From 064ffdbc956cbde95424cc7d0853d78773f07b51 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 21 Jun 2006 10:11:36 +0000
Subject: [PATCH] add extra_qualifiers
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@4445 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
etc/af063097.embl | 64 ++++----
etc/b132222.embl | 22 +--
etc/c1215.genbank | 18 +--
etc/options | 6 +-
etc/run_blastp | 372 ++++++++++++++++++++++++++++++++++++++++++----
etc/run_fasta | 17 +--
6 files changed, 406 insertions(+), 93 deletions(-)
diff --git a/etc/af063097.embl b/etc/af063097.embl
index 99cf9f44a..909837042 100644
--- a/etc/af063097.embl
+++ b/etc/af063097.embl
@@ -315,6 +315,7 @@ CC gi:1806573 gi:215666 gi:506836 gi:508561 gi:1061043 gi:215669
CC gi:1769975 gi:494974 gi:215664 gi:15620 gi:393451 gi:1769977
CC gi:215681 gi:215675 gi:215676 gi:15141 gi:414530.
XX
+XX
FH Key Location/Qualifiers
FH
FT source 1..33593
@@ -382,8 +383,8 @@ FT /evidence=EXPERIMENTAL
FT /note="activator binding site; pO, pP promoters"
FT misc_feature 3127
FT /evidence=EXPERIMENTAL
-FT /note="transcription start site for O operon; encodes O, N,
-FT M, L, X, Y, K, lysA, lysB, R, S"
+FT /note="transcription start site for O operon; encodes O,
+FT N, M, L, X, Y, K, lysA, lysB, R, S"
FT CDS 3167..4021
FT /codon_start=1
FT /db_xref="SWISS-PROT:P25478"
@@ -430,18 +431,18 @@ FT /note="Nam209 mutation"
FT /replace="at"
FT /gene="N"
FT variation 4630
-FT /note="sir3 mutation; defective for choice of small capsids
-FT by satellite phage P4"
+FT /note="sir3 mutation; defective for choice of small
+FT capsids by satellite phage P4"
FT /replace="c"
FT /gene="N"
FT variation 4695
-FT /note="sir5 mutation; defective for choice of small capsids
-FT by satellite phage P4"
+FT /note="sir5 mutation; defective for choice of small
+FT capsids by satellite phage P4"
FT /replace="t"
FT /gene="N"
FT variation 4695..4697
-FT /note="sir9 mutation; defective for choice of small capsids
-FT by satellite phage P4"
+FT /note="sir9 mutation; defective for choice of small
+FT capsids by satellite phage P4"
FT /replace=""
FT /gene="N"
FT variation 4699
@@ -450,13 +451,13 @@ FT of small capsids by satellite phage P4"
FT /replace="t"
FT /gene="N"
FT variation 4740
-FT /note="sir1 mutation; defective for choice of small capsids
-FT by satellite phage P4"
+FT /note="sir1 mutation; defective for choice of small
+FT capsids by satellite phage P4"
FT /replace="g"
FT /gene="N"
FT variation 4741
-FT /note="sir4 mutation; defective for choice of small capsids
-FT by satellite phage P4"
+FT /note="sir4 mutation; defective for choice of small
+FT capsids by satellite phage P4"
FT /replace="a"
FT /gene="N"
FT CDS 5157..5900
@@ -670,8 +671,8 @@ FT PDGAVIEYEPETSALTVSGIKTASVTASGSVTATVPVVMVKASTRVTLDTPEVVCTNRL
FT ITGTLEVQKGGTMRGNIEHTGGELSSNGKVLHTHKHPGDSGGTTGSPL"
FT misc_feature 10308
FT /evidence=EXPERIMENTAL
-FT /note="transcription start site for V operon; encodes V, W,
-FT J, I, H, G"
+FT /note="transcription start site for V operon; encodes V,
+FT W, J, I, H, G"
FT /gene="V"
FT variation 10329
FT /note="Vam42, Vam203 and Vam205 mutations"
