mimseq - npm Package Compare versions

Comparing version 1.3.5 to 1.3.6

mimseq.egg-info/entry_points.txt

 [console_scripts]
 mimseq = mimseq.mimseq:main
-

mimseq.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: mimseq
-Version: 1.3.5
+Version: 1.3.6
 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
-Platform: UNKNOWN
 Classifier: Development Status :: 4 - Beta
@@ -19,4 +18,1 @@ Classifier: Environment :: Console
 License-File: LICENSE.txt
-
-UNKNOWN
-

mimseq.egg-info/SOURCES.txt

@@ -91,4 +91,2 @@ LICENSE.txt
 mimseq/data/gorGor4-eColitK/gorGor4-tRNAs-detailed.out
-mimseq/data/gorGor4-eColitK/gorGor4-tRNAs-filtered.fa
-mimseq/data/gorGor4-eColitK/gorGor4-tRNAs-filtered2.fa
 mimseq/data/gorGor4-eColitK/gorGor4-tRNAs.bed
@@ -115,3 +113,2 @@ mimseq/data/gorGor4-eColitK/gorGor4-tRNAs.fa
 mimseq/data/hg38-eColitK/hg38-tRNAs-detailed.out
-mimseq/data/hg38-eColitK/hg38-tRNAs-filtered.fa
 mimseq/data/hg38-eColitK/hg38-tRNAs.bed
@@ -118,0 +115,0 @@ mimseq/data/hg38-eColitK/hg38-tRNAs.fa

mimseq/data/gorGor4-eColitK/README.txt

@@ -18,13 +18,2 @@ # Generate fasta file of full tRNA set using bed file and custom script to adjust tRNA naming in final fasta
 
-### Manually removed sequences due to strange sequence, poor score and issues with infernal alignment with mimseq
-### See gorGor4-tRNAs-filtered.fa
-
->Gorilla_gorilla_tRX-Ala-GGC-9-1 (tRNAscan-SE ID: chr16.trna24) Ala (GGC) 77 bp Sc: 28.0 16:71652066-71652143(-)
->Gorilla_gorilla_tRX-Phe-GAA-5-1 (tRNAscan-SE ID: chr18.trna3) Phe (GAA) 69 bp Sc: 23.1 18:59921682-59921751(-)
->Gorilla_gorilla_tRX-Lys-CTT-13-1 (tRNAscan-SE ID: chr7.trna1) Lys (CTT) 84 bp Sc: 33.0 7:12541420-12541504(+)
->Gorilla_gorilla_tRX-Cys-GCA-8-1 (tRNAscan-SE ID: chr7.trna18) Cys (GCA) 84 bp Sc: 26.8 7:149223412-149223496(+)
->Gorilla_gorilla_tRX-Lys-TTT-17-1 (tRNAscan-SE ID: chr3.trna11) Lys (TTT) 81 bp Sc: 25.2 3:45318879-45318960(-)
->Gorilla_gorilla_tRX-Cys-GCA-6-1 (tRNAscan-SE ID: chr10.trna7) Cys (GCA) 96 bp Sc: 20.7 10:6238138-6238234(-)
->Gorilla_gorilla_tRNA-Asn-GTT-12-1 (tRNAscan-SE ID: chr1.trna19) Asn (GTT) 76 bp Sc: 52.9 1:125422054-125422130(+)
-
 ##### Manually rename problem reference names #######
@@ -48,6 +37,6 @@
 
-#### NB! gorGor4-tRNAs-filtered2.fa is the one loaded by mimseq with --species Ggor ####
-####--------------------------------------------------------------------------------####
+#### NB! ####
+####-----####
 
 Gorilla_gorilla_tRNA-Pro-AGG-6-1 has been removed as NNN repeat causes problems with clustering
 This is a high-confidence tRNA so removing it might not be the best fix, but the AGG anticodon family has very very few reads aligned anyway

mimseq/data/hg38-eColitK/README.txt

@@ -27,15 +27,2 @@ # Generate fasta file of full tRNA set using bed file and custom script to adjust tRNA naming in final fasta
 
-### Manually removed sequences due to strange sequence, poor score and issues with infernal alignment with mimseq
-### See hg38-tRNAs-filtered.fa
-# Homo_sapiens_tRX-Phe-GAA-2-1 (tRNAscan-SE ID: chr1.trna134) Phe (GAA) 80 bp Sc: 26.6 chr1:121009543-121009623(-)
-# Homo_sapiens_tRX-Lys-CTT-5-1 (tRNAscan-SE ID: chr7.trna1) Lys (CTT) 84 bp Sc: 31.1 chr7:12601963-12602047(+)
-# Homo_sapiens_tRX-Lys-CTT-4-1 (tRNAscan-SE ID: chr7.trna31) Lys (CTT) 73 bp Sc: 34.5 chr7:97141572-97141645(-)
-# Homo_sapiens_tRNA-Phe-GAA-9-1 (tRNAscan-SE ID: chr1.trna124) Phe (GAA) 80 bp Sc: 32.2 chr1:143792723-143792803(-)
-# Homo_sapiens_tRX-Arg-CCT-2-1 (tRNAscan-SE ID: chr11.trna9) Arg (CCT) 79 bp Sc: 21.2 chr11:118241371-118241450(+)
-# Homo_sapiens_tRX-Ile-AAT-4-1 (tRNAscan-SE ID: chr17.trna38) Ile (AAT) 87 bp Sc: 20.5 chr17:8206072-8206159(-)
-# Homo_sapiens_tRNA-Glu-TTC-13-1 (tRNAscan-SE ID: chr2.trna6) Glu (TCA) 73 bp Sc: 21.3 chr2:74896918-74896991(+)
-# Homo_sapiens_tRNA-Tyr-GTA-11-1 (tRNAscan-SE ID: chr7.trna29) Tyr (GTA) 77 bp Sc: 37.1 chr7:149356652-149356729(-)
-# Homo_sapiens_tRNA-Asn-GTT-20-1 (tRNAscan-SE ID: chr1.trna116) Asn (GTT) 76 bp Sc: 41.0 chr1:146049197-146049273(-)
-# Homo_sapiens_tRX-Cys-GCA-4-1 (tRNAscan-SE ID: chr7.trna16) Cys (GCA) 83 bp Sc: 26.6 chr7:149628152-149628235(+)
-# Homo_sapiens_tRNA-Cys-GCA-25-1 (tRNAscan-SE ID: chr3.trna11) Cys (GCA) 80 bp Sc: 40.9 chr3:17699892-17699972(-)
 
