[med-svn] [Git][med-team/fasta3][master] install more things to /usr/share/fasta3/
Michael R. Crusoe
gitlab at salsa.debian.org
Mon Apr 20 18:23:37 BST 2020
Michael R. Crusoe pushed to branch master at Debian Med / fasta3
Commits:
bea9334a by Michael R. Crusoe at 2020-04-18T12:36:02+02:00
install more things to /usr/share/fasta3/
- - - - -
5 changed files:
- debian/changelog
- debian/examples
- debian/fasta3.install
- debian/patches/adjust-scripts
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+fasta3 (36.3.8h.2020-02-11-4) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Install scripts, matrics, and misc scripts in
+ /usr/share/fasta3/{scripts,data,misc}
+ * Install all the example SQL scripts and data
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Sat, 18 Apr 2020 12:22:35 +0200
+
fasta3 (36.3.8h.2020-02-11-3) unstable; urgency=medium
* Team upload.
=====================================
debian/examples
=====================================
@@ -1,2 +1,2 @@
-seq/prot_test.lseg
-seq/mgstm1.aa
+seq/
+sql/
=====================================
debian/fasta3.install
=====================================
@@ -1,2 +1,4 @@
bin/[a-z]* usr/bin
-scripts/* usr/share/fasta3/
+scripts/* usr/share/fasta3/scripts/
+data/* usr/share/fasta3/data/
+misc/* usr/share/fasta3/misc/
=====================================
debian/patches/adjust-scripts
=====================================
@@ -173,11 +173,11 @@ Description: adjust for installed use
$BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 0 -html > $bl0_out
$BLAST_PATH/blast_formatter -archive $bl_asn -outfmt '7 qseqid qlen sseqid slen pident length mismatch gapopen qstart qend sstart send evalue bitscore score btop' > $blt_out
-annot_blast_btop2.pl --query $QUERY --have_qslen --dom_info --ann_script "$ANN_SCRIPT" --q_ann_script "$Q_ANN_SCRIPT" $blt_out > $blt_ann
-+/usr/share/fasta3/annot_blast_btop2.pl --query $QUERY --have_qslen --dom_info --ann_script "$ANN_SCRIPT" --q_ann_script "$Q_ANN_SCRIPT" $blt_out > $blt_ann
++/usr/share/fasta3/scripts/annot_blast_btop2.pl --query $QUERY --have_qslen --dom_info --ann_script "$ANN_SCRIPT" --q_ann_script "$Q_ANN_SCRIPT" $blt_out > $blt_ann
## rename_exons.py --have_qslen --dom_info $blt_ann > $blr_out
-merge_blast_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blr_out $bl0_out
-+/usr/share/fasta3/merge_blast_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blr_out $bl0_out
++/usr/share/fasta3/scripts/merge_blast_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blr_out $bl0_out
# $BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 2 > $blm_out
--- fasta3.orig/scripts/blastp_cmd.sh
@@ -247,7 +247,7 @@ Description: adjust for installed use
$BLAST_PATH/$SRCH_CMD $cmd > $bl0_out
-$BLAST_PATH/rename_exons.py --have_qslen --dom_info $blt_out > $blr_out
-+/usr/share/fasta3/rename_exons.py --have_qslen --dom_info $blt_out > $blr_out
++/usr/share/fasta3/scripts/rename_exons.py --have_qslen --dom_info $blt_out > $blr_out
if [ ! -s $blr_out ]; then
# echo "# " `ls -l $blt_out $blr_out`
@@ -256,7 +256,7 @@ Description: adjust for installed use
fi
-$BLAST_PATH/merge_fasta_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blr_out $bl0_out
-+/usr/share/fasta3/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
--- fasta3.orig/scripts/get_genome_seq.py
+++ fasta3/scripts/get_genome_seq.py
@@ -1,4 +1,4 @@
@@ -418,15 +418,15 @@ Description: adjust for installed use
-echo 'get_genome_seq.py'
-get_genome_seq.py chr1:109687874-109687909
+#echo 'get_genome_seq.py'
-+#/usr/share/fasta3/get_genome_seq.py chr1:109687874-109687909
++#/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/get_protein.py 'sp|P09488|GSTM1_HUMAN'
-+#/usr/share/fasta3/get_protein.py 'P09488'
-+/usr/share/fasta3/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 'NP_000552'
echo '################################################################'
echo 'requires mysql database'
@@ -434,39 +434,39 @@ Description: adjust for installed use
-get_protein_sql.py 'sp|P09488|GSTM1_HUMAN'
-get_protein_sql.py 'P09488'
-get_protein_sql.py 'NP_000552'
-+/usr/share/fasta3/get_protein_sql.py 'sp|P09488|GSTM1_HUMAN'
-+/usr/share/fasta3/get_protein_sql.py 'P09488'
-+/usr/share/fasta3/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/get_protein_sql_www.py 'sp|P09488|GSTM1_HUMAN'
-+/usr/share/fasta3/get_protein_sql_www.py 'P09488'
-+/usr/share/fasta3/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/get_refseq.py NP_000552
-+/usr/share/fasta3/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'
-get_uniprot.py P09488
-get_uniprot.py 'sp|P09488|GSTM1_HUMAN'
+# SSL error
+# echo 'get_uniprot.py'
-+# /usr/share/fasta3/get_uniprot.py P09488
-+# /usr/share/fasta3/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/get_up_prot_iso_sql.py 'sp|P09488|GSTM1_HUMAN'