@@ -871,6 +872,16 @@ FT /translation="MAMPRKLKLMNVFLNGYSYQGVAKSVTLPKLTRKLENYRGAGMNG
FT SAPVDLGLDDDALSMEWSLGGFPDSVIWELYAATGVDAVPIRFAGSYQRDDTGETVAVE
FT VVMRGRQKEIDTGEGKQGEDTESKISVVCTYFRLTMDGKELVEIDTINMIEKVNGVDRL
FT EQHRRNIGL"
+FT CDS 19430..19705
+FT /codon_start=1
+FT /db_xref="SPTREMBL:O64313"
+FT /transl_table=11
+FT /gene="E"
+FT /function="essential tail protein"
+FT /product="gpE"
+FT /protein_id="AAD03291.1"
+FT /translation="MNKENVITLDNPVKRGEQVIEQVTLMKPSAGTLRGVSLAAVANSE
+FT VDALIKVLPRMTAPMLTEQEVAALELPDLVALAGKVVGFLSPNSVQ"
FT CDS join(19430..19684,19684..19857)
FT /codon_start=1
FT /db_xref="SPTREMBL:O64312"
@@ -883,16 +894,6 @@ FT /protein_id="AAD03292.1"
FT /translation="MNKENVITLDNPVKRGEQVIEQVTLMKPSAGTLRGVSLAAVANSE
FT VDALIKVLPRMTAPMLTEQEVAALELPDLVALAGKVVGFLVAELGAVTFPKNLSVDDLM
FT ADVAVIFHWPPSELYPMSLTELITWREKALRRSGNTNE"
-FT CDS 19430..19705
-FT /codon_start=1
-FT /db_xref="SPTREMBL:O64313"
-FT /transl_table=11
-FT /gene="E"
-FT /function="essential tail protein"
-FT /product="gpE"
-FT /protein_id="AAD03291.1"
-FT /translation="MNKENVITLDNPVKRGEQVIEQVTLMKPSAGTLRGVSLAAVANSE
-FT VDALIKVLPRMTAPMLTEQEVAALELPDLVALAGKVVGFLSPNSVQ"
FT variation 19473
FT /note="Ets55 mutation"
FT /replace="a"
@@ -1018,11 +1019,11 @@ FT /note="saf mutation; altered integration site specificity"
FT /replace="g"
FT variation 24376
FT /note="left end del3 deletion/insertion"
-FT variation 24378..25927
-FT /note="vir22 deletion/insertion"
FT variation 24378..25065
FT /note="del6 deletion"
FT /replace=""
+FT variation 24378..25927
+FT /note="vir22 deletion/insertion"
FT variation 24381..26340
FT /note="vir94 deletion/insertion"
FT protein_bind 24399..24472
@@ -1141,9 +1142,9 @@ FT /codon_start=1
FT /db_xref="SWISS-PROT:P07695"
FT /transl_table=11
FT /gene="cox"
-FT /function="repressor of Pc; required for prophage excision;
-FT inhibits integration; activates P11 promoter of satellite
-FT phage P4"
+FT /function="repressor of Pc; required for prophage
+FT excision; inhibits integration; activates P11 promoter of
+FT satellite phage P4"
FT /product="Cox"
FT /protein_id="AAD03299.1"
FT /translation="MSKQVTLMTDAIPYQEFAKLIGKSTGAVRRMIDKGKLPVIDMTDP
@@ -1174,8 +1175,8 @@ FT /codon_start=1
FT /db_xref="SWISS-PROT:P07696"
FT /transl_table=11
FT /gene="B"
-FT /function="essential protein; DNA replication; required for
-FT lagging strand synthesis"
+FT /function="essential protein; DNA replication; required
+FT for lagging strand synthesis"
FT /product="gpB"
FT /protein_id="AAD03301.1"
FT /translation="MTVMTLNLVEKQPAAMRRIIGKHLAVPRWQDTCDYYNQMMERERL
@@ -1338,7 +1339,6 @@ FT misc_feature complement(33426)
FT /note="transcript start 2; old-tin mRNA"
FT misc_feature 33575..33593
FT /note="cosR; right cohesive end"
-XX
SQ Sequence 33593 BP; 8398 A; 7983 C; 8870 G; 8342 T; 0 other;
ggcgaggcgg ggaaagcact gcgcgctgac ggtggtgctg attgtatttt ttcagcgtct 60
cagcgcgtcg tgacggcact tagtctgccc gttgaggcgt tgtgtgtctg cggggtgttt 120
diff --git a/etc/b132222.embl b/etc/b132222.embl
index 4e4dcccab..8dc1ddd84 100644
--- a/etc/b132222.embl
+++ b/etc/b132222.embl
@@ -137,6 +137,7 @@ XX
CC On Jul 23, 1998 this sequence version replaced gi:14895 gi:15549
CC gi:1262241 gi:974436.
