[med-svn] [Git][med-team/fasta3][master] 2 commits: Adjusted patch so that the autopkgtests run. Added bedtools as a test dependency.
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Fri Oct 25 15:37:49 BST 2024
Michael R. Crusoe pushed to branch master at Debian Med / fasta3
Commits:
7691331c by Michael R. Crusoe at 2024-10-25T16:35:44+02:00
Adjusted patch so that the autopkgtests run. Added bedtools as a test dependency.
- - - - -
078e8229 by Michael R. Crusoe at 2024-10-25T16:36:05+02:00
routine-update: Ready to upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/patches/adjust-scripts
- debian/patches/local_tests
- debian/rules
- debian/tests/control
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-fasta3 (36.3.8i.14-Nov-2020-2) UNRELEASED; urgency=medium
+fasta3 (36.3.8i.14-Nov-2020-2) unstable; urgency=medium
* Team upload.
@@ -6,13 +6,15 @@ fasta3 (36.3.8i.14-Nov-2020-2) UNRELEASED; urgency=medium
* Force use of packaged SIMDe library
* Mark Debian-specific patches as not needing forwarding. Update my
email address
+ * Adjusted patch so that the autopkgtests run. Added bedtools as a
+ test dependency.
[ Andreas Tille ]
* Cleanup after testing
Closes: #1044536
* Add python3-mysql.connector, python3-requests to Suggests and Test-Depends
- -- Michael R. Crusoe <crusoe at debian.org> Fri, 19 May 2023 18:46:30 +0200
+ -- Michael R. Crusoe <crusoe at debian.org> Fri, 25 Oct 2024 16:36:05 +0200
fasta3 (36.3.8i.14-Nov-2020-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -79,8 +79,6 @@ Architecture: all
Multi-Arch: foreign
Section: doc
Depends: ${misc:Depends}
-Breaks: fasta3 (<< 36.3.8h)
-Replaces: fasta3 (<< 36.3.8h)
Description: user guide for FASTA tools
The FASTA programs find regions of local or global similarity between
Protein or DNA sequences, either by searching Protein or DNA databases,
=====================================
debian/patches/adjust-scripts
=====================================
@@ -1,169 +1,169 @@
Author: Michael R. Crusoe <crusoe at debian.org>
Description: adjust for installed use
Forwarded: non-needed
---- a/scripts/ann_exons_all.pl
-+++ b/scripts/ann_exons_all.pl
+--- fasta3.orig/scripts/ann_exons_all.pl
++++ fasta3/scripts/ann_exons_all.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014,2015 by William R. Pearson and The Rector &
---- a/scripts/ann_exons_ens.pl
-+++ b/scripts/ann_exons_ens.pl
+--- fasta3.orig/scripts/ann_exons_ens.pl
++++ fasta3/scripts/ann_exons_ens.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014,2015 by William R. Pearson and The Rector &
---- a/scripts/ann_exons_ncbi.pl
-+++ b/scripts/ann_exons_ncbi.pl
+--- fasta3.orig/scripts/ann_exons_ncbi.pl
++++ fasta3/scripts/ann_exons_ncbi.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
# ann_exons_ncbi.pl gets an annotation file from fasta36 -V with a line of the form:
---- a/scripts/ann_exons_up_sql.pl
-+++ b/scripts/ann_exons_up_sql.pl
+--- fasta3.orig/scripts/ann_exons_up_sql.pl
++++ fasta3/scripts/ann_exons_up_sql.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014,2015 by William R. Pearson and The Rector &
---- a/scripts/ann_exons_up_sql_www.pl
-+++ b/scripts/ann_exons_up_sql_www.pl
+--- fasta3.orig/scripts/ann_exons_up_sql_www.pl
++++ fasta3/scripts/ann_exons_up_sql_www.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014,2015 by William R. Pearson and The Rector &
---- a/scripts/ann_exons_up_www.pl
-+++ b/scripts/ann_exons_up_www.pl
+--- fasta3.orig/scripts/ann_exons_up_www.pl
++++ fasta3/scripts/ann_exons_up_www.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014,2015 by William R. Pearson and The Rector &
