[med-svn] [Git][med-team/trnascan-se][master] 11 commits: Add repack suffix
Nilesh Patra
gitlab at salsa.debian.org
Thu Sep 24 20:19:04 BST 2020
Nilesh Patra pushed to branch master at Debian Med / trnascan-se
Commits:
c9eeee37 by Nilesh Patra at 2020-09-25T00:15:49+05:30
Add repack suffix
- - - - -
6c42e5bd by Nilesh Patra at 2020-09-25T00:16:19+05:30
New upstream version 2.0.6+ds
- - - - -
1a85cdc2 by Nilesh Patra at 2020-09-25T00:16:19+05:30
routine-update: New upstream version
- - - - -
b0626dd5 by Nilesh Patra at 2020-09-25T00:17:01+05:30
Update upstream source from tag 'upstream/2.0.6+ds'
Update to upstream version '2.0.6+ds'
with Debian dir abfa9b88accb93f6c16b4646c51fd566648c258b
- - - - -
cb5a9007 by Nilesh Patra at 2020-09-25T00:17:01+05:30
routine-update: Standards-Version: 4.5.0
- - - - -
3bb1d8c1 by Nilesh Patra at 2020-09-25T00:17:01+05:30
routine-update: debhelper-compat 13
- - - - -
e0df194a by Nilesh Patra at 2020-09-25T00:17:12+05:30
routine-update: Add salsa-ci file
- - - - -
c3bb48e1 by Nilesh Patra at 2020-09-25T00:17:12+05:30
routine-update: Rules-Requires-Root: no
- - - - -
bd250bbb by Nilesh Patra at 2020-09-25T00:17:32+05:30
routine-update: Ready to upload to unstable
- - - - -
9c9471dd by Nilesh Patra at 2020-09-25T00:26:31+05:30
Header files not needed
- - - - -
aec148d6 by Nilesh Patra at 2020-09-24T19:15:18+00:00
Add manpages
- - - - -
27 changed files:
- README
- + debian/EukHighConfidenceFilter.1
- debian/changelog
- debian/control
- + debian/covels-SE.1
- + debian/coves-SE.1
- + debian/createmanpages
- + debian/eufindtRNA.1
- + debian/fasta2gsi.1
- debian/manpages
- debian/rules
- + debian/salsa-ci.yml
- + debian/sstofa.1
- + debian/tRNAscan-SE.1
- + debian/trnascan-1.4.1
- debian/watch
- lib/models/TRNAinf-arch-iso
- lib/models/TRNAinf-arch-iso.i1f
- lib/models/TRNAinf-arch-iso.i1i
- lib/models/TRNAinf-arch-iso.i1m
- lib/models/TRNAinf-arch-iso.i1p
- lib/tRNAscanSE/CM.pm
- + lib/tRNAscanSE/Constants.pm
- lib/tRNAscanSE/ResultFileReader.pm
- lib/tRNAscanSE/Sequence.pm
- lib/tRNAscanSE/tRNA.pm
- tRNAscan-SE.src
Changes:
=====================================
README
=====================================
@@ -5,7 +5,7 @@ Patricia Chan, Brian Lin, and Todd Lowe
School of Engineering, University of California, Santa Cruz, CA
--------------------------------------------------------------
-Current release: 2.0.4 (September 2019)
+Current release: 2.0.6 (May 2020)
tRNAscan-SE was written in the PERL (version 5) script language.
