mimseq - npm Package Compare versions

Comparing version 1.3.4 to 1.3.5

mimseq.egg-info/entry_points.txt

 [console_scripts]
 mimseq = mimseq.mimseq:main
+

mimseq.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: mimseq
-Version: 1.3.4
+Version: 1.3.5
 Summary: Custom high-throughput tRNA sequencing alignment and quantification pipeline based on modification induced misincorporation cDNA synthesis.
@@ -9,2 +9,3 @@ Home-page: https://github.com/nedialkova-lab/mim-tRNAseq
 License: GPLv3
+Platform: UNKNOWN
 Classifier: Development Status :: 4 - Beta
@@ -18,1 +19,4 @@ Classifier: Environment :: Console
 License-File: LICENSE.txt
+
+UNKNOWN
+

mimseq.egg-info/SOURCES.txt

@@ -58,2 +58,3 @@ LICENSE.txt
 mimseq/data/ce11-eColitK/ce11-tRNAs-detailed.out
+mimseq/data/ce11-eColitK/ce11-tRNAs-filtered.fa
 mimseq/data/ce11-eColitK/ce11-tRNAs.bed
@@ -60,0 +61,0 @@ mimseq/data/ce11-eColitK/ce11-tRNAs_name_map.txt

mimseq/data/ce11-eColitK/README.txt

@@ -18,6 +18,3 @@ # Generate fasta file of full tRNA set using bed file and custom script to adjust tRNA naming in final fasta
 
-
-#### mitochondrial Tyr-GTA missing a 3'-A which leads to inaccuracies in alignment and shows as mostly CCA-less reads in CCA plots ####
-#### Gene should end on CCA and gain an additional CCA after processing
-#### manually added this A
-#### see https://www.nature.com/articles/s41467-020-18068-6#Sec24 (supplementary data 4)
+# remove tRNA-Lys-CTT-7-1 as this is definitely a weird tRNA with extra sequence in D-loop that is not an intron
+# despite high score, this is a strange tRNA (http://gtrnadb.ucsc.edu/genomes/eukaryota/Celeg11/genes/tRNA-Lys-CTT-7-1.html)

mimseq/mimseq.py

@@ -416,3 +416,3 @@ #! /usr/bin/env python3
 				if args.species == 'Cele':
-					args.trnas = os.path.dirname(os.path.realpath(__file__)) + "/data/ce11-eColitK/ce11-tRNAs-all.fa"
+					args.trnas = os.path.dirname(os.path.realpath(__file__)) + "/data/ce11-eColitK/ce11-tRNAs-filtered.fa"
 					args.trnaout = os.path.dirname(os.path.realpath(__file__)) + "/data/ce11-eColitK/ce11-tRNAs-detailed.out"
@@ -419,0 +419,0 @@ args.mito = os.path.dirname(os.path.realpath(__file__)) + "/data/ce11-eColitK/ce11-mitotRNAs.fa"

mimseq/version.py

@@ -1,1 +0,1 @@
-__version__ = "v1.3.4"
+__version__ = "v1.3.5"

PKG-INFO

 Metadata-Version: 2.1
 Name: mimseq
-Version: 1.3.4
+Version: 1.3.5
 Summary: Custom high-throughput tRNA sequencing alignment and quantification pipeline based on modification induced misincorporation cDNA synthesis.
@@ -9,2 +9,3 @@ Home-page: https://github.com/nedialkova-lab/mim-tRNAseq
 License: GPLv3
+Platform: UNKNOWN
 Classifier: Development Status :: 4 - Beta
@@ -18,1 +19,4 @@ Classifier: Environment :: Console
 License-File: LICENSE.txt
+
+UNKNOWN
+

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18166723

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178

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