
-
-  -str
-     Only structures will be collected by Seekquencer
-     If neither -str nor -seq is set, both structures and sequences will be collected by Seekquencer
-
-  -seq
-     Only sequences will be collected by Seekquencer
-     If neither -str nor -seq is set, both structures and sequences will be collected by Seekquencer
-
-
-OPTIONAL PARAMETERS:
-  -seqd <uniref100|uniref90|uniref70|uniprot>
-     Search Database for sequence homologs. Default value: uniref100
-
-  -lim <count>
-     this sets the maximum number of sequence homologs collected. Default value: 100
-
-  -blim <count>
-     this sets the -b and -v value when running blastall. Default value: 100
-
-  -pre
-     When -str is set, this will compare all structures against all using pdp-ash
-     This would ensure that all structures collected are matching
-     All structures that do not match will be removed
-
-  -noin
-     When set, inputs will not be included in the output
-
-  -mod <mafftash|mafftash-split|fasta>
-     Defines the output format
-     mafftash (default) will print a mafftash-formatted fasta file
-     mafftash-split will make 2 files separating the structures (OUTFILE.str) from sequences (OUTFILE.seq)
-     fasta will print a regular fasta file
-
-  -run <thread|normal>
-    thread will run simultaneous jobs during blast queries (faster but takes more nodes)
-    normal will run sequential blast queries (slower but takes less nodes)
-    Default value: normal
-
-  -trd <count>
-    if -run <thread> is defined, this sets the number of parallel jobs to run. Default value: 3
-
-
-HELPME
-
-    bail($str);
-}
-

abutils/bin/mafft_linux_amd64/mafft.bat

-#! /bin/bash
-# sh -> bash for debian. By J. R. Peterson. 2015/Jun.
-
-pushd "`dirname "$0"`" > /dev/null 2>&1; rootdir="$PWD"; popd > /dev/null 2>&1;
-MAFFT_BINARIES="$rootdir/mafftdir/libexec"; export MAFFT_BINARIES;
-
-"$rootdir/mafftdir/bin/mafft" "$@"
-# input file name can have space