Input consists of DNA or RNA sequences in FASTA format. tRNA
=====================================
debian/EukHighConfidenceFilter.1
=====================================
@@ -0,0 +1,23 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH EUKHIGHCONFIDENCEFILTER "1" "September 2020" "EukHighConfidenceFilter 2.0.6+ds" "User Commands"
+.SH NAME
+EukHighConfidenceFilter \- detection of transfer RNA genes in genomic sequence
+.SH SYNOPSIS
+.B EukQualityFilter
+[\fI\,options\/\fR]
+.SH DESCRIPTION
+Options
+\fB\-\-result\fR \fB\-i\fR <file> tRNAscan\-SE output file used as input
+\fB\-\-ss\fR \fB\-s\fR <file> tRNAscan\-SE secondary structure file used as input
+\fB\-\-output\fR \fB\-o\fR <file path> Directory where output files will be written
+\fB\-\-prefix\fR \fB\-p\fR <name> Prefix for output file name
+\fB\-\-remove\fR \fB\-r\fR Remove filtered tRNA hits (default: filtered tRNA hits are only tagged)
+\fB\-\-cmscore1\fR \fB\-c1\fR <num> Domain\-specific model score cutoff for secondary filtering (default = 50; \fB\-1\fR if not used for filtering)
+\fB\-\-ssscore1\fR \fB\-m1\fR <num> Secondary structure score cutoff for secondary filtering (default = 10; \fB\-1\fR if not used for filtering)
+\fB\-\-isoscore1\fR \fB\-e1\fR <num> Isotype\-specific model score cutoff for secondary filtering (default = 70; \fB\-1\fR if not used for filtering)
+\fB\-\-isoscore2\fR \fB\-e2\fR <num> Isotype\-specific model starting score cutoff for tertiary filtering (default = 70; \fB\-1\fR if not used for filtering)
+\fB\-\-isomaxscore2\fR \fB\-x\fR <num> Maximum isotype\-specific model score cutoff for tertiary filtering (default = 95)
+\fB\-\-help\fR \fB\-h\fR Print this help
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+trnascan-se (2.0.6+ds-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+
+ -- Nilesh Patra <npatra974 at gmail.com> Fri, 25 Sep 2020 00:17:32 +0530
+
trnascan-se (2.0.5-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -4,12 +4,13 @@ Uploaders: Afif Elghraoui <afif at debian.org>
Section: non-free/science
XS-Autobuild: yes
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
infernal
-Standards-Version: 4.4.1
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/trnascan-se
Vcs-Git: https://salsa.debian.org/med-team/trnascan-se.git
Homepage: http://lowelab.ucsc.edu/tRNAscan-SE
+Rules-Requires-Root: no
Package: trnascan-se
Architecture: any
=====================================
debian/covels-SE.1
=====================================
@@ -0,0 +1,42 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH COVELS-SE "1" "September 2020" "covels-SE 2.0.6+ds" "User Commands"
+.SH NAME
+covels-SE \- detection of transfer RNA genes in genomic sequence
+.SH SYNOPSIS
+.B covels
+[\fI\,-options\/\fR] \fI\,<CM file> <seqfile>\/\fR
+.SH DESCRIPTION
+covels \- scan sequences for matches to an RNA covariance model
+.IP
+version 2.4.4 (January 1996)
+.SS "where options are:"
+.TP
+\fB\-c\fR
+: do complementary strand too
+.HP
+\fB\-g\fR <fracGC> : set background expected GC content (0.5 default)
+.TP
+\fB\-h\fR
+: print short help and version info
+.TP
+\fB\-o\fR <file>
+: save hits in <file>
+.HP
+\fB\-t\fR <thresh> : set score reporting threshold
+.HP
+\fB\-w\fR <window> : set scanning window size
+.IP
+CRASH PROTECTION OPTIONS:
+.HP
+\fB\-D\fR <filename> : save name of last sequence processed
+.IP
+EXPERIMENTAL OPTIONS:
+.TP
+\fB\-E\fR
+: set epsilon for fast search
+.TP
+\fB\-F\fR
+: fast heuristic search
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/coves-SE.1
=====================================
@@ -0,0 +1,23 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH COVES-SE "1" "September 2020" "coves-SE 2.0.6+ds" "User Commands"
+.SH NAME
+coves-SE \- detection of transfer RNA genes in genomic sequence
+.SH DESCRIPTION
+FATAL: Usage: coves [\-options] <CM file> <seqfile>
+where options are:
+.TP
+\fB\-a\fR
+: show all pairs, not just Watson\-Crick
+.HP
+\fB\-g\fR <gcfrac> : set expected background GC composition (default 0.5)
+.TP
+\fB\-m\fR
+: mountain representation of structural alignment
+.TP
+\fB\-s\fR