---- a/scripts/ann_feats2ipr.pl
-+++ b/scripts/ann_feats2ipr.pl
+--- fasta3.orig/scripts/ann_feats2ipr.pl
++++ fasta3/scripts/ann_feats2ipr.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014 by William R. Pearson and The Rector &
---- a/scripts/ann_feats2ipr_e.pl
-+++ b/scripts/ann_feats2ipr_e.pl
+--- fasta3.orig/scripts/ann_feats2ipr_e.pl
++++ fasta3/scripts/ann_feats2ipr_e.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014 by William R. Pearson and The Rector &
---- a/scripts/ann_feats_up_sql.pl
-+++ b/scripts/ann_feats_up_sql.pl
+--- fasta3.orig/scripts/ann_feats_up_sql.pl
++++ fasta3/scripts/ann_feats_up_sql.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014,2015 by William R. Pearson and The Rector &
---- a/scripts/ann_feats_up_www2.pl
-+++ b/scripts/ann_feats_up_www2.pl
+--- fasta3.orig/scripts/ann_feats_up_www2.pl
++++ fasta3/scripts/ann_feats_up_www2.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014,2015 by William R. Pearson and The Rector &
---- a/scripts/ann_ipr_www.pl
-+++ b/scripts/ann_ipr_www.pl
+--- fasta3.orig/scripts/ann_ipr_www.pl
++++ fasta3/scripts/ann_ipr_www.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014 by William R. Pearson and The Rector &
---- a/scripts/ann_pdb_cath.pl
-+++ b/scripts/ann_pdb_cath.pl
+--- fasta3.orig/scripts/ann_pdb_cath.pl
++++ fasta3/scripts/ann_pdb_cath.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014 by William R. Pearson and The Rector &
---- a/scripts/ann_pdb_vast.pl
-+++ b/scripts/ann_pdb_vast.pl
+--- fasta3.orig/scripts/ann_pdb_vast.pl
++++ fasta3/scripts/ann_pdb_vast.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014, 2015 by William R. Pearson and The Rector &
---- a/scripts/ann_pfam30_tmptbl.pl
-+++ b/scripts/ann_pfam30_tmptbl.pl
+--- fasta3.orig/scripts/ann_pfam30_tmptbl.pl
++++ fasta3/scripts/ann_pfam30_tmptbl.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014,2015 by William R. Pearson and The Rector &
---- a/scripts/ann_pfam_sql.pl
-+++ b/scripts/ann_pfam_sql.pl
+--- fasta3.orig/scripts/ann_pfam_sql.pl
++++ fasta3/scripts/ann_pfam_sql.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2015 by William R. Pearson and The Rector &
---- a/scripts/ann_pfam_www.pl
-+++ b/scripts/ann_pfam_www.pl
+--- fasta3.orig/scripts/ann_pfam_www.pl
++++ fasta3/scripts/ann_pfam_www.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014, 2015 by William R. Pearson and The Rector &
---- a/scripts/ann_upfeats_pfam_www_e.pl
-+++ b/scripts/ann_upfeats_pfam_www_e.pl
+--- fasta3.orig/scripts/ann_upfeats_pfam_www_e.pl
++++ fasta3/scripts/ann_upfeats_pfam_www_e.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014 by William R. Pearson and The Rector &
---- a/scripts/annot_blast_btop2.pl
-+++ b/scripts/annot_blast_btop2.pl
+--- fasta3.orig/scripts/annot_blast_btop2.pl
++++ fasta3/scripts/annot_blast_btop2.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2017,2018 by William R. Pearson and The Rector &
---- a/scripts/annot_blast_btop3.py
-+++ b/scripts/annot_blast_btop3.py
+--- fasta3.orig/scripts/annot_blast_btop3.py
++++ fasta3/scripts/annot_blast_btop3.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
################################################################
# copyright (c) 2017,2018 by William R. Pearson and The Rector &
---- a/scripts/annot_blast_btop4.py
-+++ b/scripts/annot_blast_btop4.py
+--- fasta3.orig/scripts/annot_blast_btop4.py
++++ fasta3/scripts/annot_blast_btop4.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