abutils/bin/mafft_...4/mafftdir/libexec/mafftash_premafft.pl

-#!/usr/bin/perl
-
-#####################################################################
-# Author:  KM Amada ([e-mail])
-#
-# Ver. Date      Changelog
-#####################################################################
-# 1.0  07.26.13  Initial release
-# 2.0  09.03.13  Added extensive warnings and error messages
-# 3.0  10.28.13  Fix for retrieving large files. Added STDERR logs
-# 3.1  11.08.13  Added LWP failsafe. Made hat3 not a required output
-# 3.2  12.08.14  Removed 5-char restriction for own structure files
-#
-#####################################################################
-
-use strict;
-use Getopt::Long;
-use File::Path qw(make_path remove_tree);
-use LWP::Simple;
-use LWP::UserAgent;
-
-# to prevent error 'Header line too long (limit is 8192)' [v3.1]
-use LWP::Protocol::http;
-push(@LWP::Protocol::http::EXTRA_SOCK_OPTS, MaxLineLength => 0);
-
-
-
-my $BASEURL = "http://sysimm.ifrec.osaka-u.ac.jp/MAFFTash/REST/service.cgi/premafft";
-
-my ( $WORKDIR, $PDBLIST, $OWNLIST, $HAT3FILE, $INSTRFILE );
-
-GetOptions
-(
-    'd=s' => \$WORKDIR,
-    'p=s' => \$PDBLIST,
-    'o=s' => \$OWNLIST,
-    'h=s' => \$HAT3FILE,
-    'i=s' => \$INSTRFILE,
-);
-
-print STDERR "[MAFFTash-premafft]\n";
-
-# set temp directory
-my $TMP = "/tmp/mapremafft$$";
-make_path($TMP) unless -d $TMP;
-
-
-
-######
-# validation
-&help("Required parameter : atleast one of either '-p' or '-o'") unless ( defined $PDBLIST || defined $OWNLIST);
-&help("Required parameter : '-d'") if defined $OWNLIST && ! defined $WORKDIR;
-
-$HAT3FILE = "hat3" unless defined $HAT3FILE;
-$INSTRFILE = "instr" unless defined $INSTRFILE;
-chop $WORKDIR if defined $WORKDIR && $WORKDIR =~ m/\/$/g;
-
-
-######
-# prepare inputs
-print STDERR "Preparing inputs for service request...\n";
-
-my @files = ();
-push(@files, "strweight" => "0.5");
-push(@files, "premafft" => "1");
-
-
-# pdb entries
-if ( defined $PDBLIST )
-{
-    print STDERR "PDB List defined!\n";
-    &bail("Error: Input file $PDBLIST does not exists!") unless -e $PDBLIST;
-    my $listfile = "$TMP/pdblist.inp";
-
-
-    open(INPF,"<$PDBLIST") or &bail("Error: Cannot open file $PDBLIST for reading!");
-    open(OUTF,">$listfile") or &bail("Error: Cannot open temporary file $listfile for writing!");
-
-    while(<INPF>)
-    {
-        chomp;
-        if ( /^(\w{5})$/ )
-        {
-            print OUTF ">PDBID\n$1\n";
-        }
-    }
-
-    close OUTF;
-    close INPF;
-
-    push(@files, "inputfile" => ["$listfile"]);
-}
-
-
-
-# upload own structures
-my %ownids = ();
-
-if ( defined $OWNLIST  )
-{
-    print STDERR "OWN List defined!\n";
-    &bail("Error: Input file $OWNLIST does not exists!") unless -e $OWNLIST;
-
-
-    open(OWNINPF,"<$OWNLIST") or &bail("Error: Cannot open file $OWNLIST for reading!");
-
-    while(<OWNINPF>)
-    {
-        chomp;
-
-        if ( /^(\S+)$/ )
-        {
-            my $fileref = "$WORKDIR/$1.pdb";
-
-            unless (-e $fileref)
-            {
-                close OWNINPF;
-                &bail("Error: File $fileref does not exists!");
-            }
-
-            push(@files, "inputownfile[]" => ["$fileref"]);
-            $ownids{$1} = 1;
-        }
-    }
-
-    close OWNINPF;
-}
-
-
-
-######
-# start rest service
-print STDERR "Sending service request...\n";
-
-my $browser = LWP::UserAgent->new;
-$browser->timeout(0);
-
-
-# post: running a mafftash job
-my $postResponse = $browser->post( $BASEURL, \@files, 'Content_Type' => 'form-data' );
-&bail(sprintf("[%d] %s\n", $postResponse->code, &parseError($postResponse->content))) unless($postResponse->is_success);