+: secondary structure string representation of
+.IP
+structural alignment
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,72 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=EukHighConfidenceFilter
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+progname=sstofa
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+
+progname=tRNAscan-SE
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+progname=coves-SE
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+progname=covels-SE
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+progname=eufindtRNA
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+progname=trnascan-1.4
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
=====================================
debian/eufindtRNA.1
=====================================
@@ -0,0 +1,26 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH EUFINDTRNA "1" "September 2020" "eufindtRNA 2.0.6+ds" "User Commands"
+.SH NAME
+eufindtRNA \- detection of transfer RNA genes in genomic sequence
+.SH SYNOPSIS
+.B eufindtRNA
+[\fI\,-options\/\fR] \fI\,<sequence file>\/\fR
+.SH DESCRIPTION
+eufindtRNA 1.1, Aug 2000
+.PP
+Find tRNAs in eukaryotic sequences
+.PP
+Available options:
+\fB\-h\fR : help \- print version and usage info
+\fB\-o\fR <outfile> : save tRNAs in <outfile>
+\fB\-r\fR : relaxed mode (no terminators searched for)
+\fB\-s\fR : strict mode (discard tRNAs with missing terminators)
+\fB\-l\fR <length> : set max intron+variable loop length (default=140)
+\fB\-X\fR <Score> : manually set final score cutoff to <Score> (def=\-31.8)
+\fB\-I\fR <Score> : set cutoff for intermediate score (def=\-31.25)
+\fB\-D\fR : save tRNA score components (for Debugging)
+\fB\-F\fR : don't check for uppercase or DNA alphabet
+\fB\-i\fR <integer> : start nucleotide numbering at <integer> (def=1)
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/fasta2gsi.1
=====================================
@@ -0,0 +1,13 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH SSTOFA "1" "September 2020" "fasta2gsi 2.0.6+ds" "User Commands"
+.SH NAME
+fasta2gsi \- detection of transfer RNA genes in genomic sequence
+.SH SYNOPSIS
+.B sstofa
+\fI\,<fasta file>\/\fR
+.SH DESCRIPTION
+Convert fasta file to gsi format
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
+
=====================================
debian/manpages
=====================================
@@ -1 +1 @@
-debian/man/*
+debian/*.1
=====================================
debian/rules
=====================================
@@ -8,3 +8,7 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
# tRNAscan can't handle compressed fasta files
override_dh_compress:
dh_compress -X .fa
+
+override_dh_missing:
+ rm -rf debian/*/usr/include
+ dh_missing
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/sstofa.1
=====================================
@@ -0,0 +1,12 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH SSTOFA "1" "September 2020" "sstofa 2.0.6+ds" "User Commands"
+.SH NAME
+sstofa \- detection of transfer RNA genes in genomic sequence
+.SH SYNOPSIS
+.B sstofa
+\fI\,<sec struct file>\/\fR
+.SH DESCRIPTION
+Convert secondary structure file to fasta format
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/tRNAscan-SE.1
=====================================
@@ -0,0 +1,203 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH TRNASCAN-SE "1" "September 2020" "tRNAscan-SE 2.0.6+ds" "User Commands"
+.SH NAME
+tRNAscan-SE \- detection of transfer RNA genes in genomic sequence
+.SH SYNOPSIS
+.B tRNAscan-SE
+[\fI\,-options\/\fR] \fI\,<FASTA file(s)>\/\fR
+.SH DESCRIPTION
+tRNAscan\-SE 2.0.6 (May 2020)
+Copyright \(co 2019 Patricia Chan and Todd Lowe
+.IP
+University of California Santa Cruz
+.PP
+Freely distributed under the GNU General Public License (GPLv3)
+.IP
+Scan a sequence file for tRNAs
+.HP
+\fB\-\-\fR default: use Infernal & tRNA covariance models
+.IP
+with eukaryotic sequences
+(use 'Search Mode Options' below to scan other types of sequences)
+.PP
+Search Mode Options:
+.TP
+\fB\-E\fR
+: search for eukaryotic tRNAs (default)
+.TP
+\fB\-B\fR
+: search for bacterial tRNAs
+.TP
+\fB\-A\fR
+: search for archaeal tRNAs