XX
+XX
FH Key Location/Qualifiers
FH
FT source 1..30624
@@ -565,13 +566,13 @@ FT /evidence=EXPERIMENTAL
FT /note="two CI binding sites for repression of pB"
FT /gene="B"
FT /bound_moiety="CI"
+FT -35_signal 20549..20554
+FT /gene="B"
FT promoter 20549..20584
FT /evidence=EXPERIMENTAL
FT /note="pB; repressed by CI"
FT /gene="B"
FT /function="transcription of B gene"
-FT -35_signal 20549..20554
-FT /gene="B"
FT -10_signal 20572..20577
FT /gene="B"
FT CDS 20609..20827
@@ -611,8 +612,8 @@ FT tRNA 20985..21030
FT /note="truncated"
FT /product="tRNA-Ile"
FT misc_feature 20995..21030
-FT /note="in common with attB in Escherichia coli, which is in
-FT the 3' end of ileY"
+FT /note="in common with attB in Escherichia coli, which is
+FT in the 3' end of ileY"
FT misc_feature 21023..21029
FT /note="attP; predicted crossover region with attB"
FT variation 21030..22865
@@ -732,10 +733,6 @@ FT /note="FR"
FT /bound_moiety="CI"
FT /function="probably responsible for CI repression of pE
FT promoter"
-FT protein_bind 23435..23462
-FT /gene="cII"
-FT /bound_moiety="CII"
-FT /function="activate pE"
FT CDS 23435..23944
FT /codon_start=1
FT /db_xref="SWISS-PROT:P21678"
@@ -752,6 +749,10 @@ FT /translation="MFDFQVSKHPHYDEACRAFAQRHNMAKLAERAGMNVQTLRNKLNP
FT EQPHQFTPPELWLLTDLTEDSTLVDGFLAQIHCLPCVPVNELAKDKLQSYVMRAMSELG
FT ELASGAVSDERLTTARKHNMIESVNSGIRMLSLSALALHARLQTNPAMSSVVDTMSGIG
FT ASFGLI"
+FT protein_bind 23435..23462
+FT /gene="cII"
+FT /bound_moiety="CII"
+FT /function="activate pE"
FT variation 23440
FT /note="prevents CII binding to pE; cIV476"
FT /replace="a"
@@ -790,8 +791,8 @@ FT /note="CP78am; dhram"
FT /replace="a"
FT /gene="dhr"
FT terminator 24384..24412
-FT /note="tR1; one of a number of transcription terminators in
-FT this region that are anti-terminated during early lytic
+FT /note="tR1; one of a number of transcription terminators
+FT in this region that are anti-terminated during early lytic
FT development by an unknown mechanism"
FT CDS 24433..24666
FT /codon_start=1
@@ -996,7 +997,6 @@ FT /replace=""
FT /gene="orf97"
FT terminator 30436..30463
FT /note="t95b; p95 transcript terminator"
-XX
SQ Sequence 30624 BP; 7461 A; 7801 C; 8456 G; 6906 T; 0 other;
ggcgtggcgg ggaaagcatt gcgcgccaga ggtggcgcgt gaatgataaa aattatcgtc 60
tgagcgcctc gtaatggcgc tatcgtggtg ctgttggttc gttggtggtc gtgtgtgttt 120
diff --git a/etc/c1215.genbank b/etc/c1215.genbank
index 9e3c3d873..6ba609013 100644
--- a/etc/c1215.genbank
+++ b/etc/c1215.genbank
@@ -63,8 +63,6 @@ FEATURES Location/Qualifiers
rRNA 415..581
/note="SPRG5SD K00771 Yeast (s.pombe) 5s rrna gene and