-
-
-# get response from post request
-my ($status, $mafftashid) = &parseResponse($postResponse->content);
-
-
-
-my $MAXTRIES = 3;
-my $STIMER = 4;
-my $longtimer = 0;
-
-print STDERR "Request sent! Waiting for response...[$mafftashid]\n";
-
-
-# wait for results until it becomes available
-while(1)
-{
-    $longtimer = $longtimer <= ($STIMER*3) ? $longtimer+$STIMER : $STIMER;
-    sleep $longtimer;
-
-
-    # get: get results for mafftash job
-    my $getResponse = $browser->get("$BASEURL/$mafftashid");
-
-    if ( $getResponse->is_success )
-    {
-
-        # get response from get request
-        ($status, $mafftashid) = &parseResponse($getResponse->content);
-        next unless ( $status eq "done" );
-
-
-        # if job is finished and ready
-        print STDERR "Results found!\n";
-        my $csfile = "$TMP/checksum.tar.gz";
-        my $try1 = 1;
-
-
-        while(1)
-        {
-            print STDERR "Fetching Results... [Trial $try1]\n";
-
-            if ( is_success(getstore("$BASEURL/getmdlist/$mafftashid", $csfile)) && -e $csfile && -s $csfile )
-            {
-                # get response from get request
-                my $checklist = &extractchecksum($csfile);
-                &bail("Error retrieving list of compressed files!") unless ( scalar %$checklist > 0 );
-
-
-                foreach my $id ( keys %$checklist )
-                {
-                    my $checkfile = "$TMP/$id";
-                    my $checkid = $checklist->{$id};
-                    my $try2 = 1;
-
-                    while(1)
-                    {
-                        unlink $checkfile if -e $checkfile;
-
-                        if ( is_success(getstore("$BASEURL/get/$mafftashid/$id", $checkfile)) && -e $checkfile && -s $checkfile )
-                        {
-                            my $hashid = &getchecksum($checkfile);
-                            #print STDERR "[hashid]$hashid [checkid]$checkid\n";
-
-                            if ($hashid ne "" && $hashid ne $checkid )
-                            {
-                                unlink $checkfile if -e $checkfile;
-                                &bail("Error retrieving compressed file from server! [Checksum Failed]") if $try2 >= $MAXTRIES;
-                                $try2++;
-                                sleep $STIMER;
-                            }
-                            else
-                            {
-                                last;
-                            }
-                        }
-                        else
-                        {
-                            &bail("Error retrieving compressed file from server!") if $try2 >= $MAXTRIES;
-                            $try2++;
-                            sleep $STIMER;
-                        }
-                    }
-                }
-
-                last;
-            }
-            else
-            {
-                &bail("Error retrieving list of compressed files from server!") if $try1 >= $MAXTRIES;
-                $try1++;
-                sleep $STIMER;
-            }
-        }
-
-        last;
-
-    }
-    else
-    {
-        &bail(sprintf("[%d] %s\n", $getResponse->code, &parseError($getResponse->content)));
-    }
-
-}
-
-
-# make sure outputs were generated
-# decompress
-print STDERR "Assembling final results...\n";
-
-&backticks("cat $TMP/archive.tar.gz* | tar -zxf - -C $TMP/");
-&backticks("mv -f $TMP/instr $INSTRFILE") if -e "$TMP/instr";
-&backticks("mv -f $TMP/hat3 $HAT3FILE") if -e "$TMP/hat3";
-
-# sometimes no hat3 file is generated [v3.1]
-#&bail("Error: Output file $HAT3FILE not found!") unless -e $HAT3FILE;