################################################################
# copyright (c) 2017,2018 by William R. Pearson and The Rector &
---- a/scripts/blastp_annot_cmd.sh
-+++ b/scripts/blastp_annot_cmd.sh
-@@ -82,19 +82,19 @@ $BLAST_PATH/blast_formatter -archive $bl
+--- fasta3.orig/scripts/blastp_annot_cmd.sh
++++ fasta3/scripts/blastp_annot_cmd.sh
+@@ -82,19 +82,19 @@
# annot_cmd="annot_blast_btop2.pl --query $QUERY --raw --have_qslen --dom_info --ann_script "$ANN_SCRIPT" --q_ann_script "$Q_ANN_SCRIPT" $blt_out > $blt_ann"
# echo "# $annot_cmd"
@@ -186,9 +186,9 @@ Forwarded: non-needed
fi
# $BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 2 > $blm_out
---- a/scripts/blastp_cmd.sh
-+++ b/scripts/blastp_cmd.sh
-@@ -22,7 +22,7 @@ blt_out="$OUTNAME.bl_tab"
+--- fasta3.orig/scripts/blastp_cmd.sh
++++ fasta3/scripts/blastp_cmd.sh
+@@ -22,7 +22,7 @@
# echo "OUTFILE = ${OUTNAME}"
#export BLAST_PATH="/ebi/extserv/bin/ncbi-blast+/bin"
@@ -197,49 +197,49 @@ Forwarded: non-needed
$BLAST_PATH/blastp -outfmt 11 $cmd > $bl_asn
$BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 0 -html > $bl0_out
---- a/scripts/exp_up_ensg.pl
-+++ b/scripts/exp_up_ensg.pl
+--- fasta3.orig/scripts/exp_up_ensg.pl
++++ fasta3/scripts/exp_up_ensg.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2010, 2014 by William R. Pearson and The Rector &
---- a/scripts/expand_links.pl
-+++ b/scripts/expand_links.pl
+--- fasta3.orig/scripts/expand_links.pl
++++ fasta3/scripts/expand_links.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2010, 2014 by William R. Pearson and The Rector &
---- a/scripts/expand_refseq_isoforms.pl
-+++ b/scripts/expand_refseq_isoforms.pl
+--- fasta3.orig/scripts/expand_refseq_isoforms.pl
++++ fasta3/scripts/expand_refseq_isoforms.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2010, 2014 by William R. Pearson and The Rector &
---- a/scripts/expand_uniref50.pl
-+++ b/scripts/expand_uniref50.pl
+--- fasta3.orig/scripts/expand_uniref50.pl
++++ fasta3/scripts/expand_uniref50.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2010, 2014 by William R. Pearson and The Rector &
---- a/scripts/expand_up_isoforms.pl
-+++ b/scripts/expand_up_isoforms.pl
+--- fasta3.orig/scripts/expand_up_isoforms.pl
++++ fasta3/scripts/expand_up_isoforms.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2010, 2014 by William R. Pearson and The Rector &
---- a/scripts/fasta_annot_cmd.sh
-+++ b/scripts/fasta_annot_cmd.sh
-@@ -54,7 +54,7 @@ bla_out="${OUTNAME}_an.html"
+--- fasta3.orig/scripts/fasta_annot_cmd.sh
++++ fasta3/scripts/fasta_annot_cmd.sh
+@@ -54,7 +54,7 @@
blt_out="$OUTNAME.fa_tab"
blr_out="$OUTNAME.fa_tab_rn"
@@ -248,7 +248,7 @@ Forwarded: non-needed
# BLAST_PATH="../bin"
cmd="$cmd -mF8CBL=$blt_out $QUERY $DATABASE"
-@@ -73,7 +73,7 @@ cmd="$cmd -mF8CBL=$blt_out $QUERY $DATAB
+@@ -73,7 +73,7 @@
# run the program
$BLAST_PATH/$SRCH_CMD $cmd > $bl0_out
@@ -257,239 +257,207 @@ Forwarded: non-needed
if [ ! -s $blr_out ]; then
# echo "# " `ls -l $blt_out $blr_out`
-@@ -81,4 +81,4 @@ if [ ! -s $blr_out ]; then
+@@ -81,4 +81,4 @@
# echo "# " `ls -l $blt_out $blr_out`
fi
-$BLAST_PATH/merge_fasta_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blr_out $bl0_out
+/usr/share/fasta3/scripts/merge_fasta_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blr_out $bl0_out
---- a/scripts/get_genome_seq.py
-+++ b/scripts/get_genome_seq.py
+--- fasta3.orig/scripts/get_genome_seq.py
++++ fasta3/scripts/get_genome_seq.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
################
## get_hg38_bed.py parses an HG38 coordinate into a pseudo-bed entry,
---- a/scripts/get_protein.py