flanks"
- gene join(1501..1760,1844..2456)
- /gene="SPBC1215.01"
CDS join(1501..1760,1844..2456)
/gene="SPBC1215.01"
/note="SPBC1215.01, len:290, SIMILARITY:Saccharomyces
@@ -82,17 +80,15 @@ FEATURES Location/Qualifiers
PKGPVVIEGLLRQHTDKPRFMMKNEPEKNSFYFLNVREFAQLKGTLPILITELQPSLT
PLQEADHVKRGLPLGHPLKVEIFNSHTEYIITWYSLSVVSAIMLYVYFKRGSGTSSLN
SAYERSKILNNKRL"
+ gene join(1501..1760,1844..2456)
+ /gene="SPBC1215.01"
misc_feature 1761..1766
/gene="SPBC1215.01"
/note="gtacgt, splice donor sequence"
misc_feature 1827..1843
/gene="SPBC1215.01"
/note="ctaacataatcacttag, splice branch and acceptor"
- gene complement(join(2495..2602,2663..2881,2953..4071,
- 4111..4372,4413..4849,4889..5007,5251..5389,5434..5466))
- /gene="SPBC1215.02c"
- CDS complement(join(2495..2602,2663..2881,2953..4071,
- 4111..4372,4413..4849,4889..5007,5251..5389,5434..5466))
+ CDS complement(join(2495..2602,2663..2881,2953..4071,4111..4372,4413..4849,4889..5007,5251..5389,5434..5466))
/gene="SPBC1215.02c"
/note="SPBC1215.02c, len:811, SIMILARITY:Saccharomyces
cerevisiae, DEC1_YEAST, dec1 protein, (796 aa), fasta
@@ -118,6 +114,8 @@ FEATURES Location/Qualifiers
LIESFDYENSTPLSQLTKYTEIINDLITCLNSFLYHVSATKKKEFTRQYQLLKNISSN
KLGSISGITKHKKKAARKYVSELLSNSWLSNLSETQVPYDPKFAKQVGEGMIDSYIQT
TDAVSKLPKFVKF"
+ gene complement(join(2495..2602,2663..2881,2953..4071,4111..4372,4413..4849,4889..5007,5251..5389,5434..5466))
+ /gene="SPBC1215.02c"
misc_feature complement(2603..2612)
/gene="SPBC1215.02c"
/note="ctaataatag, splice branch and acceptor"
@@ -163,8 +161,8 @@ FEATURES Location/Qualifiers
misc_feature 6387..6490
/note="nominal overlap with cosmid SPBC83 S. pombe
chromosome 2"
-BASE COUNT 2097 a 1138 c 1138 g 2117 t
-ORIGIN
+BASE COUNT 0 a 0 c 0 g 0 t
+ORIGIN
1 tatatataat ttaataaata cattccgacg atactgcctc tatggcttag tggtacagca
61 tcgcacttgt aatgcgaaga tccttggttc gattccgagt ggaggcatat acattatatt
121 atattctttt tcatgcggaa aaaagatttc aaatttttgg gtatgatatt aatatgactg
@@ -273,5 +271,5 @@ ORIGIN
6301 gattattgtt gaaaagcgca gacgaagttt agagaattac tagcgtattt taaatttaat
6361 caacggacta ttttttattc ctttgagatc cgactttatc gctttgcttc taattttcca
6421 aaattcagtc tatctacgcg atccagccct gtttgcgtaa atttcatatt atttttcttt
- 6481 aaacgtttgg
+ 6481 aaacgtttgg
//
diff --git a/etc/options b/etc/options
index 1c447a161..22498c000 100644
--- a/etc/options
+++ b/etc/options
@@ -2,7 +2,7 @@
# (Note that comment lines start with a hash (#) symbol)
-# $Header: //tmp/pathsoft/artemis/etc/options,v 1.21 2005-07-11 08:52:08 tjc Exp $
+# $Header: //tmp/pathsoft/artemis/etc/options,v 1.22 2006-06-21 10:11:36 tjc Exp $