-&bail("Error: Output file $INSTRFILE not found!") unless -e $INSTRFILE;
-
-
-# warn if some ownids were ommitted
-if ( scalar keys(%ownids) > 0 )
-{
-    my %instrids = ();
-
-    open(INSTRF,"<$INSTRFILE") or &bail("Error: Cannot open file $INSTRFILE for reading!");
-
-    while(<INSTRF>)
-    {
-        chomp;
-
-        if ( /^>\d+_(\S+)$/ )
-        {
-            $instrids{$1} = 1;
-        }
-    }
-
-    close INSTRF;
-
-    foreach my $id ( keys %ownids )
-    {
-        warn "Warning: Own structure $id was excluded from instr/hat3.\n" unless $instrids{$id};
-    }
-
-}
-
-
-
-&cleanup();
-
-
-
-####################
-####################
-
-
-
-sub parseResponse
-{
-    my $response = shift;
-
-    #"status":"wait","mafftashid":"Ma8211432R"
-
-    my $status = "";
-    my $mafftashid = "";
-
-    if ( $response =~ /^([^\s:]+):([^\s:]+)$/ )
-    {
-        $mafftashid = $1;
-        $status = $2;
-    }
-
-    return ($status, $mafftashid);
-
-}
-
-
-sub extractchecksum
-{
-    my $infile = shift;
-    my %dataset = ();
-
-    open CSUM, "tar -zxf $infile -O|" or return \%dataset;
-
-    while(<CSUM>)
-    {
-        chomp;
-        if ( /^(\S+)\s+(\S+)$/ )
-        {
-            $dataset{$2} = $1;
-        }
-
-    }
-
-    close CSUM;
-
-    return \%dataset;
-
-}
-
-
-sub parseError
-{
-    my $response = shift;
-
-    #"error":"Invalid number of inputs found."
-    my $errorstr = ( $response =~ /\"error\"\s*:\s*\"([^\"]+)\"/ ) ? $1 : "";
-    return $errorstr;
-}
-
-
-sub getchecksum
-{
-    my $infile = shift;
-
-    # md5 binary check
-    my $MD5BIN = "";
-
-    if ( -x "/usr/bin/md5sum" )
-    {
-        $MD5BIN = "/usr/bin/md5sum";
-    }
-    elsif ( -x "/sbin/md5" )
-    {
-        $MD5BIN = "/sbin/md5 -q";
-    }
-
-    return "" if $MD5BIN eq "";
-
-
-    my $checksum = "";
-    open MD5EXE, "$MD5BIN $infile|" or return "";
-
-    while(<MD5EXE>)
-    {
-        if (/^(\S+)\s+(\S+)$/)
-        {
-            $checksum = $1;
-            last;
-        }
-        elsif (/^(\S+)$/)
-        {
-            $checksum = $1;
-            last;
-        }
-    }
-
-    close MD5EXE;
-
-    return $checksum;
-
-}
-
-
-sub backticks
-{
-    my $command = shift;
-
-    `$command`;
-    return ($? == -1) ? 0 : 1;
-}
-
-
-sub bail
-{
-    my $str = shift;
-    print STDERR "$str\n" if defined $str;
-
-    &cleanup();
-    exit(1);
-}
-
-
-sub cleanup
-{
-    return if ($TMP eq "" || !-d $TMP);
-
-    opendir(MAINDIR, $TMP);
-    my @files = readdir(MAINDIR);
-    closedir(MAINDIR);
-
-    foreach my $file (@files)
-    {
-        unlink "$TMP/$file" if -e "$TMP/$file";
-    }
-
-    remove_tree($TMP);
-
-}
-
-
-sub help
-{
-    my $str = shift;
-
-    print <<'HELPME';
-
-USAGE
-  ./mafftash_premafft.pl -p [FILE]
-  ./mafftash_premafft.pl -o [FILE] -d [DIRECTORY]
-  ./mafftash_premafft.pl -p [FILE] -o [FILE] -d [DIRECTORY]
-
-
-PARAMETERS
-  -p [FILE]
-     FILE contains a list of PDBIDs (one entry per line); make sure that the PDBIDs are in the standard 5-character pdbid+chain naming format
-
-  -o [FILE] -d [DIRECTORY]
-     FILE contains a list of IDs from your own structure/pdb files (one entry per line)
-     for each ID in the list make sure that a corresponding structure file (same ID with .pdb extension) is stored in DIRECTORY
-
-  -h [HATFILE]
-     save the output hat3 file in HATFILE; if not set, the output is written to a file named 'hat3' in your current directory
-
-  -i [INSTRFILE]
-     save the output instr file in INSTRFILE; if not set, the output is written to a file named 'instr' in your current directory
-
-HELPME
-
-    &bail($str);
-}
-
-
-

