[med-svn] [Git][med-team/pftools][master] Use upstream patch instead of own one
Andreas Tille
gitlab at salsa.debian.org
Thu Dec 17 14:35:49 GMT 2020
Andreas Tille pushed to branch master at Debian Med / pftools
Commits:
a5d923a3 by Andreas Tille at 2020-12-17T15:35:16+01:00
Use upstream patch instead of own one
- - - - -
3 changed files:
- + debian/patches/0001-Harmonize-bin-env-path-Cleaning.patch
- debian/patches/fix_perl_interpreter.patch
- debian/patches/series
Changes:
=====================================
debian/patches/0001-Harmonize-bin-env-path-Cleaning.patch
=====================================
@@ -0,0 +1,265 @@
+From 342a8a5730c5b664741dff90a293f35818cb06d1 Mon Sep 17 00:00:00 2001
+From: smoretti <sebastien.moretti at sib.swiss>
+Date: Wed, 16 Dec 2020 18:08:06 +0100
+Subject: [PATCH] Harmonize bin/env path + Cleaning
+
+---
+ src/Perl/fasta_to_fastq.pl | 2 +-
+ src/Perl/make_iupac_cmp.pl | 2 +-
+ src/Perl/scramble_fasta.pl | 2 +-
+ src/Perl/sort_fasta.pl | 2 +-
+ tests/examples/test_V3.sh.cmake | 68 +++++++++----------
+ tests/examples/test_V3_output.sh.cmake | 3 -
+ tests/examples/test_pfsearchV3_iupac.pl.cmake | 2 +-
+ tests/examples/test_scan_search.pl.cmake | 2 +-
+ 8 files changed, 40 insertions(+), 43 deletions(-)
+
+--- a/src/Perl/fasta_to_fastq.pl
++++ b/src/Perl/fasta_to_fastq.pl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env perl
+ #Copyright (c) 2010 LUQMAN HAKIM BIN ABDUL HADI (csilhah at nus.edu.sg)
+ #
+ #Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files
+--- a/src/Perl/make_iupac_cmp.pl
++++ b/src/Perl/make_iupac_cmp.pl
+@@ -1,4 +1,4 @@
+-#!/bin/env perl
++#!/usr/bin/env perl
+
+ use strict;
+ use Getopt::Std;
+--- a/src/Perl/scramble_fasta.pl
++++ b/src/Perl/scramble_fasta.pl
+@@ -1,4 +1,4 @@
+-#!/bin/env perl
++#!/usr/bin/env perl
+
+ use strict;
+
+--- a/src/Perl/sort_fasta.pl
++++ b/src/Perl/sort_fasta.pl
+@@ -1,4 +1,4 @@
+-#!/bin/env perl
++#!/usr/bin/env perl
+
+ use strict;
+ use Getopt::Std;
+--- a/tests/examples/test_V3.sh.cmake
++++ b/tests/examples/test_V3.sh.cmake
+@@ -19,9 +19,9 @@ PFW=$<TARGET_FILE:pfw>
+ PTOH=$<TARGET_FILE:ptoh>
+ PTOF=$<TARGET_FILE:ptof>
+ P2FT=$<TARGET_FILE:2ft> # NB: sh does not allow variable name starting with a digit
+-
+-SORT_PSA=@PERL_SCRIPT_DIR@/sort_fasta.pl # FIXME: use cmake syntax
+-MAKE_IUPAC_CMP=@PERL_SCRIPT_DIR@/make_iupac_cmp.pl # FIXME: use cmake syntax
++
++SORT_PSA=@PERL_SCRIPT_DIR@/sort_fasta.pl # FIXME: use cmake syntax
++MAKE_IUPAC_CMP=@PERL_SCRIPT_DIR@/make_iupac_cmp.pl # FIXME: use cmake syntax
+ SCRAMBLE=@PERL_SCRIPT_DIR@/scramble_fasta.pl # FIXME: use cmake syntax
+
+ CMPDIR=@DATA_DIR@/Matrices
+@@ -29,15 +29,15 @@ TMPDIR=/tmp/test_V3
+ mkdir -p $TMPDIR
+
+ #----------------------------------------------------------------------#
+-# The PFTOOLS is a powerful software to align biological sequences.
+-# Owing to the 'generalized profile syntax', it allows the fine-tuning
+-# of an alignent scoring system, beyond what is feasible by most other
+-# software. Despite the PFTOOLS are crippled by a lot of legacy code,
+-# they are still extremely useful for precision work .
++# The PFTOOLS is a powerful software to align biological sequences.