@@ -42,0 +29,0 @@ #### mitochondrial Tyr-GTA missing a 3'-A which leads to inaccuracies in alignment and shows as mostly CCA-less reads in CCA plots ####

mimseq/deseq.R

@@ -353,3 +353,3 @@ #!/usr/bin/Rscript
             scale_size_manual(values = c(1,2), guide = "none") + theme_bw() +
-            labs(x = paste('log10', combinations[[i]][2], 'counts', sep = ' '), y = paste('log10', combinations[[i]][1], 'counts', sep = ' ')) +
+            labs(x = paste(combinations[[i]][2], 'counts', sep = ' '), y = paste(combinations[[i]][1], 'counts', sep = ' ')) +
             annotate("label", 0, Inf, hjust = 0, vjust = 1, label = paste("italic(r) == ", anticodon_cor), parse = TRUE)
@@ -365,3 +365,3 @@
             scale_size_manual(values = c(1,2), guide = "none") + theme_bw() +
-            labs(x = paste('log10', combinations[[i]][2], 'counts', sep = ' '), y = paste('log10', combinations[[i]][1], 'counts', sep = ' ')) +
+            labs(x = paste(combinations[[i]][2], 'counts', sep = ' '), y = paste(combinations[[i]][1], 'counts', sep = ' ')) +
             annotate("label", 0, Inf, hjust = 0, vjust = 1, label = paste("italic(r) == ", isodecoder_cor), parse = TRUE)
@@ -368,0 +368,0 @@

mimseq/mimseq.py

@@ -362,3 +362,3 @@ #! /usr/bin/env python3
 				if args.species == 'Ggor':
-					args.trnas = os.path.dirname(os.path.realpath(__file__)) + "/data/gorGor4-eColitK/gorGor4-tRNAs-filtered2.fa"
+					args.trnas = os.path.dirname(os.path.realpath(__file__)) + "/data/gorGor4-eColitK/gorGor4-tRNAs-all.fa"
 					args.trnaout = os.path.dirname(os.path.realpath(__file__)) + "/data/gorGor4-eColitK/gorGor4-tRNAs-detailed.out"
@@ -371,3 +371,3 @@ args.mito = os.path.dirname(os.path.realpath(__file__)) + "/data/gorGor4-eColitK/gorGor4-mitotRNAs.fa"
 				if args.species == 'Hsap':
-					args.trnas = os.path.dirname(os.path.realpath(__file__)) + "/data/hg38-eColitK/hg38-tRNAs-filtered.fa"
+					args.trnas = os.path.dirname(os.path.realpath(__file__)) + "/data/hg38-eColitK/hg38-tRNAs-all.fa"
 					args.trnaout = os.path.dirname(os.path.realpath(__file__)) + "/data/hg38-eColitK/hg38-tRNAs-detailed.out"
@@ -374,0 +374,0 @@ args.mito = os.path.dirname(os.path.realpath(__file__)) + "/data/hg38-eColitK/hg38-mitotRNAs.fa"

mimseq/version.py

@@ -1,1 +0,1 @@
-__version__ = "v1.3.5"
+__version__ = "v1.3.6"

PKG-INFO

 Metadata-Version: 2.1
 Name: mimseq
-Version: 1.3.5
+Version: 1.3.6
 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
-Platform: UNKNOWN
 Classifier: Development Status :: 4 - Beta
@@ -19,4 +18,1 @@ Classifier: Environment :: Console
 License-File: LICENSE.txt
-
-UNKNOWN
-

README.md

@@ -39,3 +39,3 @@ <p align="center">
 
-To use mim-tRNAseq, it is recommended to install the package using `conda`, preferably in its own environment. Significant time improvements can be made to installing mimseq using mamba which we will use within the mimseq environment:
+To use mim-tRNAseq, it is recommended to install the package using `conda`, preferably in its own environment. Significant time and dependency-related improvements can be made to using conda for managing environment and installing mimseq using the [Mambaforge](https://github.com/conda-forge/miniforge) version of conda Miniforge. We recommend installing Mambaforge and then followin the steps below:
 ```bash
@@ -42,0 +42,0 @@ conda create -n mimseq python=3.7

Alert delta unavailable

Currently unable to show alert delta for PyPI packages.

Worsened metrics

Total package byte prevSize

17834212

-1.83%

Number of package files

175

-1.69%