+.TP
+\fB\-M\fR <model>
+: search for mitochondrial tRNAs
+options: mammal, vert
+.TP
+\fB\-O\fR
+: search for other organellar tRNAs
+.TP
+\fB\-G\fR
+: use general tRNA model (cytoslic tRNAs from all 3 domains included)
+.TP
+\fB\-\-mt\fR <model>
+: use mito tRNA models for cytosolic/mito detemination
+(if not specified, only cytosolic isotype\-specific model scan will be performed)
+.TP
+\fB\-I\fR
+: search using Infernal
+default use with \fB\-E\fR, \fB\-B\fR, \fB\-A\fR, or \fB\-G\fR; optional for \fB\-O\fR
+.TP
+\fB\-\-max\fR
+: maximum sensitivity mode \- search using Infernal without hmm filter (very slow)
+.TP
+\fB\-L\fR
+: search using the legacy method (tRNAscan, EufindtRNA, and COVE)
+use with \fB\-E\fR, \fB\-B\fR, \fB\-A\fR or \fB\-G\fR
+.TP
+\fB\-C\fR \fB\-\-cove\fR
+: search using COVE analysis only (legacy, extremely slow)
+default use with \fB\-O\fR
+.TP
+\fB\-H\fR \fB\-\-breakdown\fR
+: show breakdown of primary and secondary structure components to
+covariance model bit scores
+.TP
+\fB\-D\fR \fB\-\-nopseudo\fR
+: disable pseudogene checking
+.PP
+Output options:
+.TP
+\fB\-o\fR \fB\-\-output\fR <file>
+: save final results in <file>
+.TP
+\fB\-f\fR \fB\-\-struct\fR <file>
+: save tRNA secondary structures to <file>
+.TP
+\fB\-s\fR \fB\-\-isospecific\fR <file>
+: save results using isotype\-specific models in <file>
+.TP
+\fB\-m\fR \fB\-\-stats\fR <file>
+: save statistics summary for run in <file>
+(speed, # tRNAs found in each part of search, etc)
+.TP
+\fB\-b\fR \fB\-\-bed\fR <file>
+: save results in BED file format of <file>
+.TP
+\fB\-a\fR \fB\-\-fasta\fR <file>
+: save predicted tRNA sequences in FASTA file format of <file>
+.TP
+\fB\-l\fR \fB\-\-log\fR <file>
+: save log of program progress in <file>
+.TP
+\fB\-\-detail\fR
+: display prediction outputs in detailed view
+.TP
+\fB\-\-brief\fR
+: brief output format (no column headers)
+.TP
+\-? #
+: '#' in place of <file> chooses default name for output files
+.TP
+\fB\-p\fR \fB\-\-prefix\fR <label>
+: use <label> prefix for all default output file names
+.TP
+\fB\-d\fR \fB\-\-progress\fR
+: display program progress messages
+.TP
+\fB\-q\fR \fB\-\-quiet\fR
+: quiet mode (credits & run option selections suppressed)
+.TP
+\fB\-y\fR \fB\-\-hitsrc\fR
+: show origin of hits (Ts=tRNAscan 1.4, Eu=EufindtRNA,
+Bo=Both Ts and Eu, Inf=Infernal)
+.PP
+Specify Alternate Cutoffs / Data Files:
+.TP
+\fB\-X\fR \fB\-\-score\fR <score>
+: set cutoff score (in bits) for reporting tRNAs (default=20)
+.TP
+\fB\-g\fR \fB\-\-gencode\fR <file>
+: use alternate genetic codes specified in <file> for
+determining tRNA type
+.TP
+\fB\-z\fR \fB\-\-pad\fR <number>
+: use <number> nucleotides padding when passing first\-pass
+tRNA bounds predictions to CM analysis (default=8)
+.TP
+\fB\-\-len\fR <length>
+: set max length of tRNA intron+variable region for legacy search mode
+(default=116bp)
+.PP
+Misc Options:
+.TP
+\fB\-h\fR \fB\-\-help\fR
+: print this help message
+.TP
+\fB\-c\fR \fB\-\-conf\fR <file>
+: tRNAscan\-SE configuration file (default: tRNAscan\-SE.conf)
+.TP
+\fB\-Q\fR \fB\-\-forceow\fR
+: do not prompt user before overwriting pre\-existing
+result files (for batch processing)
+.TP
+\fB\-\-match\fR <EXPR>
+: search only sequences with names matching <EXPR> string
+(<EXPR> may contain * or ? wildcard chars)
+.TP
+\fB\-\-search\fR <EXPR>
+: start search at sequence with name matching <EXPR> string
+and continue to end of input sequence file(s)
+.PP
+Special Advanced Options (for testing & special purposes)
+.TP
+\fB\-U\fR
+: search for tRNAs with alternate models defined in configuration file
+.TP
+\fB\-t\fR \fB\-\-tscan\fR
+: search using tRNAscan only (defaults to strict params)
+.TP
+\fB\-\-tmode\fR <mode>
+: explicitly set tRNAscan params, where <mode>=R or S
+(R=relaxed, S=strict tRNAscan v1.3 params)
+.TP
+\fB\-v\fR \fB\-\-verbose\fR <file>
+: save verbose tRNAscan 1.3 output to <file>
+.TP
+\fB\-\-nomerge\fR
+: Keep redundant tRNAscan 1.3 hits (don't filter out multiple
+predictions per tRNA identification)
+.TP
+\fB\-e\fR \fB\-\-eufind\fR