abutils/bin/mafft_...afftdir/libexec/seekquencer_premafft.pl

-#!/usr/bin/perl
-
-####################################################################################
-# Author:  KM Amada ([e-mail])
-#
-# Ver. Date      Changelog
-####################################################################################
-# 1.0  11.01.13  Initial release
-#
-# **Skipped version 2 to standardise version numbers to seekquencer.pl script**
-#
-# 3.0  04.24.14  Added split option -mod <mafftash-split> for output
-#                Uses seekquencer_v3 backend
-#
-# 4.0  05.12.14  Added new options: -run <thread|normal> -trd <count> -noin
-#                Sets -seqa fast in seekquencer.pl
-#                Uses seekquencer_v4 backend
-#
-# 4.1  05.19.14  Added a check on running REST requests before proceeding
-#                to avoid server load problems
-#
-# 4.2  05.27.14  Seq limit processing done in seekquencer.pl script
-#                to avoid server load problems
-#
-# 4.3  07.22.14  Added new option: -seqd <uniref100|uniref90|uniref70|uniprot>
-#                Blast limit changed from factor of 10 to -blim option
-#                Timing on sleep changed; added srand() for making seed
-#                Moved the job limit processing to server side
-#
-# 4.4  08.05.14  Modified to work in multiple OS
-#
-#
-####################################################################################
-
-use strict;
-use Getopt::Long;
-use File::Path qw(make_path remove_tree);
-use Cwd;
-use LWP::Simple;
-use LWP::UserAgent;
-
-# to prevent error: Header line too long (limit is 8192)
-use LWP::Protocol::http;
-push(@LWP::Protocol::http::EXTRA_SOCK_OPTS, MaxLineLength => 0);
-
-
-
-my $BASEURL = "http://sysimm.ifrec.osaka-u.ac.jp/seekquencer/REST/service.cgi/premafft";
-my ( $INPUTFILE, $IDLISTFILE, $SEQFASTAFILE, $OUTPUTFILE, $SEQFLAG, $STRFLAG, $EVALFLAG, $NOINFLAG );
-my $OUTTYPE = "mafftash";
-
-my $SEQDATABASE = "uniref100";
-my $SEQLIMIT = 100;
-my $SEQBLASTLIMIT = 100;
-
-my $RUNMODE = "normal";    # thread|normal
-my $THREADCOUNT = 3;
-
-
-GetOptions
-(
-    'inp=s'  => \$INPUTFILE,
-    'idf=s'  => \$IDLISTFILE,
-    'seqf=s' => \$SEQFASTAFILE,
-    'out=s'  => \$OUTPUTFILE,
-    'str'    => \$STRFLAG,
-    'seq'    => \$SEQFLAG,
-    'seqd=s' => \$SEQDATABASE,
-    'lim=i'  => \$SEQLIMIT,
-    'blim=i' => \$SEQBLASTLIMIT,
-    'pre'    => \$EVALFLAG,
-    'noin'   => \$NOINFLAG,
-    'mod=s'  => \$OUTTYPE,
-    'run=s'  => \$RUNMODE,
-    'trd=i'  => \$THREADCOUNT,
-
-
-);
-
-my $ISWINDOWS = ( $^O =~ /^MSWin/ ) ? 1 : 0;
-print STDERR "[Seekquencer-premafft 4.4 on $^O]\n";
-
-
-# set temp directory
-my $CWD = getcwd;
-my $TMP = "$CWD/seekpremafft$$";
-make_path($TMP) unless -d $TMP;
-
-
-
-######
-# validation
-help("Required parameter: define input as '-inp' or '-idf' or '-seqf'") if ( !defined $INPUTFILE && !defined $IDLISTFILE && !defined $SEQFASTAFILE );
-help("'-inp' is already defined") if ( defined $INPUTFILE && (defined $IDLISTFILE || defined $SEQFASTAFILE) );
-help("Input file $INPUTFILE does not exist (or filesize is 0)") if ( defined $INPUTFILE && (! -e $INPUTFILE || !-s $INPUTFILE) );
-help("Input file $IDLISTFILE does not exist (or filesize is 0)") if ( defined $IDLISTFILE && (! -e $IDLISTFILE || !-s $IDLISTFILE) );
-help("Input file $SEQFASTAFILE does not exist (or filesize is 0)") if ( defined $SEQFASTAFILE && (! -e $SEQFASTAFILE || !-s $SEQFASTAFILE) );
-help("Required parameter: output file '-out'") unless ( defined $OUTPUTFILE );
-help("Set either '-str' or '-seq' or dont set any at all") if ( defined $STRFLAG && defined $SEQFLAG );
-
-help("Invalid value for '-seqd <uniref100|uniref90|uniref70|uniprot>'") if ( $SEQDATABASE ne "uniref100" && $SEQDATABASE ne "uniref90" && $SEQDATABASE ne "uniref70" && $SEQDATABASE ne "uniprot");
-help("Invalid value for '-mod <fasta|mafftash|mafftash-split>'") if ( $OUTTYPE ne "fasta" && $OUTTYPE ne "mafftash" && $OUTTYPE ne "mafftash-split" );
-help("Invalid value for '-run <thread|normal>'") if ( $RUNMODE ne "thread" && $RUNMODE ne "normal" );