# This file should contain option settings that look like this:
#
@@ -496,10 +496,13 @@ extra_qualifiers = \
obsolete_product "text" \
origid "text" \
ortholog "text" \
+ other_transcript "text" \
paralog "text" \
pepstats_file "text" \
percent_id text \
pfam_match "text" \
+ previous_other_transcript "text" \
+ previous_shared_id "text" \
previous_systematic_id "text" \
primary_name "text" \
prosite_match "text" \
@@ -510,6 +513,7 @@ extra_qualifiers = \
score text \
sequence_source "text" \
sequence_status "text" \
+ shared_id "text" \
sigcleave_file "text" \
signal "text" \
similarity "text" \
diff --git a/etc/run_blastp b/etc/run_blastp
index 9b557691b..2ee1b2a1b 100755
--- a/etc/run_blastp
+++ b/etc/run_blastp
@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below
-RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastp,v 1.4 2005-12-20 11:50:59 tjc Exp $"
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastp,v 1.5 2006-06-21 10:11:36 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
@@ -21,17 +21,17 @@ else
then
DATABASE=$2 export DATABASE
else
- echo usage: $0 -onefile input_file output_file database
- echo or: $0 file_of_filenames database
+ echo usage: $0 -onefile input_file output_file database 1>&2
+ echo or: $0 file_of_filenames database 1>&2
exit 1
fi
fi
+
# expand any ~ or environment variables
EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
-
### change this function to suit your site:
run_one_prog () {
@@ -41,18 +41,7 @@ run_one_prog () {
### change these lines:
- EXEC=${EXEC-`which blastall 2>/dev/null`}
-
- if [ ! -x "$EXEC" ]; then
- EXEC=`find Artemis* -name blastall 2>/dev/null`
- fi
-
- if [ ! -d "$BLASTDB" ]; then
- DATABASE_TMP="$PWD/"`find Artemis* -name blast-data 2>/dev/null`"/$DATABASE"
- if [ -f "$DATABASE_TMP" ]; then
- DATABASE="$DATABASE_TMP"
- fi
- fi
+ EXEC=blastall
echo "about to start $EXEC with input from $INPUT_FILE and output to"
echo "$OUTPUT_FILE using database $DATABASE"
@@ -60,10 +49,30 @@ run_one_prog () {
EXTRA_ARGS=
+ HOSTNAME=`hostname`
+ REMOTE=N
+
+ case $HOSTNAME in
+ deskpro*)
+ REMOTE=Y ;;
+ *)
+ esac
+
+ if [ $REMOTE = "Y" ]; then
+ WDIR=`pwd`
+ export WDIR
+# rsh babel "cd $WDIR; lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v \
+# blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastp \
+# $EXTRA_ARGS >! $OUTPUT_FILE"
+ ssh babel "cd $WDIR; bsub -q longblastq -o $OUTPUT_FILE -e ${PROG}_errors.new -I flexi_blast.pl -p $DATABASE $INPUT_FILE $EXTRA_ARGS"
+ else
# add/change the flags to suit your site:
- nice -19 $EXEC -d $DATABASE -i $INPUT_FILE -p blastp \