++# Owing to the 'generalized profile syntax', it allows the fine-tuning
++# of an alignent scoring system, beyond what is feasible by most other
++# software. Despite the PFTOOLS are crippled by a lot of legacy code,
++# they are still extremely useful for precision work.
+ #
+ # Nota bene to use this script as a testsuite:
+-# (1) The output order of pfsearch is reproducible, as well as the one of
+-# pfsearchV3 with -t 1.
++# (1) The output order of pfsearch is reproducible, as well as the one of
++# pfsearchV3 with -t 1.
+ # (2) Refrain using any pipe.
+ #----------------------------------------------------------------------#
+
+@@ -45,7 +45,7 @@ mkdir -p $TMPDIR
+ # Searching for the occurence of the SH3 domain within the VAV oncogene,
+ # using pfsearch V2 ...
+ #----------------------------------------------------------------------#
+-$PFSEARCH -f ./sh3.prf ./VAV_HUMAN.seq
++$PFSEARCH -f ./sh3.prf ./VAV_HUMAN.seq
+
+ #----------------------------------------------------------------------#
+ # ...and using pfsearch V3:
+@@ -53,8 +53,8 @@ $PFSEARCH -f ./sh3.prf ./VAV_HUMAN.seq
+ $PFSEARCHV3 -n -t 1 -f ./sh3.prf ./VAV_HUMAN.seq
+
+ #----------------------------------------------------------------------#
+-# Create a database of sequences and a database of profiles, each one
+-# with two entries.
++# Create a database of sequences and a database of profiles, each one
++# with two entries.
+ #----------------------------------------------------------------------#
+ cat ./VAV_HUMAN.seq ./VAV_RAT.seq > $TMPDIR/VAV.seq
+ cat ./sh2.prf ./sh3.prf > $TMPDIR/SHX.prf
+@@ -79,10 +79,10 @@ $PFSEARCHV3 -f -n -t 2 -o 6 ./sh3.prf -f
+ $PFSCANV3 -f -n -o 6 $TMPDIR/SHX.prf $TMPDIR/VAV.seq > $TMPDIR/SHX.pfscan3.hit
+
+ #----------------------------------------------------------------------#
+-# All these commands produces exactly the same list of matched
+-# sequences, with the same raw scores and coordinates.
++# All these commands produces exactly the same list of matched
++# sequences, with the same raw scores and coordinates.
+ #
+-# However the output order is not necessarily preserved here.
++# However the output order is not necessarily preserved here.
+ #
+ # Let's verify that the output are comparable after fixing FASTA headers
+ #----------------------------------------------------------------------#
+@@ -95,7 +95,7 @@ diff $TMPDIR/SHX.pfscan2.out $TMPDIR/SHX
+ diff $TMPDIR/SHX.pfscan2.out $TMPDIR/SHX.pfsearch3.out # expecting no difference
+
+ #----------------------------------------------------------------------#
+-# Pfsearch/pfscan V2 supports the following input formats for sequence:
++# Pfsearch/pfscan V2 supports the following input formats for sequence:
+ # FASTA, Swiss-Prot and EMBL.
+ #----------------------------------------------------------------------#
+ $PFSEARCH -f ./sh3.prf ./VAV_HUMAN.seq # FASTA
+@@ -105,10 +105,10 @@ $PFSEARCH ./sh3.prf ./GTPA_HUMAN.dat
+ $PFSCAN ./GTPA_HUMAN.dat ./sh3.prf # SwissProt
+
+ $PFSEARCH ./ecp.prf ./CVPBR322.embl # EMBL
+-$PFSCAN ./CVPBR322.embl ./ecp.prf # EMBL
++$PFSCAN ./CVPBR322.embl ./ecp.prf # EMBL
+
+ #----------------------------------------------------------------------#
+-# Pfsearch/pfscan V3 supports the following input formats for sequence:
++# Pfsearch/pfscan V3 supports the following input formats for sequence:
+ # FASTA and FASTQ.
