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executable file 448 lines (356 sloc) 9.674 kb
#!/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.sanger.linux,v 1.1 2008-01-24 10:48:29 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: $0 file_of_filenames database 1>&2
exit 1
fi
fi
#
# Exchange DB name for fasta reference
#
if [ "$DATABASE" = "%uniprot" ]; then
DATABASE="%U";
elif [ "$DATABASE" = "%uniprot_archaea" ]; then
DATABASE="%A";
elif [ "$DATABASE" = "%uniprot_bacteria" ]; then
DATABASE="%B";
elif [ "$DATABASE" = "%uniprot_eukaryota" ]; then
DATABASE="%E";
elif [ "$DATABASE" = "%uniprot_viruses" ]; then
DATABASE="%V";
elif [ "$DATABASE" = "%uniprot_rest" ]; then
DATABASE="%R";
elif [ "$DATABASE" = "%malaria" ]; then
DATABASE="%M";
elif [ "$DATABASE" = "%kineto_aa" ]; then
DATABASE="%K";
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
### strip out directory from command line
IN=`echo $INPUT_FILE | sed -n -e "s|$PWD//||p"`
if test "$IN" != "" && test -f $IN; then
INPUT_FILE="$IN"
fi
echo "\n\nIN=$IN\nPWD=$PWD\nINPUT_FILE=$INPUT_FILE\n\n"
### change these lines:
### get sequence size
seq_size=`infoseq "$INPUT_FILE" -length -only -auto | awk '{ sum += $1 } END { print sum }'`
FASTLIBS=/nfs/disk222/yeastpub/bio-soft/fasta/pubseqgbs export FASTLIBS
# EXEC=/nfs/disk222/yeastpub/bio-soft/fasta/fasta33_t
# EXEC=/nfs/disk222/yeastpub/bio-soft/fasta/fasta33
EXEC=/software/pathogen/external/applications/fasta/fasta35
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 100 -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 > $OUTPUT_FILE |
if [ "$seq_size" -lt 50000 ]
then
bsub -q normal -n 1 -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -I $COMMAND 2>&1 > $OUTPUT_FILE |
tee ${PROG}_errors.new 1>&2
else
bsub -q "longblastq" -n 1 -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -I $COMMAND 2>&1 > $OUTPUT_FILE |
tee ${PROG}_errors.new 1>&2
fi
#### 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
}
PERL_PROG_1='
local *BSUB;
my $file = $ARGV[0];
my $database = $ARGV[1];
my $pwd = $ARGV[2];
chomp $file;
chomp $database;
$ENV{'FASTLIBS'} = "/nfs/disk222/yeastpub/bio-soft/fasta/pubseqgbs_test";
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="/nfs/disk222/yeastpub/bio-soft/fasta/fasta33_t";
$EXEC="/software/pathogen/external/applications/fasta/fasta35";
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,})(fasta\/\S+)/)
{
my $inFile_tmp = $1;
if( -e $inFile_tmp )
{
print BSUB "cd $inFile_tmp\n";
$inFile = $2;
}
}
}
print BSUB "$EXEC -B -S -q -b 100 -H $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;
$ENV{'FASTLIBS'} = "/nfs/disk222/yeastpub/bio-soft/fasta/pubseqgbs_test";
open(LIST_FILE,$file);
$EXEC="/nfs/disk222/yeastpub/bio-soft/fasta/fasta33";
$EXEC="/software/pathogen/external/applications/fasta/fasta35";
$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,})(fasta\/\S+)/)
{
my $inFile_tmp = $1;
if( -e $inFile_tmp )
{
$NEW_WDIR=$inFile_tmp;
$inFile = $2;
}
}
}
# find number of leading zero
if($inFile =~ m/^(.*)(fasta\/)([^\/]*)(0{4})(\d{1})$/)
{
push(@jobs10, $inFile);
}
elsif($inFile =~ m/^(.*)(fasta\/)([^\/]*)(0{3})(\d{2})$/)
{
push(@jobs100, $inFile);
}
elsif($inFile =~ m/^(.*)(fasta\/)([^\/]*)(0{2})(\d{3})$/)
{
push(@jobs1000, $inFile);
}
elsif($inFile =~ m/^(.*)(fasta\/)([^\/]*)(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/^(.*)(\/fasta\/)([^\/]*)(\d{5})/)
{
$prefix = $1.$2.$3;
push(@starts, "$4");
}
elsif($jobs[0] =~ m/^(fasta\/)([^\/]*)(\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/^(.*)(fasta\/)([^\/]*)(\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/^(.*)(fasta\/)([^\/]*)(\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$end";
}
bsub($prefix, $index, $num);
}
}
# start job arrays
sub bsub
{
my ($prefix, $index, $num) = @_;
my $name = $prefix;
if($prefix =~ m/(\/fasta\/)(.*)/)
{
$name = "$2";
}
my $random = int( rand( 999+1 ) );
push(@bsub_jobs, "$name$random\_fasta");
my $QUEUE="long";
if($NUM_JOBS <= 6)
{
$QUEUE="normal";
}
open(BSUB, "| bsub -q $QUEUE -o /dev/null -n 1 -R \"select[mem > 500] rusage[mem=500]\" -J$name$random\_fasta\"[$index]%16\"") or die "could not open bsub pipe : $!";
print BSUB "cd $NEW_WDIR\n";
print BSUB "$EXEC -B -S -q -b 100 -H $prefix$num";
print BSUB "\${LSB_JOBINDEX} $database ktup 2 > $prefix$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
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
exit 0
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