-+++ b/scripts/get_protein.py
+--- fasta3.orig/scripts/get_protein.py
++++ fasta3/scripts/get_protein.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
## get_protein_www.py --
## get a protein sequence from the Uniprot or NCBI/Refseq web sites using the accession
---- a/scripts/get_protein_sql.py
-+++ b/scripts/get_protein_sql.py
+--- fasta3.orig/scripts/get_protein_sql.py
++++ fasta3/scripts/get_protein_sql.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
## get_protein_sql.py --
## get a protein sequence from a local Uniprot or NCBI/Refseq mySQL database using the accession
---- a/scripts/get_protein_sql_www.py
-+++ b/scripts/get_protein_sql_www.py
+--- fasta3.orig/scripts/get_protein_sql_www.py
++++ fasta3/scripts/get_protein_sql_www.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
## get_protein.py --
## get a protein sequence from Uniprot or NCBI/Refseq using the accession
---- a/scripts/get_refseq.py
-+++ b/scripts/get_refseq.py
+--- fasta3.orig/scripts/get_refseq.py
++++ fasta3/scripts/get_refseq.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
import sys
import re
---- a/scripts/get_uniprot.py
-+++ b/scripts/get_uniprot.py
+--- fasta3.orig/scripts/get_uniprot.py
++++ fasta3/scripts/get_uniprot.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
import sys
import re
---- a/scripts/get_up_prot_iso_sql.py
-+++ b/scripts/get_up_prot_iso_sql.py
+--- fasta3.orig/scripts/get_up_prot_iso_sql.py
++++ fasta3/scripts/get_up_prot_iso_sql.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
import sys
import re
---- a/scripts/lav2plt.pl
-+++ b/scripts/lav2plt.pl
+--- fasta3.orig/scripts/lav2plt.pl
++++ fasta3/scripts/lav2plt.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
# lav2plt.pl - produce plotfrom lav output */
---- a/scripts/lavplt_ps.pl
-+++ b/scripts/lavplt_ps.pl
+--- fasta3.orig/scripts/lavplt_ps.pl
++++ fasta3/scripts/lavplt_ps.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
#
################################################################
# copyright (c) 2012, 2014 by William R. Pearson and The Rector &
---- a/scripts/lavplt_svg.pl
-+++ b/scripts/lavplt_svg.pl
+--- fasta3.orig/scripts/lavplt_svg.pl
++++ fasta3/scripts/lavplt_svg.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
#
################################################################
# copyright (c) 2012, 2014 by William R. Pearson and The Rector &
---- a/scripts/links2sql.pl
-+++ b/scripts/links2sql.pl
+--- fasta3.orig/scripts/links2sql.pl
++++ fasta3/scripts/links2sql.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014 by William R. Pearson and The Rector &
---- a/scripts/m8_btop_msa.pl
-+++ b/scripts/m8_btop_msa.pl
+--- fasta3.orig/scripts/m8_btop_msa.pl
++++ fasta3/scripts/m8_btop_msa.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014,2015 by William R. Pearson and The Rector &
---- a/scripts/m9B_btop_msa.pl
-+++ b/scripts/m9B_btop_msa.pl
+--- fasta3.orig/scripts/m9B_btop_msa.pl
++++ fasta3/scripts/m9B_btop_msa.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014,2015 by William R. Pearson and The Rector &
---- a/scripts/map_exon_coords.py
-+++ b/scripts/map_exon_coords.py
+--- fasta3.orig/scripts/map_exon_coords.py
++++ fasta3/scripts/map_exon_coords.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
#
# given a -m8CB file with exon annotations for the query and subject,
# provide a function that maps subject coordinates to query, or vice versa
---- a/scripts/merge_blast_btab.pl
-+++ b/scripts/merge_blast_btab.pl
+--- fasta3.orig/scripts/merge_blast_btab.pl