+ #----------------------------------------------------------------------#
+ $PFSEARCHV3 -n -t 1 -f ./sh3.prf ./VAV_HUMAN.seq # FASTA
+@@ -117,7 +117,7 @@ cat ./CVPBR322.embl \
+ | perl -ne 'if(/^ID +(\w+)/){print ">$1\n"}elsif(/^ /){s/[\s\d]+//g;print "$_\n";}' \
+ > $TMPDIR/CVPBR322.fa # Extract FASTA from EMBL
+ $PFSEARCHV3 -n -t 1 -f ./ecp.prf $TMPDIR/CVPBR322.fa
+-$PFSCANV3 -n -t 1 -f ./ecp.prf $TMPDIR/CVPBR322.fa
++$PFSCANV3 -n -t 1 -f ./ecp.prf $TMPDIR/CVPBR322.fa
+
+ $PFSEARCHV3 -n -t 1 -q ./hiv.prf ./hiv.fastq # FASTQ
+ $PFSCANV3 -n -t 1 -q ./hiv.prf ./hiv.fastq # FASTQ
+@@ -136,8 +136,8 @@ $PFSEARCHV3 -n -fb ./ecp.prf $TMPDIR/CVP
+ diff -b $TMPDIR/ecp.CVPBR322.2.hit $TMPDIR/ecp.CVPBR322.3.hit # expecting no difference
+
+ #----------------------------------------------------------------------#
+-# The different PSA (i.e FASTA) output formats differ by the content
+-# their headers. The usage of XPSA (-o 6) is strongly recommended, the
++# The different PSA (i.e FASTA) output formats differ by the content
++# their headers. The usage of XPSA (-o 6) is strongly recommended, the
+ # other formats being preserved for legacy.
+ #----------------------------------------------------------------------#
+ $PFSEARCHV3 -n -f -o 1 -N 15 ./sh3.prf ./VAV_HUMAN.seq | $SORT_PSA -
+@@ -147,10 +147,10 @@ $PFSEARCHV3 -n -f -o 4 -N 15 ./sh3.prf .
+ $PFSEARCHV3 -n -f -o 6 -N 15 ./sh3.prf ./VAV_HUMAN.seq | $SORT_PSA - # recommended
+
+ #----------------------------------------------------------------------#
+-# Multiple sequence alignment (MSA) can easily be produced from PSA
++# Multiple sequence alignment (MSA) can easily be produced from PSA
+ # using psa2msa (V2)
+ #----------------------------------------------------------------------#
+-$PFSEARCHV3 -n -f -o 6 ./ecp.prf $TMPDIR/CVPBR322.fa | $SORT_PSA - | $PSA2MSA
++$PFSEARCHV3 -n -f -o 6 ./ecp.prf $TMPDIR/CVPBR322.fa | $SORT_PSA - | $PSA2MSA
+
+ #----------------------------------------------------------------------#
+ # V3 has two new output formats: TSV and SAM
+@@ -169,15 +169,15 @@ $PFSEARCHV3 -n -t 1 -q -o 8 ./hiv.prf
+ $PFSEARCHV3 -n -t 1 -q -b -o 8 ./hiv.prf ./hiv.fastq # FASTQ to SAM
+
+ #----------------------------------------------------------------------#
+-# Index can optionaly be used to speed-up database upload for pfsearch.
+-# This should be especially usefull for repetitive database searches
+-# using the heuristic.
++# Index can optionaly be used to speed-up database upload for pfsearch.
++# This should be especially usefull for repetitive database searches
++# using the heuristic.
+ #----------------------------------------------------------------------#
+
+ $PFINDEX -f -o $TMPDIR/CVPBR322.fa.idx $TMPDIR/CVPBR322.fa
+ $PFSEARCHV3 -n -f -o 7 ./ecp.prf $TMPDIR/CVPBR322.fa | sort > $TMPDIR/A.out # FASTA to TSV
+ $PFSEARCHV3 -n -f -i $TMPDIR/CVPBR322.fa.idx -o 7 ./ecp.prf $TMPDIR/CVPBR322.fa | sort > $TMPDIR/B.out # FASTA to TSV
+-diff $TMPDIR/A.out $TMPDIR/B.out
++diff $TMPDIR/A.out $TMPDIR/B.out
+
+ $PFINDEX -q -o $TMPDIR/hiv.fastq.idx ./hiv.fastq
+ $PFSEARCHV3 -n -q -b -o 8 ./hiv.prf ./hiv.fastq | sort > $TMPDIR/A.out
+@@ -185,23 +185,23 @@ $PFSEARCHV3 -n -q -b -o 8 -i $TMPDIR/hiv
+ diff $TMPDIR/A.out $TMPDIR/B.out
+
+ #----------------------------------------------------------------------#
+-# Profile and/or sequence can be reversed on the fly. If both are
++# Profile and/or sequence can be reversed on the fly. If both are
+ # reversed the match score is the same
+ #----------------------------------------------------------------------#
+ $PFSEARCHV3 -f -a rand_dna.prf rand_dna.seq
+ $PFSEARCHV3 -f -a -r -R rand_dna.prf rand_dna.seq
+
+ #----------------------------------------------------------------------#
+-# There is a much better support of rev/comp search in DNA sequences,
++# There is a much better support of rev/comp search in DNA sequences,
+ # featuring the full IUPAC code.