+: search using Eukaryotic tRNA finder (EufindtRNA) only
+(defaults to Normal seach parameters when run alone,
+or to Relaxed search params when run with Cove)
+.TP
+\fB\-\-emode\fR <mode>
+: explicitly set EufindtRNA params, where <mode>=R, N, or S
+(relaxed, normal, or strict)
+.TP
+\fB\-\-iscore\fR <score>
+: manually set "intermediate" cutoff score for EufindtRNA
+.TP
+\fB\-r\fR \fB\-\-fsres\fR <file>
+: save first\-pass scan results from EufindtRNA, tRNAscan, or
+Infernal hmm in <file> in tabular results format
+.TP
+\fB\-\-mid\fR
+: fast scan mode \- search using Infernal with mid\-level strictness of hmm filter
+.TP
+\fB\-F\fR \fB\-\-falsepos\fR <file>
+: save first\-pass candidate tRNAs in <file> that were then
+found to be false positives by second\-pass analysis
+.TP
+\fB\-\-missed\fR <file>
+: save all seqs that do NOT have at least one
+tRNA prediction in them (aka "missed" seqs)
+.TP
+\fB\-\-thread\fR <number>
+: number of threads used for running infernal (default is to use available threads)
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/trnascan-1.4.1
=====================================
@@ -0,0 +1,23 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH TRNASCAN-1.4 "1" "September 2020" "trnascan-1.4 2.0.6+ds" "User Commands"
+.SH NAME
+trnascan-1.4 \- detection of transfer RNA genes in genomic sequence
+.SH SYNOPSIS
+.B trnascan
+[\fI\,-options\/\fR] \fI\,<seqfile>\/\fR
+.SH DESCRIPTION
+trnascan: scan a sequence for tRNAs
+.IP
+version 1.4 (Feb 96)
+.PP
+where supported options are:
+\fB\-s\fR : use original tRNAscan 1.3 parameters (default)
+\fB\-r\fR : use relaxed search parameters (used with tRNAscan\-SE)
+\fB\-a\fR : use alternate (user\-set) search parameters
+\fB\-c\fR : suppress credits
+\fB\-o\fR <outfile> : write results to <outfile>
+\fB\-i\fR <integer> : start sequence numbering at <integer> (def=1)
+\fB\-h\fR : print (this) short help message
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
version=4
-opts="uversionmangle=s/rc/~rc/i,repack,compression=gz" \
+opts="repacksuffix=+ds,dversionmangle=auto,repack,compression=gz" \
http://trna.ucsc.edu/software/trnascan-se-(.*)\.tar\.gz
=====================================
lib/models/TRNAinf-arch-iso
=====================================
The diff for this file was not included because it is too large.
=====================================
lib/models/TRNAinf-arch-iso.i1f
=====================================
Binary files a/lib/models/TRNAinf-arch-iso.i1f and b/lib/models/TRNAinf-arch-iso.i1f differ
=====================================
lib/models/TRNAinf-arch-iso.i1i
=====================================
Binary files a/lib/models/TRNAinf-arch-iso.i1i and b/lib/models/TRNAinf-arch-iso.i1i differ
=====================================
lib/models/TRNAinf-arch-iso.i1m
=====================================
Binary files a/lib/models/TRNAinf-arch-iso.i1m and b/lib/models/TRNAinf-arch-iso.i1m differ
=====================================
lib/models/TRNAinf-arch-iso.i1p
=====================================
Binary files a/lib/models/TRNAinf-arch-iso.i1p and b/lib/models/TRNAinf-arch-iso.i1p differ
=====================================
lib/tRNAscanSE/CM.pm
=====================================
@@ -3,7 +3,7 @@
#
# --------------------------------------------------------------
# This module is part of the tRNAscan-SE program.
-# Copyright (C) 2017 Patricia Chan and Todd Lowe
+# Copyright (C) 2020 Patricia Chan and Todd Lowe
# --------------------------------------------------------------
#
@@ -992,7 +992,7 @@ sub decode_nci_tRNA_properties
for (my $i = 0; $i < scalar(@introns); $i++)
{
- if ($acodon_index > $introns[$i]->{rel_start})
+ if ($acodon_index >= $introns[$i]->{rel_start})
{
$acodon_index += ($introns[$i]->{rel_end} - $introns[$i]->{rel_start} + 1);
}
=====================================
lib/tRNAscanSE/Constants.pm
=====================================
@@ -0,0 +1,105 @@
+# tRNAscanSE/Constants.pm
+# This class defines global constants used in tRNAscan-SE.
+#
+# --------------------------------------------------------------
+# This module is part of the tRNAscan-SE program.