- $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
- tee ${PROG}_errors.new 1>&2
+# lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v \
+# blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastp \
+# $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
+# tee ${PROG}_errors.new 1>&2
+ bsub -q longblastq -o $OUTPUT_FILE -e ${PROG}_errors.new -I flexi_blast.pl -p $DATABASE $INPUT_FILE $EXTRA_ARGS
+ fi
#### end of changes
@@ -73,24 +82,337 @@ run_one_prog () {
if [ -s ${PROG}_errors.new ]
then
- ( echo ERROR running $PROG: ; echo;
+ ( echo ERROR running $PROG: ; echo;
echo ===================================================
cat ${PROG}_errors.new ) >> $OUTPUT_FILE
cat ${PROG}_errors.new >> ${PROG}_errors
fi
}
+PERL_PROG_1='
+
+local *BSUB;
+
+my $file = $ARGV[0];
+my $database = $ARGV[1];
+my $pwd = $ARGV[2];
+chomp $file;
+chomp $database;
+
+open(BSUB, "| bsub -q normal -o fasta_errors -n 1 -R \"select[blast && mem > 500] rusage[r1m=1:mem=500]\" -K") or die "could not open bsub pipe : $!";
+open(LIST_FILE,$file);
+
+$EXEC="blastall";
+
+while(my $inFile = <LIST_FILE>)
+{
+ chomp($inFile);
+
+ if($inFile =~ m/^($pwd)(.*)/)
+ {
+ my $inFile_tmp = $2;
+ while($inFile_tmp =~ m/^(\/)(.*)/)
+ {
+ $inFile_tmp = $2;
+ }
+
+ if( -e $inFile_tmp )
+ {
+ $inFile = $inFile_tmp;
+ }
+ }
+
+ if($inFile =~ m/^(\S{100})/)
+ {
+ if($inFile =~ m/^(\S{90,})(blastp\/\S+)/)
+ {
+ my $inFile_tmp = $1;
+
+ if( -e $inFile_tmp )
+ {
+ print BSUB "cd $inFile_tmp\n";
+ $inFile = $2;
+ }
+ }
+ }
+
+ print BSUB "flexi_blast.pl -p $database $inFile $database ktup 2 > $inFile\.out\n";
+ print BSUB "gzip -9 $inFile\.out\n";
+}
+close BSUB or die "--Could not submit job : $!";
+close LIST_FILE;
+'
+
+
+
+PERL_PROG='
+
+local *BSUB;
+
+my $file = $ARGV[0];
+my $database = $ARGV[1];
+my $pwd = $ARGV[2];
+chomp $file;
+chomp $database;
+
+open(LIST_FILE,$file);
+
+$NEW_WDIR=".";
+$NUM_JOBS=0;
+
+while(my $inFile = <LIST_FILE>)
+{
+ $NUM_JOBS++;
+ chomp($inFile);
+
+ if($inFile =~ m/^($pwd)(.*)/)
+ {
+ my $inFile_tmp = $2;
+ while($inFile_tmp =~ m/^(\/)(.*)/)
+ {
+ $inFile_tmp = $2;
+ }
+
+ if( -e $inFile_tmp )
+ {
+ $inFile = $inFile_tmp;
+ }
+ }
+
+
+ if($inFile =~ m/^(\S{100})/)
+ {
+ if($inFile =~ m/^(\S{90,})(blastp\/\S+)/)
+ {
+ my $inFile_tmp = $1;
+
+ if( -e $inFile_tmp )
+ {
+ $NEW_WDIR=$inFile_tmp;
+ $inFile = $2;
+ }
+ }
+ }
+ # find number of leading zero
+
+ if($inFile =~ m/^(.*)(blastp\/)([^\/]*)(0{4})(\d{1})$/)
+ {
+ push(@jobs10, $inFile);
+ }
+ elsif($inFile =~ m/^(.*)(blastp\/)([^\/]*)(0{3})(\d{2})$/)
+ {
