mimseq
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mimseq - npm Package Compare versions
@@ -1,4 +0,4 @@ | ||
| Metadata-Version: 1.1 | ||
| Metadata-Version: 2.1 | ||
| Name: mimseq | ||
| Version: 1.3.2 | ||
| Version: 1.3.3 | ||
| Summary: Custom high-throughput tRNA sequencing alignment and quantification pipeline based on modification induced misincorporation cDNA synthesis. | ||
@@ -9,3 +9,2 @@ Home-page: https://github.com/nedialkova-lab/mim-tRNAseq | ||
| License: GPLv3 | ||
| Description: UNKNOWN | ||
| Platform: UNKNOWN | ||
@@ -19,1 +18,5 @@ Classifier: Development Status :: 4 - Beta | ||
| Classifier: Topic :: Scientific/Engineering :: Bio-Informatics | ||
| License-File: LICENSE.txt | ||
| UNKNOWN | ||
@@ -87,4 +87,4 @@ #! /usr/bin/env python3 | ||
| if (sum(modTable[isodecoder][pos].values()) >= misinc_thresh and (any(cov >= min_cov) or 'mito' in isodecoder) and pos-1 not in knownTable[isodecoder]): # misinc above threshold, cov above threshold and not previously known | ||
| # if one nucleotide dominates misinc. pattern (i.e. >= 0.9 of all misinc, likely a true SNP or misalignment) | ||
| if (max(modTable[isodecoder][pos].values()) / sum(modTable[isodecoder][pos].values()) > 0.95): | ||
| # if one nucleotide dominates misinc. pattern (i.e. >= 0.97 of all misinc, likely a true SNP or misalignment) | ||
| if (max(modTable[isodecoder][pos].values()) / sum(modTable[isodecoder][pos].values()) > 0.97): | ||
| # if mod seems to be an inosine (i.e. A with G misinc at 34) add to list and modification SNPs file (see tRNAtools.ModsParser()) | ||
@@ -94,3 +94,3 @@ if (tRNA_dict[isodecoder]['sequence'][pos-1] == 'A' and list(modTable[isodecoder][pos].keys())[list(modTable[isodecoder][pos].values()).index(max(modTable[isodecoder][pos].values()))] == 'G' and pos-1 == min(anticodon)): | ||
| new_inosines_isodecoder[isodecoder].append(pos-1) | ||
| elif (max(modTable[isodecoder][pos].values()) / sum(modTable[isodecoder][pos].values()) <= 0.95 and not (pos-1 == min(anticodon))): | ||
| elif (max(modTable[isodecoder][pos].values()) / sum(modTable[isodecoder][pos].values()) <= 0.97 and not (pos-1 == min(anticodon))): | ||
| new_mods_cluster[cluster].append(pos-1) #modTable has 1 based values - convert back to 0 based for mod_lists | ||
@@ -97,0 +97,0 @@ new_mods_isodecoder[isodecoder].append(pos-1) |
@@ -294,3 +294,3 @@ #! /usr/bin/env python3 | ||
| temp_chrom = input + "_chrom.txt" | ||
| cmd = "samtools view -H " + input + " | grep @SQ|sed 's/@SQ\tSN:\|LN://g' > " + temp_chrom | ||
| cmd = "samtools view -H " + input + " | grep @SQ | sed 's/@SQ\tSN:\|@sq\tSN:\|LN://g' > " + temp_chrom | ||
| subprocess.call(cmd, shell = True) | ||
@@ -450,6 +450,6 @@ ### each bam file might have a reduced set of chromosomes compared to the bedTool object and so sorting on all doesn't always work | ||
| if "/" in seq: | ||
| tempSeq = seq.split("/")[0] | ||
| tempSeq = seq.split("/")[0] + "-" | ||
| isodecoder_list = [x for x in tRNA_dict.keys() if tempSeq in x and not "chr" in x] | ||
| iso_min = min([x.split("-")[-1] for x in isodecoder_list]) | ||
| newSeq = tempSeq + "-" + str(iso_min) | ||
| newSeq = tempSeq + str(iso_min) | ||
| else: | ||
@@ -456,0 +456,0 @@ newSeq = seq |
@@ -50,3 +50,3 @@ #! /usr/bin/env python3 | ||
| # cons_pos_dict is a dictionary of 1 based positions and canonical positions to create extra column in mods tables (mismatchTable and RTstopTable) mapping ungapped positions to canonical ones | ||
| ss_cons = "".join([line.split()[-1] for line in open(stkname) if line.startswith("#=GC SS_cons")]) | ||
| ss_cons = stk.column_annotations['secondary_structure'] | ||
| if ungapped: | ||
@@ -76,3 +76,3 @@ ss_cons_orig = ss_cons | ||
| elif cons_pos == 20: | ||
| elif cons_pos == 20: | ||
| if not '20' in cons_pos_list: | ||
@@ -189,3 +189,4 @@ cons_pos_dict[pos+1] = '20' | ||
| anticodon = list() | ||
| rf_cons = "".join([line.split()[-1] for line in open(stkname) if line.startswith("#=GC RF")]) | ||
| stk = AlignIO.read(stkname, "stockholm") | ||
| rf_cons = stk.column_annotations['reference_annotation'] | ||
| # use '*' in rf_cons from stk to delimit the anticodon positions | ||
@@ -195,3 +196,3 @@ for pos, char in enumerate(rf_cons): | ||
| anticodon.append(pos) | ||
| return(anticodon) | ||
@@ -225,3 +226,3 @@ | ||
| mod_sites = ['9', '20', '26', '32', '34', '37', '58'] | ||
| for mod in mod_sites: | ||
@@ -232,3 +233,3 @@ sites_dict[mod] = list(cons_pos_dict.keys())[list(cons_pos_dict.values()).index(mod)] | ||
| stk = AlignIO.read(stkname, "stockholm") | ||
| stk = AlignIO.read(stkname, "stockholm") | ||
| for record in stk: | ||
@@ -247,3 +248,3 @@ gene = record.id | ||
| canon_pos = cons_pos_dict[pos] | ||
| upstream_dict[gene][canon_pos].append(identity) | ||
| upstream_dict[gene][canon_pos].append(identity) | ||
| upstream_dict[gene][canon_pos].append(seq[up]) # upstream base | ||
@@ -274,3 +275,3 @@ upstream_dict[gene][canon_pos].append(seq[down]) # downstream base | ||
| # read in stk file generated above and define structural regions for each tRNA input | ||
| struct_dict = dict() | ||
@@ -277,0 +278,0 @@ # get conserved tRNA structure from alignment |
@@ -1,1 +0,1 @@ | ||
| __version__ = "v1.3.2" | ||
| __version__ = "v1.3.3" |
+6
-3
@@ -1,4 +0,4 @@ | ||
| Metadata-Version: 1.1 | ||
| Metadata-Version: 2.1 | ||
| Name: mimseq | ||
| Version: 1.3.2 | ||
| Version: 1.3.3 | ||
| Summary: Custom high-throughput tRNA sequencing alignment and quantification pipeline based on modification induced misincorporation cDNA synthesis. | ||
@@ -9,3 +9,2 @@ Home-page: https://github.com/nedialkova-lab/mim-tRNAseq | ||
| License: GPLv3 | ||
| Description: UNKNOWN | ||
| Platform: UNKNOWN | ||
@@ -19,1 +18,5 @@ Classifier: Development Status :: 4 - Beta | ||
| Classifier: Topic :: Scientific/Engineering :: Bio-Informatics | ||
| License-File: LICENSE.txt | ||
| UNKNOWN | ||
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