++++ fasta3/scripts/merge_blast_btab.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2018 by William R. Pearson and The Rector &
---- a/scripts/merge_fasta_btab.pl
-+++ b/scripts/merge_fasta_btab.pl
+--- fasta3.orig/scripts/merge_fasta_btab.pl
++++ fasta3/scripts/merge_fasta_btab.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2018 by William R. Pearson and The Rector &
---- a/scripts/relabel_domains.py
-+++ b/scripts/relabel_domains.py
+--- fasta3.orig/scripts/relabel_domains.py
++++ fasta3/scripts/relabel_domains.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
# Given a blast_tabular file with search results from one or more
# protein queries, modify the domain color numbers (e.g. ~1, ~2) so
---- a/scripts/rename_exons.py
-+++ b/scripts/rename_exons.py
+--- fasta3.orig/scripts/rename_exons.py
++++ fasta3/scripts/rename_exons.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
#
# given a -m8CB file with exon annotations for the query and subject,
# adjust the subject exon names to match the query exon names
---- a/scripts/summ_domain_ident.pl
-+++ b/scripts/summ_domain_ident.pl
+--- fasta3.orig/scripts/summ_domain_ident.pl
++++ fasta3/scripts/summ_domain_ident.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014 by William R. Pearson and The Rector &
---- a/scripts/test_py.sh
-+++ b/scripts/test_py.sh
-@@ -5,57 +5,58 @@
+--- fasta3.orig/scripts/test_py.sh
++++ fasta3/scripts/test_py.sh
+@@ -5,39 +5,39 @@
## test python scripts
##
-echo 'get_genome_seq.py'
-get_genome_seq.py chr1:109687874-109687909
-+#echo 'get_genome_seq.py'
-+#/usr/share/fasta3/scripts/get_genome_seq.py chr1:109687874-109687909
++# echo 'get_genome_seq.py'
++# /usr/share/fasta3/scripts/get_genome_seq.py chr1:109687874-109687909
echo 'get_protein.py'
-get_protein.py 'sp|P09488|GSTM1_HUMAN'
-get_protein.py 'P09488'
-get_protein.py 'NP_000552'
-+#/usr/share/fasta3/scripts/get_protein.py 'sp|P09488|GSTM1_HUMAN'
-+#/usr/share/fasta3/scripts/get_protein.py 'P09488'
++/usr/share/fasta3/scripts/get_protein.py 'sp|P09488|GSTM1_HUMAN'
++/usr/share/fasta3/scripts/get_protein.py 'P09488'
+/usr/share/fasta3/scripts/get_protein.py 'NP_000552'
- echo '################################################################'
- echo 'requires mysql database'
- echo 'get_protein_sql.py'
--get_protein_sql.py 'sp|P09488|GSTM1_HUMAN'
--get_protein_sql.py 'P09488'
--get_protein_sql.py 'NP_000552'
-+/usr/share/fasta3/scripts/get_protein_sql.py 'sp|P09488|GSTM1_HUMAN'
-+/usr/share/fasta3/scripts/get_protein_sql.py 'P09488'
-+/usr/share/fasta3/scripts/get_protein_sql.py 'NP_000552'
-
- echo 'get_protein_sql_www.py'
--get_protein_sql_www.py 'sp|P09488|GSTM1_HUMAN'
--get_protein_sql_www.py 'P09488'
--get_protein_sql_www.py 'NP_000552'
-+/usr/share/fasta3/scripts/get_protein_sql_www.py 'sp|P09488|GSTM1_HUMAN'
-+/usr/share/fasta3/scripts/get_protein_sql_www.py 'P09488'
-+/usr/share/fasta3/scripts/get_protein_sql_www.py 'NP_000552'
-
echo 'get_refseq.py'
-get_refseq.py NP_000552
-get_refseq.py NP_0000552
+/usr/share/fasta3/scripts/get_refseq.py NP_000552
+/usr/share/fasta3/scripts/get_refseq.py NP_0000552
--echo 'get_uniprot.py'
+ echo 'get_uniprot.py'
-get_uniprot.py P09488
-get_uniprot.py 'sp|P09488|GSTM1_HUMAN'
-+# SSL error
-+# echo 'get_uniprot.py'
-+# /usr/share/fasta3/scripts/get_uniprot.py P09488
-+# /usr/share/fasta3/scripts/get_uniprot.py 'sp|P09488|GSTM1_HUMAN'
++/usr/share/fasta3/scripts/get_uniprot.py P09488
++/usr/share/fasta3/scripts/get_uniprot.py 'sp|P09488|GSTM1_HUMAN'
echo '################################################################'