-help("Invalid value for '-trd <count>'; count should be between 1 and 5 (inclusive)") if ( $RUNMODE eq "thread" && ($THREADCOUNT <= 0 || $THREADCOUNT > 5) );
-
-
-######
-# check existing requests
-print STDERR "Checking server status...\n";
-
-# generate seed
-srand($$);
-
-# sleep a bit to give time for lsf response
-sleep(int(rand(6))+1);
-
-
-my $browser = LWP::UserAgent->new;
-$browser->timeout(0);
-
-# get: check if you can send a new request this time
-my $jobsResponse = $browser->get("$BASEURL/isAllowed");
-
-if ( $jobsResponse->is_success )
-{
-    my $status = parseJobQueryResponse($jobsResponse->content);
-    bail("Max jobs reached. The server cannot process your request right now; try again later.", 0) unless $status > 0;
-}
-else
-{
-    bail(sprintf("[%d] %s\n", $jobsResponse->code, parseError($jobsResponse->content)));
-}
-
-
-######
-# make a temporary input if lists were provided
-unless ( defined $INPUTFILE )
-{
-    $INPUTFILE = "$TMP/input.homemade";
-    open INPF, ">$INPUTFILE" or bail("Error writing to input file.");
-
-    if ( defined $IDLISTFILE )
-    {
-        open IDLIST, "<$IDLISTFILE" or bail("Error reading input file.");
-        while( <IDLIST> )
-    	{
-        	chomp;
-        	if ( /(\w{5})/ )
-        	{
-        	    print INPF ">PDBID\n$1\n";
-        	}
-        }
-        close IDLIST;
-    }
-
-
-    if ( defined $SEQFASTAFILE )
-    {
-        open FASTA, "<$SEQFASTAFILE" or bail("Error reading input file.");
-        while( <FASTA> )
-    	{
-        	chomp;
-            print INPF "$_\n";
-        }
-        close FASTA;
-    }
-
-    close INPF;
-}
-
-
-######
-# prepare parameters
-print STDERR "Preparing parameters for service request...\n";
-
-my @parameters = ();
-push(@parameters, "fileinput" => ["$INPUTFILE"]);
-push(@parameters, "out_type" => $OUTTYPE);
-
-push(@parameters, "rest_flag" => "1");
-push(@parameters, "cls_flag" => "1");
-push(@parameters, "pre_flag" => "1") if defined $EVALFLAG;
-push(@parameters, "noin_flag" => "1") if defined $NOINFLAG;
-
-push(@parameters, "run_mode" => $RUNMODE);
-push(@parameters, "thread_count" => $THREADCOUNT) if $RUNMODE eq "thread";
-
-
-if ( defined $STRFLAG )
-{
-    push(@parameters, "str_flag" => "1");
-    push(@parameters, "ash_flag" => "1");
-}
-elsif ( defined $SEQFLAG )
-{
-    push(@parameters, "seq_flag" => "1");
-    push(@parameters, "seq_algorithm" => "fast");
-    push(@parameters, "seq_database" => $SEQDATABASE);
-    push(@parameters, "seq_blastlimit" => $SEQBLASTLIMIT);
-    push(@parameters, "seq_outputlimit" => $SEQLIMIT);
-}
-else
-{
-    push(@parameters, "str_flag" => "1");
-    push(@parameters, "ash_flag" => "1");
-    push(@parameters, "seq_flag" => "1");
-    push(@parameters, "seq_algorithm" => "fast");
-    push(@parameters, "seq_database" => $SEQDATABASE);
-    push(@parameters, "seq_blastlimit" => $SEQBLASTLIMIT);
-    push(@parameters, "seq_outputlimit" => $SEQLIMIT);
-}
-
-
-
-######
-# start rest service
-print STDERR "Sending service request...\n";
-
-# post: running a mafftash job
-my $postResponse = $browser->post( $BASEURL, \@parameters, 'Content_Type' => 'form-data' );
-bail(sprintf("[%d] %s\n", $postResponse->code, parseError($postResponse->content))) unless($postResponse->is_success);
-
-
-# get response from post request
-my ($status, $seekid) = parseResponse($postResponse->content);
-
-my $MAXTRIES = 3;
-my $STIMER = 5;
-my $timer = 0;
-
-print STDERR "Request sent! Waiting for response...[$seekid]\n";
-
-my $checklist = {};
-
-# wait for results until it becomes available
-while(1)
-{
-    # sleeps for 5+random, 10+random, 15+random, 20+random, 25+random, 30+random ,,, 60+random, 60+random,,,
-    $timer = $timer >= 60 ? 60 : $timer+$STIMER;
-    sleep($timer+int(rand(4)));
-
-    # get: get results for mafftash job
-    my $getResponse = $browser->get("$BASEURL/$seekid");
-
-    if ( $getResponse->is_success )
-    {
-
-        # get response from get request
-        ($status, $seekid) = parseResponse($getResponse->content);
-        next unless ( $status eq "done" );
-
-
-        # if job is finished and ready