+ # To illustrate these capabilities, let build a profile for bacterial
+-# 16S sequence, starting from the Rfam seed RF00177.msa. First create
++# 16S sequence, starting from the Rfam seed RF00177.msa. First create
+ # an adhoc substitution matrix
+ #----------------------------------------------------------------------#
+ $MAKE_IUPAC_CMP -M 20 -m -30 > $TMPDIR/iupac20-30.cmp
+
+ #----------------------------------------------------------------------#
+-# ... let build a profile for bacterial 16S sequence, starting from
++# ... let build a profile for bacterial 16S sequence, starting from
+ # the Rfam seed RF00177.msa.
+ #----------------------------------------------------------------------#
+ cat ./RF00177.msa \
+@@ -224,7 +224,7 @@ cat ./SRR9619541.sample.fastq \
+ > $TMPDIR/permut.fa
+
+ # $PFCALIBRATEV3 -F $TMPDIR/permut.fa $TMPDIR/16S.prf.tmp > $TMPDIR/16S.prf
+-# $PFSEARCHV3 -t 1 -n -q $TMPDIR/16S.prf $TMPDIR/small.sample.fastq
++# $PFSEARCHV3 -t 1 -n -q $TMPDIR/16S.prf $TMPDIR/small.sample.fastq
+
+ #----------------------------------------------------------------------#
+ # Verify handling of characters not in the profile alphabet
+@@ -240,7 +240,7 @@ ACGTWACGT
+ EOI
+ $PFMAKE -m -3 -S 0.01 -F 100 $TMPDIR/ACGTAACGT.seq $CMPDIR/dna_50_40.cmp > $TMPDIR/ACGTAACGT.prf
+
+-$PFSEARCHV3 -fa -o 6 $TMPDIR/ACGTAACGT.prf $TMPDIR/ACGTAACGT.seq # raw_score=450 PSA=ACGTAACGT
++$PFSEARCHV3 -fa -o 6 $TMPDIR/ACGTAACGT.prf $TMPDIR/ACGTAACGT.seq # raw_score=450 PSA=ACGTAACGT
+ $PFSEARCHV3 -fa -o 6 $TMPDIR/ACGTAACGT.prf $TMPDIR/ACGTWACGT.seq # raw_score=383 PSA=ACGTWACGT (not ACGTXACGT)
+
+
+--- a/tests/examples/test_V3_output.sh.cmake
++++ b/tests/examples/test_V3_output.sh.cmake
+@@ -13,6 +13,3 @@ mkdir -p $TMPDIR
+ sh -ve ./test_V3.sh > $TMPDIR/test_V3.out 2>/dev/null
+ diff ./test_V3.out $TMPDIR/test_V3.out
+
+-
+-
+-
+--- a/tests/examples/test_pfsearchV3_iupac.pl.cmake
++++ b/tests/examples/test_pfsearchV3_iupac.pl.cmake
+@@ -1,4 +1,4 @@
+-#!/bin/env perl
++#!/usr/bin/env perl
+
+ use strict;
+
+--- a/tests/examples/test_scan_search.pl.cmake
++++ b/tests/examples/test_scan_search.pl.cmake
+@@ -1,4 +1,4 @@
+-#!/bin/env perl
++#!/usr/bin/env perl
+
+ use strict;
+
=====================================
debian/patches/fix_perl_interpreter.patch
=====================================
@@ -10,3 +10,11 @@ Description: Fix interpreter of perl script to fix build time test
use strict;
use Getopt::Std;
+--- a/src/Perl/make_iupac_cmp.pl
++++ b/src/Perl/make_iupac_cmp.pl
+@@ -1,4 +1,4 @@
+-#!/bin/env perl
++#!/usr/bin/perl
+
+ use strict;
+ use Getopt::Std;
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
spelling.patch
-fix_perl_interpreter.patch
+# fix_perl_interpreter.patch
+0001-Harmonize-bin-env-path-Cleaning.patch
View it on GitLab: https://salsa.debian.org/med-team/pftools/-/commit/a5d923a3d3284c95a6ba13cf0fa6409fcad015db
--
View it on GitLab: https://salsa.debian.org/med-team/pftools/-/commit/a5d923a3d3284c95a6ba13cf0fa6409fcad015db
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