- echo 'requires mysql database'
- echo 'get_up_prot_iso_sql.py'
--get_up_prot_iso_sql.py 'sp|P09488|GSTM1_HUMAN'
--get_up_prot_iso_sql.py P09488
-+/usr/share/fasta3/scripts/get_up_prot_iso_sql.py 'sp|P09488|GSTM1_HUMAN'
-+/usr/share/fasta3/scripts/get_up_prot_iso_sql.py P09488
-
--echo '################################################################'
--echo 'map_exon_coords.py -- look for chrA:start-stop::chrB:start-stop in output'
-+# echo '################################################################'
-+# echo 'map_exon_coords.py -- look for chrA:start-stop::chrB:start-stop in output'
+ echo 'map_exon_coords.py -- look for chrA:start-stop::chrB:start-stop in output'
# (a) produce an appropriate alignment file
-fasta36 -q -m 8CBL -V \!ann_exons_up_sql.pl+--gen_coord+--exon_label -V q\!ann_exons_up_sql.pl+--gen_coord+--exon_label \!get_protein.py+P30711 \!get_protein.py+P20135 > hum_chk_map_test.m8CBL
-+#fasta36 -q -m 8CBL -V \!/usr/share/fasta3/scripts/ann_exons_up_sql.pl+--gen_coord+--exon_label -V q\!/usr/share/fasta3/scripts/ann_exons_up_sql.pl+--gen_coord+--exon_label \!/usr/share/fasta3/scripts/get_protein.py+P30711 \!/usr/share/fasta3/scripts/get_protein.py+P20135 > hum_chk_map_test.m8CBL
++fasta36 -q -m 8CBL -V \!/usr/share/fasta3/scripts/ann_exons_up_sql.pl+--gen_coord+--exon_label -V q\!/usr/share/fasta3/scripts/ann_exons_up_sql.pl+--gen_coord+--exon_label \!/usr/share/fasta3/scripts/get_protein.py+P30711 \!/usr/share/fasta3/scripts/get_protein.py+P20135 > hum_chk_map_test.m8CBL
# (b) expand chromosome locations on subject and query exons to both genomes
-map_exon_coords.py hum_chk_map_test.m8CBL
-+# /usr/share/fasta3/scripts/map_exon_coords.py hum_chk_map_test.m8CBL
++/usr/share/fasta3/scripts/map_exon_coords.py hum_chk_map_test.m8CBL
--echo 'rename_exons.py -- look for exon_X in output'
+ echo 'rename_exons.py -- look for exon_X in output'
-rename_exons.py hum_chk_map_test.m8CBL # produces a renamed exon_x
-+# echo 'rename_exons.py -- look for exon_X in output'
-+# /usr/share/fasta3/scripts/rename_exons.py hum_chk_map_test.m8CBL # produces a renamed exon_x
-
+-
-echo '################################################################'
-echo 'annot_blast_btop4.py -- put annotations on blast BTOP alignment with (or without) raw_score'
-# (a) from FASTA -m8CBl -- no raw score
@@ -499,18 +467,20 @@ Forwarded: non-needed
-## .bl_tab uses --ann_script because of multiple HSPs
-echo '.bl_tab yes raw score'
-annot_blast_btop4.py --raw_score --have_qslen --query ../seq/mgstm1.aa --q_ann_file gstm1_mouse.annot --ann_script ann_pfam_sql.pl mgstm1_v_a1zb72.bl_tab
++/usr/share/fasta3/scripts/rename_exons.py hum_chk_map_test.m8CBL # produces a renamed exon_x
+
+# echo '################################################################'
+# echo 'annot_blast_btop4.py -- put annotations on blast BTOP alignment with (or without) raw_score'
+# # (a) from FASTA -m8CBl -- no raw score
+# echo '.fa_tab no raw score'
-+# /usr/share/fasta3/scripts/annot_blast_btop4.py --no_raw_score --have_qslen --query /usr/share/doc/fasta3/examples/mgstm1.aa --q_ann_file gstm1_mouse.annot --ann_file a1zb72_drome.annot mgstm1_v_a1zb72_dr.fa_tab
++# /usr/share/fasta3/scripts/annot_blast_btop4.py --no_raw_score --have_qslen --query /usr/share/doc/fasta3/examples/seq/mgstm1.aa --q_ann_file gstm1_mouse.annot --ann_file a1zb72_drome.annot mgstm1_v_a1zb72_dr.fa_tab
+#
+# ## .bl_tab uses --ann_script because of multiple HSPs
+# echo '.bl_tab yes raw score'