+ push(@jobs100, $inFile);
+ }
+ elsif($inFile =~ m/^(.*)(blastp\/)([^\/]*)(0{2})(\d{3})$/)
+ {
+ push(@jobs1000, $inFile);
+ }
+ elsif($inFile =~ m/^(.*)(blastp\/)([^\/]*)(0{1})(\d{4})$/)
+ {
+ push(@jobs10000, $inFile);
+ }
+ else
+ {
+ push(@jobs100000, $inFile);
+ }
+}
+close LIST_FILE;
+
+if(defined @jobs10)
+{
+ my( $num ) = sprintf( "%04d", 0);
+ submit($num, @jobs10);
+}
+
+if(defined @jobs100)
+{
+ my( $num ) = sprintf( "%03d", 0);
+ submit($num, @jobs100);
+}
+
+if(defined @jobs1000)
+{
+ my( $num ) = sprintf( "%02d", 0);
+ submit($num, @jobs1000);
+}
+
+if(defined @jobs10000)
+{
+ my( $num ) = sprintf( "%01d", 0);
+ submit($num, @jobs10000);
+}
+
+if(defined @jobs100000)
+{
+ submit("", @jobs100000);
+}
+
+for($count = 0; $count < @bsub_jobs; $count++)
+{
+ open(BSUB, "| bsub -q normal -R \"select[mem > 1] rusage[mem=1]\" -o /dev/null -e /dev/null -w \"ended($bsub_jobs[$count])\" -K -J \"$bsub_jobs[$count]\_fin\"") or die "could not open bsub pipe : $!";
+ print BSUB "\"echo finished > /dev/null\" > /dev/null 2> /dev/null";
+ close BSUB; # or die "--Could not submit job : $!";
+}
+
+
+sub submit
+{
+ my ($num, @jobs) = @_;
+
+ my $prefix;
+ my @starts;
+ my @prefixes;
+
+ if($jobs[0] =~ m/^(.*)(\/blastp\/)([^\/]*)(\d{5})/)
+ {
+ $prefix = $1.$2.$3;
+ push(@starts, "$4");
+ }
+ elsif($jobs[0] =~ m/^(blastp\/)([^\/]*)(\d{5})/)
+ {
+ $prefix = $1.$2;
+ push(@starts, "$3");
+ }
+
+ # escape characters
+ if($prefix =~ /(\+|\?|\*|\[|\])/)
+ {
+ $prefix =~ s/\+/\\+/;
+ $prefix =~ s/\?/\\?/;
+ $prefix =~ s/\*/\\*/;
+ $prefix =~ s/\[/\\[/;
+ $prefix =~ s/\]/\\]/;
+ }
+ push(@prefixes, $prefix);
+
+
+ #different entries have different prefixes
+ for($count =0; $count < @jobs; $count++)
+ {
+ if($jobs[$count] !~ m/^$prefix(.*)/)
+ {
+ if($jobs[$count] =~ m/^(.*)(blastp\/)([^\/]*)(\d{5})/)
+ {
+ $prefix = $1.$2.$3;
+
+ push(@starts, "$4");
+
+ if($prefix =~ /(\+|\?|\*|\[|\])/)
+ {
+ $prefix =~ s/\+/\\+/;
+ $prefix =~ s/\?/\\?/;
+ $prefix =~ s/\*/\\*/;
+ $prefix =~ s/\[/\\[/;
+ $prefix =~ s/\]/\\]/;
+ }
+
+ push(@prefixes, $prefix);
+ }
+ }
+ }
+
+ for($count =0; $count < @prefixes; $count++)
+ {
+ $prefix = $prefixes[$count];
+ $start = $starts[$count];
+
+ # build the index description that need to be run
+ $index="$start-";
+ $end="$start";
+ for($j =0; $j < @jobs; $j++)
+ {
+ if($jobs[$j] =~ m/^$prefix(.*)/)
+ {
+ if($jobs[$j] =~ m/^(.*)(blastp\/)([^\/]*)(\d{5})/)
+ {
+ if($j == @jobs-1)
+ {
+ $index = "$index$4";
+ }
+ elsif($end+1 >= $4)
+ {
+ $end = "$4";
+ }
+ else
+ {
+ $index = "$index$end,$4-"
+ }
+ }
+ }
+ }
+
+ if($index =~ m/(\-)$/)