+# Copyright (C) 2017 Patricia Chan and Todd Lowe
+# --------------------------------------------------------------
+#
+
+package tRNAscanSE::Constants;
+
+use strict;
+use tRNAscanSE::Utils;
+
+sub new {
+ my $class = shift;
+ my $self = {};
+
+ initialize($self);
+
+ bless ($self, $class);
+ return $self;
+}
+
+sub DESTROY
+{
+ my $self = shift;
+}
+
+sub initialize
+{
+ my $self = shift;
+
+ $self->{REALLY_BIG_NUMBER} = 1000000000; # largest sequence length imaginable
+
+ # Source of first-pass hits table
+ # C = Cove, T = tRNAscan, E = EufindtRNA, B = both
+
+ my @source_tab = ('Cv', 'Ts', 'Eu', 'Bo');
+ $self->{source_tab} = \@source_tab;
+
+ $self->{upstream_len} = 60;
+ $self->{downstream_len} = 60;
+}
+
+sub REALLY_BIG_NUMBER
+{
+ my $self = shift;
+ return $self->{REALLY_BIG_NUMBER};
+}
+
+sub source_tab
+{
+ my $self = shift;
+ return $self->{source_tab};
+}
+
+sub upstream_len
+{
+ my $self = shift;
+ return $self->{upstream_len};
+}
+
+sub downstream_len
+{
+ my $self = shift;
+ return $self->{downstream_len};
+}
+
+sub set_temp_file_names
+{
+ my $self = shift;
+ my $temp_dir = shift;
+
+ $self->{tmp_raw} = &tempname($temp_dir, ".raw"); # for raw tscan output
+ $self->{tmp_fa} = &tempname($temp_dir, ".fa"); # for current fasta seq file
+ $self->{tmp_trnaseq_file} = &tempname($temp_dir, ".trna"); # for current tRNA seq
+ $self->{tmp_masked_fa} = &tempname($temp_dir, ".masked.fa"); # for current tRNA seq
+}
+
+sub tmp_raw
+{
+ my $self = shift;
+ return $self->{tmp_raw};
+}
+
+sub tmp_fa
+{
+ my $self = shift;
+ return $self->{tmp_fa};
+}
+
+sub tmp_trnaseq_file
+{
+ my $self = shift;
+ return $self->{tmp_trnaseq_file};
+}
+
+sub tmp_masked_fa
+{
+ my $self = shift;
+ return $self->{tmp_masked_fa};
+}
+
+1;
=====================================
lib/tRNAscanSE/ResultFileReader.pm
=====================================
@@ -16,7 +16,7 @@ use tRNAscanSE::LogFile;
require Exporter;
our @ISA = qw(Exporter);
-our @EXPORT = qw(read_out_file read_ss_file read_sprinzl_pos_map read_noncanomical);
+our @EXPORT = qw(read_out_file read_ss_file read_sprinzl_pos_map read_noncanomical read_name_map);
sub read_out_file
{
@@ -226,39 +226,63 @@ sub read_ss_file
my $tRNA = undef;
my $intron = {};
my $line = "";
- my ($startpos, $endpos);
+ my ($startpos, $endpos, $coords);
$log->status("Reading tRNAs from $file");
open(SSFILE, "$file") || die "Error: Fail to open $file\n";
while ($line = <SSFILE>)
{
- if ($line =~ /^(\S+)\s+\((\d+)\-(\d+)\)\s+Length:\s(\d+)\sbp/)
+ if ($line =~ /^(\S+)\s+\((\S+)\)\s+Length:\s(\d+)\sbp/)
{
if (defined $tRNA and $tRNA->tRNAscan_id() ne "")
{
$tRNA->set_mature_tRNA();
$tRNAs->put($tRNA);
}
+ my $id = $1;
+ $coords = $2;
$tRNA = tRNAscanSE::tRNA->new;
$tRNA->tRNAscan_id($1);
- $startpos = $2;
- $endpos = $3;
$tRNA->seqname(substr($tRNA->tRNAscan_id(), 0, rindex($tRNA->tRNAscan_id(), ".")));
- if ($startpos < $endpos)
+ if (index($coords, ",") == -1)
{
- $tRNA->start($startpos);
- $tRNA->end($endpos);
- $tRNA->strand("+");
+ ($startpos, $endpos) = split(/-/, $coords);
+ if ($startpos < $endpos)
+ {
