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Commit c89c8669 authored by tjc's avatar tjc
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old version 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@1652 ee4ac58c-ac51-4696-9907-e4b3aa274f04
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etc/run_fasta_orig deleted 100755 → 0
+ 0
− 90
View file @ dacea578
#!/bin/sh -
# this script will run a search program on a sequence input file or on each
# file in a file of filenames
# to customise this script see the function called run_one_prog below
RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fasta_orig,v 1.1 2004-06-09 10:03:04 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
if [ $# = 4 -a x$1 = x-onefile ]
then
shift
ONEFILE=t
DATABASE=$3 export DATABASE
else
if [ $# = 2 ]
then
DATABASE=$2 export DATABASE
else
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 () {
INPUT_FILE=$1
OUTPUT_FILE=$2
DATABASE=$3
### change these lines:
FASTLIBS=/nfs/disk222/yeastpub/bio-soft/fasta/pubseqgbs export FASTLIBS
EXEC=/nfs/disk222/yeastpub/bio-soft/fasta/fasta33
echo "about to start $EXEC with input from $INPUT_FILE and output to" 1>&2
echo "$OUTPUT_FILE using database $DATABASE" 1>&2
# add/change the flags to suit your site:
COMMAND="$EXEC -B -S -q -b 40 -H $INPUT_FILE $DATABASE ktup 2"
echo "command line: $COMMAND" 1>&2
lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v \
$COMMAND 2>&1 > $OUTPUT_FILE |
tee ${PROG}_errors.new 1>&2
#### end of changes
# Artemis can read compressed files
gzip -9 $OUTPUT_FILE &
if [ -s ${PROG}_errors.new ]
then
( echo ERROR running $PROG: ; echo;
echo ===================================================
cat ${PROG}_errors.new ) >> $OUTPUT_FILE
cat ${PROG}_errors.new >> ${PROG}_errors
fi
}
(echo "#!/bin/sh -"; echo "kill $$") > $PROG.kill
chmod a+x $PROG.kill
if [ x$ONEFILE = x ]
then
for i in `cat $1`
do
run_one_prog $i $i.out $EXPANDED_DATABASE
done
else
run_one_prog $1 $2 $EXPANDED_DATABASE
fi
exit 0
etc/run_jalview.orig deleted 100755 → 0
+ 0
− 167
View file @ dacea578
#!/bin/sh -
# This script needs one argument - a file of file names.
# Each name should refer to a file that contains a EMBL format feature.
# The feature must have a /fasta_file= qualifier which is used to read the
# FASTA search results for the feature and to find the protein sequence of the
# feature. The sequence and the sequence of the FASTA hits will be passed to
# jalview.
PERL_PROG='
use strict;
if (@ARGV != 1) {
die "$0 needs one argument - a file of feature file names\n";
}
sub process_fasta
{
my $feature_file = shift;
my $fasta_results_file = shift;
my $sequence_file;
if ($fasta_results_file =~ /(.*).out/) {
$sequence_file = $1;
} else {
die "cannot understand $fasta_results_file\n";
}
if (! -e $sequence_file) {
die "cannot find $sequence_file\n";
}
my $fasta_seq_for_alignment = "";
open SEQ_FILE, $sequence_file or die "cannot open $sequence_file: $!\n";
while (<SEQ_FILE>) {
$fasta_seq_for_alignment .= $_;
}
close SEQ_FILE;
if (-e $fasta_results_file) {
open FASTA_OUTPUT, $fasta_results_file
or die "cannot open $fasta_results_file: $!\n";
} else {
my $gzip_fasta_results_file = $fasta_results_file . ".gz";
if (-e $gzip_fasta_results_file) {
open FASTA_OUTPUT, "gzip -d < $gzip_fasta_results_file |"
or die "cannot open $gzip_fasta_results_file: $!\n";
} else {
die "cannot find $fasta_results_file or $gzip_fasta_results_file\n";
}
}
my $top_re = "^The best scores are:";
my $seen_top = 0;
my $seen_bottom = 0;
my @protein_ids = ();
while (<FASTA_OUTPUT>) {
if (/$top_re/) {
$seen_top = 1;
next;
}
if ($seen_top && /^\s*$/) {
$seen_bottom = 1;
next;
}
if ($seen_top && !$seen_bottom) {
if (/^(\S+)/) {
if (@protein_ids < 20) {
push @protein_ids, "$1"
} else {
last;
}
} else {
warn "cannot understand this line:\n$_\n";
}
}
}
my %hash = ();
@hash{@protein_ids} = (1) x @protein_ids;
@protein_ids = sort keys %hash;
my $protein_db = "swall";
# look for each of the IDs from the FASTA output in each of the DBs
for my $id (@protein_ids) {
my $fetch = "getz -sf fasta -f seq [swall-id:$id]";
my $temp_seq = "";
open FETCH, "$fetch |" or
die "cannot open pipe to $fetch: $!\n";
while (<FETCH>) {
$temp_seq .= $_;
}
close FETCH;
if ($? == 0) {
$fasta_seq_for_alignment .= $temp_seq;
} else {
print STDERR "$id was not found in $protein_db\n";
}
}
my $msf_file = "$feature_file.fasta_msf";
my $emboss_prog = "emma";
my $emboss_command_line = "$emboss_prog -filter -stdout -osf msf -dendoutfile /dev/null > $msf_file";
open EMBOSS, "|$emboss_command_line" or
die "cannot open pipe to $emboss_prog: $!\n";
print EMBOSS $fasta_seq_for_alignment;
close EMBOSS;
my $jalview_prog = "jalview";
print STDERR "\nstarting $jalview_prog:\n";
system "$jalview_prog", "$msf_file";
}
my $file;
while (defined ($file = <>)) {
chomp $file;
if (-e $file) {
open IN_FILE, "$file\n" or die "cannot open $file\n";
my $line;
while (defined ($line = <IN_FILE>)) {
if ($line =~ m!/fasta_file="(.*)"!) {
my $fasta_results_file = $1;
process_fasta $file, $fasta_results_file;
last;
}
}
close IN_FILE;
}
}'
perl -w -e "$PERL_PROG" "$@"
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