-+# /usr/share/fasta3/scripts/annot_blast_btop4.py --raw_score --have_qslen --query /usr/share/doc/fasta3/examples/mgstm1.aa --q_ann_file gstm1_mouse.annot --ann_script ann_pfam_sql.pl mgstm1_v_a1zb72.bl_tab
-
---- a/scripts/test_ann_scripts.sh
-+++ b/scripts/test_ann_scripts.sh
++# /usr/share/fasta3/scripts/annot_blast_btop4.py --raw_score --have_qslen --query /usr/share/doc/fasta3/examples/seq/mgstm1.aa --q_ann_file gstm1_mouse.annot --ann_script ann_pfam_sql.pl mgstm1_v_a1zb72.bl_tab
++#
+--- fasta3.orig/scripts/test_ann_scripts.sh
++++ fasta3/scripts/test_ann_scripts.sh
@@ -9,22 +9,22 @@
# SP:GSTM1_HUMAN -- ebi searches without accession
##
@@ -545,9 +515,9 @@ Forwarded: non-needed
+ done < ${ex_file}
+ echo '***DONE***' "$script" "$(date)"
+done < ${script_file}
---- a/scripts/ann_script_list
-+++ b/scripts/ann_script_list
-@@ -1,9 +1,7 @@
+--- fasta3.orig/scripts/ann_script_list
++++ fasta3/scripts/ann_script_list
+@@ -1,9 +1,5 @@
-ann_exons_up_sql.pl
-ann_exons_up_www.pl
-ann_feats2ipr.pl
@@ -557,46 +527,44 @@ Forwarded: non-needed
-ann_pfam30.pl
-ann_pfam_www.pl
-ann_upfeats_pfam_www_e.pl
-+/usr/share/fasta3/scripts/ann_exons_up_sql.pl
+/usr/share/fasta3/scripts/ann_exons_up_www.pl
-+/usr/share/fasta3/scripts/ann_feats2ipr.pl
+/usr/share/fasta3/scripts/ann_feats_up_sql.pl
+/usr/share/fasta3/scripts/ann_feats_up_www2.pl
+/usr/share/fasta3/scripts/ann_ipr_www.pl
+/usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl
---- a/psisearch2/clustal2fasta.pl
-+++ b/psisearch2/clustal2fasta.pl
+--- fasta3.orig/psisearch2/clustal2fasta.pl
++++ fasta3/psisearch2/clustal2fasta.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014,2015 by William R. Pearson and The Rector &
---- a/psisearch2/clustal2fasta.py
-+++ b/psisearch2/clustal2fasta.py
+--- fasta3.orig/psisearch2/clustal2fasta.py
++++ fasta3/psisearch2/clustal2fasta.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
################################################################
# copyright (c) 2014,2015 by William R. Pearson and The Rector &
---- a/psisearch2/m89_btop_msa2.pl
-+++ b/psisearch2/m89_btop_msa2.pl
+--- fasta3.orig/psisearch2/m89_btop_msa2.pl
++++ fasta3/psisearch2/m89_btop_msa2.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2014,2015 by William R. Pearson and The Rector &
---- a/psisearch2/psisearch2_msa.pl
-+++ b/psisearch2/psisearch2_msa.pl
+--- fasta3.orig/psisearch2/psisearch2_msa.pl
++++ fasta3/psisearch2/psisearch2_msa.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
################################################################
# copyright (c) 2016,2020 by William R. Pearson and The Rector &
-@@ -54,7 +54,7 @@ use vars qw( $prev_m89res $m_format $pre
+@@ -54,7 +54,7 @@
# (3) NCBI blast+ programs: psiblast/makeblastdb
# (4) NCBI datatool (required only for ssearch36 PSSMs)
@@ -605,15 +573,15 @@ Forwarded: non-needed
my $pgm_data = "/seqprg/data";
my $ssearch_bin = "$pgm_bin/ssearch36";
---- a/psisearch2/psisearch2_msa.py
-+++ b/psisearch2/psisearch2_msa.py
+--- fasta3.orig/psisearch2/psisearch2_msa.py
++++ fasta3/psisearch2/psisearch2_msa.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
################################################################
# copyright (c) 2016 by William R. Pearson and The Rector &
-@@ -45,7 +45,7 @@ import re
+@@ -45,7 +45,7 @@
# (3) NCBI blast+ programs: psiblast/makeblastdb
# (4) NCBI datatool (required only for ssearch36 PSSMs)
@@ -622,7 +590,7 @@ Forwarded: non-needed
pgm_data = "/seqprg/data"
ssearch_bin = pgm_bin+"/ssearch36"
psiblast_bin = pgm_bin+"/psiblast"
-@@ -54,9 +54,9 @@ datatool_bin = "%s/datatool -m %s/NCBI_a
+@@ -54,9 +54,9 @@