+ $tRNA->start($startpos);
+ $tRNA->end($endpos);
+ $tRNA->strand("+");
+ }
+ else
+ {
+ $tRNA->end($startpos);
+ $tRNA->start($endpos);
+ $tRNA->strand("-");
+ }
}
else
{
- $tRNA->end($startpos);
- $tRNA->start($endpos);
- $tRNA->strand("-");
+ my @loci = split(/\,/, $coords);
+ for (my $exon_count = 0; $exon_count < scalar(@loci); $exon_count++)
+ {
+ ($startpos, $endpos) = split(/-/, $loci[$exon_count]);
+ if ($startpos < $endpos)
+ {
+ $tRNA->exon_start($exon_count+1, $startpos);
+ $tRNA->exon_end($exon_count+1, $endpos);
+ $tRNA->exon_strand($exon_count+1, "+");
+ }
+ else
+ {
+ $tRNA->exon_end($exon_count+1, $startpos);
+ $tRNA->exon_start($exon_count+1, $endpos);
+ $tRNA->exon_strand($exon_count+1, "-");
+ }
+ }
}
if ($tRNA->seqname() eq "chrM" or $tRNA->seqname() eq "M" or $tRNA->seqname() eq "chrMT" or $tRNA->seqname() eq "MT")
{
- $tRNA->category("mt");
+ $tRNA->category("mito");
}
else
{
@@ -280,30 +304,34 @@ sub read_ss_file
}
$tRNA->score($5);
$tRNA->set_domain_model("infernal", $tRNA->score());
+ my $frag = index($tRNA->isotype(), "-exon");
+ if ($frag > -1)
+ {
+ $tRNA->isotype(substr($tRNA->isotype(), 0, $frag));
+ }
$tRNA->tRNAscan_id($tRNA->tRNAscan_id()."-".$tRNA->isotype().$tRNA->anticodon());
+ $tRNA->gtrnadb_id($tRNA->tRNAscan_id());
if ($tRNA->isotype() eq "Undet")
{
- $tRNA->category("und");
+ $tRNA->category("undetermined_ac");
}
}
elsif ($line =~ /^HMM Sc=(\S+)\s+Sec struct Sc=(\S+)/)
{
- my $inf_score = $3;
$tRNA->hmm_score($1);
$tRNA->ss_score($2);
- $tRNA->update_domain_model("infernal", $inf_score, $inf_score, $tRNA->hmm_score(), $tRNA->ss_score());
+ $tRNA->update_domain_model("infernal", $tRNA->score(), $tRNA->score(), $tRNA->hmm_score(), $tRNA->ss_score());
}
- elsif ($line =~ /^Possible pseudogene:\s+HMM Sc=(\S+)\s+Sec struct Sc=(\S+)/)
+ elsif ($line =~ /pseudogene:\s+HMM Sc=(\S+)\s+Sec struct Sc=(\S+)/)
{
- my $inf_score = $3;
$tRNA->hmm_score($1);
$tRNA->ss_score($2);
- $tRNA->update_domain_model("infernal", $inf_score, $inf_score, $tRNA->hmm_score(), $tRNA->ss_score());
+ $tRNA->update_domain_model("infernal", $tRNA->score(), $tRNA->score(), $tRNA->hmm_score(), $tRNA->ss_score());
$tRNA->pseudo(1);
}
elsif ($line =~ /^Possible intron: (\d+)-(\d+) \((\d+)-(\d+)\)/)
{
- $tRNA->add_intron($1, $2, $3, $4, "");
+ $tRNA->add_intron($1, $2, $3, $4, "", "");
}
elsif ($line =~ /^Seq:\s(\S+)$/)
{
@@ -436,4 +464,36 @@ sub read_noncanomical
close(FILE_IN);
}
+sub read_name_map
+{
+ my ($global_vars, $file) = @_;
+ my $log = $global_vars->{log_file};
+ my $tRNAs = $global_vars->{tRNAs};
+ my $line = "";
+ my @columns = ();
+ my $index = -1;
+
+ $tRNAs->sort_array("tRNAscanid");
+
+ $log->status("Reading GtRNAdb name map from $file");
+ open(FILE_IN, "$file") or die "Fail to open $file\n";
+
+ $line = <FILE_IN>;
+ chomp($line);
+ my @header = split(/\t/, $line);
+
+ while ($line = <FILE_IN>)
+ {
+ chomp($line);
+ @columns = split(/\t/, $line, -1);
+ $index = $tRNAs->bsearch_id($columns[0], "tRNAscanid");
+ if ($index > -1)
+ {
+ $tRNAs->get($index)->gtrnadb_id($columns[1]);
+ }
+ }
+
+ close(FILE_IN);
+}
+
1;