-        print STDERR "Results found!\n";
-        my $csfile = "$TMP/checksum";
-        my $try1 = 1;
-
-
-        while(1)
-        {
-            print STDERR "Fetching Results... [Trial $try1]\n";
-
-            if ( is_success(getstore("$BASEURL/get/$seekid/checksum", $csfile)) && -e $csfile && -s $csfile )
-            {
-                # get response from get request
-                $checklist = extractchecksum($csfile);
-                bail("Error retrieving list of compressed files!") unless ( scalar %$checklist > 0 );
-
-
-                foreach my $id ( sort keys %$checklist )
-                {
-                    sleep 1;
-                    my $checkfile = "$TMP/$id";
-                    my $checkid = $checklist->{$id};
-                    my $try2 = 1;
-
-                    while(1)
-                    {
-                        unlink $checkfile if -e $checkfile;
-
-                        if ( is_success(getstore("$BASEURL/get/$seekid/$id", $checkfile)) && -e $checkfile && -s $checkfile )
-                        {
-                            last if $ISWINDOWS;
-
-                            my $hashid = getchecksum($checkfile);
-                            #print STDERR "[hashid]$hashid [checkid]$checkid\n";
-
-                            if ($hashid ne "" && $hashid ne $checkid )
-                            {
-                                #unlink $checkfile if -e $checkfile;
-                                bail("Error retrieving compressed file from server! [Checksum Failed]") if $try2 >= $MAXTRIES;
-                                $try2++;
-                                sleep $STIMER;
-                            }
-                            else
-                            {
-                                last;
-                            }
-                        }
-                        else
-                        {
-                            bail("Error retrieving compressed file from server!") if $try2 >= $MAXTRIES;
-                            $try2++;
-                            sleep $STIMER;
-                        }
-                    }
-                }
-
-                last;
-            }
-            else
-            {
-                bail("Error retrieving list of compressed files from server!") if $try1 >= $MAXTRIES;
-                $try1++;
-                sleep $STIMER;
-            }
-        }
-
-        last;
-
-    }
-    else
-    {
-        bail(sprintf("[%d] %s\n", $getResponse->code, parseError($getResponse->content)));
-    }
-
-}
-
-
-# make sure outputs were generated
-# decompress
-print STDERR "Assembling final results...\n";
-
-foreach my $id ( sort keys %$checklist )
-{
-    if ( $id =~ /^$seekid\.out(\.str|\.seq)?/  )
-    {
-        bail("Error: Output file corrupted!") unless -e "$TMP/$id";
-        appendToFile("$TMP/$id","$OUTPUTFILE".$1);
-    }
-}
-
-cleanup();
-
-
-
-####################
-####################
-
-
-sub parseResponse
-{
-    my $response = shift;
-    my $status = "";
-    my $seekid = "";
-
-    if ( $response =~ /^([^\s:]+):([^\s:]+)$/ )
-    {
-        $seekid = $1;
-        $status = $2;
-    }
-
-    return ($status, $seekid);
-}
-
-
-sub parseJobQueryResponse
-{
-    my $response = shift;
-    my $jobs = 100;
-
-    if ( $response =~ /^(\d+)$/ )
-    {
-        $jobs = $1;
-    }
-
-    return $jobs;
-}
-
-
-sub extractchecksum
-{
-    my $infile = shift;
-    my %dataset = ();
-
-    #open CSUM, "tar -zxf $infile -O|" or return \%dataset;
-    open CSUM, "<$infile" or return \%dataset;
-
-    while(<CSUM>)
-    {
-        chomp;
-        if ( /^(\S+)\s+(\S+)$/ )
-        {
-            $dataset{$2} = $1;
-        }
-    }
-
-    close CSUM;
-
-    return \%dataset;
-}
-
-
-sub parseError
-{
-    my $response = shift;
-
-    #"error":"Invalid number of inputs found."
-    my $errorstr = ( $response =~ /\"error\"\s*:\s*\"([^\"]+)\"/ ) ? $1 : $response;
-    return $errorstr;
-}
-
-
-sub getchecksum
-{
-    my $infile = shift;
-
-    # md5 binary check
-    my $MD5BIN = "";
-