align2msa_lib = "m89_btop_msa2.pl"
clustal2fasta = "clustal2fasta.py"
@@ -635,8 +603,8 @@ Forwarded: non-needed
num_iter = 5
srch_pgm = 'ssearch'
---- a/psisearch2/psisearch2_msa_iter.sh
-+++ b/psisearch2/psisearch2_msa_iter.sh
+--- fasta3.orig/psisearch2/psisearch2_msa_iter.sh
++++ fasta3/psisearch2/psisearch2_msa_iter.sh
@@ -7,8 +7,8 @@
#
@@ -648,8 +616,8 @@ Forwarded: non-needed
FA_DB=/slib2/fa_dbs/qfo78.lseg
BL_DB=/slib2/bl_dbs/qfo78
DB=$FA_DB
---- a/psisearch2/psisearch2_msa_iter_bl.sh
-+++ b/psisearch2/psisearch2_msa_iter_bl.sh
+--- fasta3.orig/psisearch2/psisearch2_msa_iter_bl.sh
++++ fasta3/psisearch2/psisearch2_msa_iter_bl.sh
@@ -6,7 +6,7 @@
# psisearch2_msa.pl --pgm psiblast --query query.aa --num_iter 5 --db /slib2/bl_dbs/qfo78
#
=====================================
debian/patches/local_tests
=====================================
@@ -203,3 +203,37 @@ Forwarded: not-needed
echo "starting lalign36" `date`
../bin/lalign36 -q -XM2G -k 1000 ../seq/mchu.aa ../seq/mchu.aa > results/test2G_mc.lal
../bin/lalign36 -q -XM2G -z 3 ../seq/mchu.aa ../seq/mchu.aa > results/test2G_mc.lal_z3
+--- fasta3.orig/scripts/test_py.sh
++++ fasta3/scripts/test_py.sh
+@@ -13,18 +13,6 @@
+ get_protein.py 'P09488'
+ get_protein.py 'NP_000552'
+
+-echo '################################################################'
+-echo 'requires mysql database'
+-echo 'get_protein_sql.py'
+-get_protein_sql.py 'sp|P09488|GSTM1_HUMAN'
+-get_protein_sql.py 'P09488'
+-get_protein_sql.py 'NP_000552'
+-
+-echo 'get_protein_sql_www.py'
+-get_protein_sql_www.py 'sp|P09488|GSTM1_HUMAN'
+-get_protein_sql_www.py 'P09488'
+-get_protein_sql_www.py 'NP_000552'
+-
+ echo 'get_refseq.py'
+ get_refseq.py NP_000552
+ get_refseq.py NP_0000552
+@@ -34,12 +22,6 @@
+ get_uniprot.py 'sp|P09488|GSTM1_HUMAN'
+
+ echo '################################################################'
+-echo 'requires mysql database'
+-echo 'get_up_prot_iso_sql.py'
+-get_up_prot_iso_sql.py 'sp|P09488|GSTM1_HUMAN'
+-get_up_prot_iso_sql.py P09488
+-
+-echo '################################################################'
+ echo 'map_exon_coords.py -- look for chrA:start-stop::chrB:start-stop in output'
+ # (a) produce an appropriate alignment file
+ fasta36 -q -m 8CBL -V \!ann_exons_up_sql.pl+--gen_coord+--exon_label -V q\!ann_exons_up_sql.pl+--gen_coord+--exon_label \!get_protein.py+P30711 \!get_protein.py+P20135 > hum_chk_map_test.m8CBL
=====================================
debian/rules
=====================================
@@ -19,9 +19,8 @@ export DEB_LDFLAGS_MAINT_APPEND +=-flto
%:
dh $@ --sourcedirectory src
-override_dh_auto_configure:
+execute_before_dh_auto_configure:
rm -Rf src/simde
- dh_auto_configure
override_dh_auto_build:
dh_auto_build --sourcedirectory make --builddirectory src --buildsystem makefile -- -f $(MAKEFILE)
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: fasta3, libdbi-perl, libwww-perl, libxml-twig-perl, libdbd-mysql-perl, libjson-perl, python3-mysqldb, python3-mysql.connector, python3-requests
+Depends: fasta3, libdbi-perl, libwww-perl, libxml-twig-perl, libdbd-mysql-perl, libjson-perl, python3-mysqldb, python3-mysql.connector, python3-requests, bedtools
Restrictions: allow-stderr
View it on GitLab: https://salsa.debian.org/med-team/fasta3/-/compare/a18b954b79675bd9a4fd8819c3100488433441dc...078e8229c70586d44636c8ee808045117fff8d8a
--
View it on GitLab: https://salsa.debian.org/med-team/fasta3/-/compare/a18b954b79675bd9a4fd8819c3100488433441dc...078e8229c70586d44636c8ee808045117fff8d8a
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