-+/usr/share/fasta3/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'
@@ -474,15 +474,15 @@ Description: adjust for installed use
+# 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/ann_exons_up_sql.pl+--gen_coord+--exon_label -V q\!/usr/share/fasta3/ann_exons_up_sql.pl+--gen_coord+--exon_label \!/usr/share/fasta3/get_protein.py+P30711 \!/usr/share/fasta3/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/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'
-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/rename_exons.py hum_chk_map_test.m8CBL # produces a renamed exon_x
++# /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'
@@ -497,11 +497,11 @@ Description: adjust for installed use
+# 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/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/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/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
++# /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
--- fasta3.orig/scripts/test_ann_scripts.sh
+++ fasta3/scripts/test_ann_scripts.sh
@@ -514,7 +514,7 @@ Description: adjust for installed use
script_file=$1
else
- script_file=ann_script_list
-+ script_file=/usr/share/fasta3/ann_script_list
++ script_file=/usr/share/fasta3/scripts/ann_script_list
fi
-if [ ! $1=='' ]; then
@@ -522,7 +522,7 @@ Description: adjust for installed use
ex_file=$1
else
- ex_file=acc_examples
-+ ex_file=/usr/share/fasta3/acc_examples
++ ex_file=/usr/share/fasta3/scripts/acc_examples
fi
-for script in `cat $script_file `; do
@@ -551,10 +551,105 @@ Description: adjust for installed use
-ann_pfam30.pl
-ann_pfam_www.pl
-ann_upfeats_pfam_www_e.pl
-+/usr/share/fasta3/ann_exons_up_sql.pl
-+/usr/share/fasta3/ann_exons_up_www.pl
-+/usr/share/fasta3/ann_feats2ipr.pl
-+/usr/share/fasta3/ann_feats_up_sql.pl
-+/usr/share/fasta3/ann_feats_up_www2.pl
-+/usr/share/fasta3/ann_ipr_www.pl
-+/usr/share/fasta3/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
+--- 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 &
+--- 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 &
+--- 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 &
+--- 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 by William R. Pearson and The Rector &
+@@ -48,7 +48,7 @@
+ # (3) NCBI blast+ programs: psiblast/makeblastdb
+ # (4) NCBI datatool (required only for ssearch36 PSSMs)
+
+-my $pgm_bin = "/seqprg/bin";
++my $pgm_bin = "/usr/bin";
+ my $pgm_data = "/seqprg/data";
+ my $ssearch_bin = "$pgm_bin/ssearch36";
+ my $psiblast_bin = "$pgm_bin/psiblast";
+--- 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 @@
+ # (3) NCBI blast+ programs: psiblast/makeblastdb
+ # (4) NCBI datatool (required only for ssearch36 PSSMs)
+
+-pgm_bin = "/seqprg/bin"
++pgm_bin = "/usr/bin"
+ pgm_data = "/seqprg/data"
+ ssearch_bin = pgm_bin+"/ssearch36"
+ psiblast_bin = pgm_bin+"/psiblast"
+@@ -54,9 +54,9 @@
+ align2msa_lib = "m89_btop_msa2.pl"
+ clustal2fasta = "clustal2fasta.py"
+
+-annot_cmds = {'rpd3': '"!../scripts/ann_pfam28.pl --pfacc --db RPD3 --vdoms --split_over"',
+- 'rpd3nv':'"!../scripts/ann_pfam28.pl --pfacc --db RPD3 --split_over"',
+- 'pfam':'"!../scripts/ann_pfam30.pl --pfacc --vdoms --split_over"'}
++annot_cmds = {'rpd3': '"!/usr/share/fasta3/scripts/ann_pfam28.pl --pfacc --db RPD3 --vdoms --split_over"',
++ 'rpd3nv':'"!/usr/share/fasta3/scripts/ann_pfam28.pl --pfacc --db RPD3 --split_over"',
++ 'pfam':'"!/usr/share/fasta3/scripts/ann_pfam30.pl --pfacc --vdoms --split_over"'}
+
+ num_iter = 5
+ srch_pgm = 'ssearch'
+--- fasta3.orig/psisearch2/psisearch2_msa_iter.sh
++++ fasta3/psisearch2/psisearch2_msa_iter.sh
+@@ -7,8 +7,8 @@
+ #
+
+
+-PS_BIN=~/Devel/fa36_v3.8/psisearch2
+-Q_DIR="../seq"
++PS_BIN=/usr/share/fasta3/psisearch2
++Q_DIR=/usr/share/doc/fasta3/examples/
+ FA_DB=/slib2/fa_dbs/qfo78.lseg
+ BL_DB=/slib2/bl_dbs/qfo78
+ DB=$FA_DB
+--- 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
+ #
+
+-PS_BIN=~/Devel/fa36_v3.8/psisearch2
++PS_BIN=/usr/share/fasta3/psisearch2
+ q_file=$1
+
+ db=/slib2/bl_dbs/pir1
=====================================
debian/tests/run-unit-test
=====================================
@@ -12,10 +12,10 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
-cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+cp -a /usr/share/doc/${pkg}/examples/seq/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
-/usr/share/fasta3/test_ann_scripts.sh
-/usr/share/fasta3/test_py.sh
+/usr/share/fasta3/scripts/test_ann_scripts.sh
+/usr/share/fasta3/scripts/test_py.sh
fasta36 -q mgstm1.aa prot_test.lseg
View it on GitLab: https://salsa.debian.org/med-team/fasta3/-/commit/bea9334a1300247f232198c2a84e6f01f5e32373
--
View it on GitLab: https://salsa.debian.org/med-team/fasta3/-/commit/bea9334a1300247f232198c2a84e6f01f5e32373
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