-    if ( -x "/usr/bin/md5sum" )
-    {
-        $MD5BIN = "/usr/bin/md5sum";
-    }
-    elsif ( -x "/sbin/md5" )
-    {
-        $MD5BIN = "/sbin/md5 -q";
-    }
-
-    return "" if $MD5BIN eq "";
-
-
-    my $checksum = "";
-    open MD5EXE, "$MD5BIN $infile|" or return "";
-
-    while(<MD5EXE>)
-    {
-        if (/^(\S+)\s+(\S+)$/)
-        {
-            $checksum = $1;
-            last;
-        }
-        elsif (/^(\S+)$/)
-        {
-            $checksum = $1;
-            last;
-        }
-    }
-
-    close MD5EXE;
-
-    return $checksum;
-
-}
-
-
-sub backticks
-{
-    my $command = shift;
-
-    `$command`;
-    return ($? == -1) ? 0 : 1;
-}
-
-
-sub bail
-{
-    my $str = shift;
-    my $status = shift;
-
-    #0 for success and 1 for error
-    $status = 1 unless defined;
-
-    print STDERR "$str\n" if defined $str;
-
-    cleanup();
-
-    exit($status);
-}
-
-
-sub cleanup
-{
-    return if ($TMP eq "" || !-d $TMP);
-
-    opendir(MAINDIR, $TMP);
-    my @files = readdir(MAINDIR);
-    closedir(MAINDIR);
-
-    foreach my $file (@files)
-    {
-        unlink "$TMP/$file" if -e "$TMP/$file";
-    }
-
-    remove_tree($TMP);
-
-}
-
-
-sub appendToFile
-{
-    my $inpfile = shift;
-    my $outfile = shift;
-
-    open INPF, "<$inpfile" or bail("Server Error: Error in reading file.");
-    open OUTF, ">>$outfile" or bail("Server Error: Error in writing to file.");
-
-    while(<INPF>)
-    {
-        print OUTF $_;
-    }
-
-    close OUTF;
-    close INPF;
-}
-
-
-
-sub help
-{
-    my $str = shift;
-
-    print <<'HELPME';
-
-USAGE
-  ./seekquencer_premafft.pl -inp <INFILE> -out <OUTFILE> [-str|-seq]
-  ./seekquencer_premafft.pl -idf <LISTFILE> -seqf <SEQFASTA> -out <OUTFILE> [-str|-seq]
-
-
-PARAMETERS
-  -inp <INFILE>
-     INFILE is a FASTA-formatted file
-     PDB entries are written as:
-        >PDBID
-        [5-character pdbid+chain]
-
-     While sequence entries are written as:
-        >[id]
-        [sequence]
-
-  -idf <LISTFILE>
-     IDLISTFILE is a file containing a list of pdbids
-     pdbids should be a 5-character pdbid + chain
-
-  -seqf <SEQFASTA>
-     SEQFASTA is a fasta file
-     entries are written as:
-        >[id]
-        [sequence]
-
-  -out <OUTFILE>
-     Results are writen to a file named OUTFILE
-
-  -str
-     Only structures will be collected by Seekquencer
-     If neither -str nor -seq is set, both structures and sequences will be collected by Seekquencer
-
-  -seq
-     Only sequences will be collected by Seekquencer
-     If neither -str nor -seq is set, both structures and sequences will be collected by Seekquencer
-
-
-OPTIONAL PARAMETERS:
-  -seqd <uniref100|uniref90|uniref70|uniprot>
-     Search Database for sequence homologs. Default value: uniref100
-
-  -lim <count>
-     this sets the maximum number of sequence homologs collected. Default value: 100
-
-  -blim <count>
-     this sets the -b and -v value when running blastall. Default value: 100
-
-  -pre
-     When -str is set, this will compare all structures against all using pdp-ash
-     This would ensure that all structures collected are matching
-     All structures that do not match will be removed
-
-  -noin
-     When set, inputs will not be included in the output
-
-  -mod <mafftash|mafftash-split|fasta>
-     Defines the output format
-     mafftash (default) will print a mafftash-formatted fasta file
-     mafftash-split will make 2 files separating the structures (OUTFILE.str) from sequences (OUTFILE.seq)
-     fasta will print a regular fasta file
-
-  -run <thread|normal>
-    thread will run simultaneous jobs during blast queries (faster but takes more nodes)
-    normal will run sequential blast queries (slower but takes less nodes)
-    Default value: normal
-
-  -trd <count>
-    if -run <thread> is defined, this sets the number of parallel jobs to run. Default value: 3
-
-
-HELPME
-
-    bail($str);
-}
-

Alert delta unavailable

Currently unable to show alert delta for PyPI packages.

Worsened metrics

Total package byte prevSize

937413

-99.62%

Number of package files

82

-63.56%