+ {
+ $index = "$index$end";
+ }
+
+ print "$prefix, $index, $num";
+ bsub($prefix, $index, $num);
+ }
+}
+
+
+# start job arrays
+sub bsub
+{
+ my ($prefix, $index, $num) = @_;
+
+ my $name = $prefix;
+
+ if($prefix =~ m/(\/blastp\/)(.*)/)
+ {
+ $name = "$2";
+ }
+
+ my $random = int( rand( 999+1 ) );
+
+ push(@bsub_jobs, "$name$random\_blastp");
+
+ my $QUEUE="longblastq";
+ if($NUM_JOBS <= 6)
+ {
+ $QUEUE="normal";
+ }
+
+ print "flexi_blast.pl -p $database $prefix$num\n";
+
+ open(BSUB, "| bsub -q $QUEUE -o /dev/null -n 1 -R \"select[blast && mem > 500] rusage[mem=500]\" -J$name$random\_blastp\"[$index]%16\"") or die "could not open bsub pipe : $!";
+ print BSUB "cd $NEW_WDIR\n";
+ print BSUB "flexi_blast.pl -p $database $prefix$num";
+ print BSUB "\${LSB_JOBINDEX} > $prefix$num";
+ print BSUB "\${LSB_JOBINDEX}\.out\n";
+
+ print BSUB "gzip -9f $prefix$num";
+ print BSUB "\${LSB_JOBINDEX}\.out\n";
+
+ close BSUB or die "--Could not submit job : $!";
+}
+
+'
+
(echo "#!/bin/sh -"; echo "kill $$") > $PROG.kill
chmod a+x $PROG.kill
+HOSTNAME=`hostname`
+REMOTE=N
+
+case $HOSTNAME in
+ deskpro*)
+ REMOTE=Y ;;
+ *)
+esac
+
if [ x$ONEFILE = x ]
then
- for i in `cat $1`
- do
- run_one_prog $i $i.out $EXPANDED_DATABASE
- done
-
+ if [ $REMOTE = "Y" ]; then
+ WDIR=`pwd`
+ export WDIR
+ CMD=`echo $PERL_PROG_1`
+ ssh babel "cd $WDIR; perl -w -e '$CMD' \"$1\" \"$EXPANDED_DATABASE\" \"$PWD\""
+ else
+ perl -w -e "$PERL_PROG" "$1" "$EXPANDED_DATABASE" "$PWD"
+ fi
else
run_one_prog $1 $2 $EXPANDED_DATABASE
fi
diff --git a/etc/run_fasta b/etc/run_fasta
index 13f597b31..286300de9 100755
--- a/etc/run_fasta
+++ b/etc/run_fasta
@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below
-RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fasta,v 1.14 2005-12-20 13:44:18 tjc Exp $"
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fasta,v 1.15 2006-06-21 10:11:36 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
@@ -41,20 +41,9 @@ run_one_prog () {
### change these lines:
- EXEC=${EXEC-`which fasta34 2>/dev/null`}
- if [ ! -x "$EXEC" ]; then
- EXEC=`find Artemis* -name fasta34 2>/dev/null`
- fi
-
- if [ ! -f "$FASTLIBS" ]; then
- DATABASE_TMP=`echo $DATABASE | sed 's|\%||'`
- DATABASE_TMP="$PWD/"`find Artemis* -name blast-data 2>/dev/null`"/$DATABASE_TMP"
- if [ -f "$DATABASE_TMP" ]; then
- DATABASE="$DATABASE_TMP"
- fi
- fi
-
+ EXEC=fasta34
+
echo "about to start $EXEC with input from $INPUT_FILE and output to" 1>&2
echo "$OUTPUT_FILE using database $DATABASE" 1>&2
--
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