=====================================
lib/tRNAscanSE/Sequence.pm
=====================================
@@ -3,12 +3,9 @@
#
# --------------------------------------------------------------
# This module is part of the tRNAscan-SE program.
-# Copyright (C) 2017 Patricia Chan and Todd Lowe
+# Copyright (C) 2020 Patricia Chan and Todd Lowe
# --------------------------------------------------------------
#
-# Perl code for reading FASTA-formatted sequence files
-# SRE, Sat Feb 19 19:10:43 1994
-
# These subroutines read a FASTA formatted file one sequence at a time.
# Open(filename, open_mode) opens a file for reading or wrting.
# Close() closes it when you're done.
@@ -21,7 +18,6 @@
# $seq_length = length of sequence
# $sequence = sequence, gaps and newlines removed
#
-# Modified by TMJL 11/95 for use in tRNAscan-SE
package tRNAscanSE::Sequence;
@@ -416,7 +412,14 @@ sub read_fasta_subseq
$seqlen += length($self->{saved_line});
}
- $self->{sequence} = substr($tempseq, 0, $subseq_len);
+ if ($seqlen < $subseq_len)
+ {
+ $self->{sequence} = substr($tempseq, 0, $seqlen);
+ }
+ else
+ {
+ $self->{sequence} = substr($tempseq, 0, $subseq_len);
+ }
$self->{sequence} = uc($self->{sequence});
$self->{sequence} =~ s/U/T/g;
@@ -497,7 +500,14 @@ sub read_fasta_subseq_slow
$seqlen += length($self->{saved_line});
}
- $self->{sequence} = substr($tempseq, 0, $subseq_len);
+ if ($seqlen < $subseq_len)
+ {
+ $self->{sequence} = substr($tempseq, 0, $seqlen);
+ }
+ else
+ {
+ $self->{sequence} = substr($tempseq, 0, $subseq_len);
+ }
$self->{sequence} = uc($self->{sequence});
$self->{sequence} =~ s/U/T/g;
=====================================
lib/tRNAscanSE/tRNA.pm
=====================================
@@ -571,7 +571,7 @@ sub get_intron
my $self = shift;
my $index = shift;
- if ($index >= 0 and $index < get_intron_count())
+ if ($index >= 0 and $index < $self->get_intron_count())
{
return $self->{data}->[_ar_introns]->[$index];
}
=====================================
tRNAscan-SE.src
=====================================
@@ -4,13 +4,13 @@
# tRNAscan-SE: a program for improved detection of transfer RNA
# genes in genomic sequence
#
-# Version 2.0.5
+# Version 2.0.6
#
-# Copyright (C) 2019 Patricia Chan and Todd Lowe
+# Copyright (C) 2020 Patricia Chan and Todd Lowe
#
# School of Engineering, University of California, Santa Cruz
-# lowe at soe.ucsc.edu
-# http://lowelab.ucsc.edu/
+# trna at soe.ucsc.edu
+# http://trna.ucsc.edu/
# --------------------------------------------------------------------
#
# Usage:
@@ -39,8 +39,8 @@ use tRNAscanSE::IntResultFile;
use tRNAscanSE::MultiResultFile;
use tRNAscanSE::SS;
-our $version = "2.0.5";
-our $release_date = "October 2019";
+our $version = "2.0.6";
+our $release_date = "May 2020";
our $program_id = "tRNAscan-SE-".$version;
# modified by 'make'
@@ -1531,10 +1531,10 @@ sub set_options
{
$opts->infernal_fp(0);
}
- elsif ($opt_mito)
- {
- $opt_mid = 0;
- }
+ elsif ($opt_mito)
+ {
+ $opt_mid = 0;
+ }
}
# set hmm filter flag for infernal
@@ -1879,8 +1879,8 @@ sub set_options
$cm->cm_cutoff($opt_score);
if ($opt_score < $cm->infernal_fp_cutoff())
{
- $cm->infernal_fp_cutoff($opt_score);
- }
+ $cm->infernal_fp_cutoff($opt_score);
+ }
}
if ($opt_thread != 999)
View it on GitLab: https://salsa.debian.org/med-team/trnascan-se/-/compare/1fddc5eff8fd3cf3432acea62b58acb2bc560973...aec148d60d97f347982a95905b4c01ad0178e6f5
--
View it on GitLab: https://salsa.debian.org/med-team/trnascan-se/-/compare/1fddc5eff8fd3cf3432acea62b58acb2bc560973...aec148d60d97f347982a95905b4c01ad0178e6f5
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200924/30677cbb/attachment-0001.html>
More information about the debian-med-commit
mailing list