| 1 |
gpertea |
23 |
#!/usr/bin/perl |
| 2 |
|
|
use strict; |
| 3 |
|
|
use FindBin; |
| 4 |
|
|
|
| 5 |
|
|
umask 0002; |
| 6 |
|
|
#the line below is needed if pvmsx is used |
| 7 |
|
|
# also, the error condition is set only by the presence of $file |
| 8 |
|
|
#chdir($ENV{PVMSX_WD}) if ($ENV{PVMSX_WD}); |
| 9 |
|
|
|
| 10 |
|
|
|
| 11 |
|
|
$ENV{'PATH'}=$FindBin::Bin.':'.$ENV{'PATH'}; |
| 12 |
|
|
|
| 13 |
|
|
#so for pvmsx to consider the task was successful, $file must be deleted! |
| 14 |
|
|
#============== |
| 15 |
|
|
# 1 is the name of the fasta sequence input file |
| 16 |
|
|
# 2 is the # of sequences in ${1} should = 1 for this script |
| 17 |
|
|
# 3 is the slice no. being processed by sx |
| 18 |
|
|
# 4 is 0 if not the last file, 1 if the last file |
| 19 |
|
|
# 5 is the # of sequences skipped initially |
| 20 |
|
|
# 6 is the # of sequences to be processed (-1 = ALL) |
| 21 |
|
|
# 7 user parameter |
| 22 |
|
|
# 1 2 3 4 5 6 |
| 23 |
|
|
my ($file, $numpass, $slice_num, $last, $skipped, $total, $userparams)=@ARGV; |
| 24 |
|
|
#user parameters: |
| 25 |
|
|
# 1) database (full path) |
| 26 |
|
|
# 2) PID cutoff (using 94 if not specified) |
| 27 |
|
|
# 3) maximum overhang |
| 28 |
|
|
# 4) minimum overlap |
| 29 |
|
|
# 5) extra flags (optional) |
| 30 |
|
|
# flags: M = no masking, D= separate database (not all-vs-all) |
| 31 |
|
|
# G = show gaps |
| 32 |
|
|
my ($searchdb,$pid,$maxovh,$minovl, $xflags)=split(/:/,$userparams); |
| 33 |
|
|
my $blast_res=$file.'.tab'; |
| 34 |
|
|
my $nomasking = $xflags=~/M/; |
| 35 |
|
|
my $gapinfo = $xflags=~/G/; |
| 36 |
|
|
my $otherDb = $xflags=~/D/; |
| 37 |
|
|
|
| 38 |
|
|
$pid=25 unless $pid>20; #not used for this blastn search |
| 39 |
|
|
$minovl=40 unless $minovl; #not used for this blastn |
| 40 |
|
|
my $log_file='log_std'; |
| 41 |
|
|
my $err_file='err_log'; |
| 42 |
|
|
open(STDERR, '>>'.$err_file); |
| 43 |
|
|
open(STDOUT, '>>'.$log_file); |
| 44 |
|
|
|
| 45 |
|
|
my $toskip = $skipped+$numpass*($slice_num-1); |
| 46 |
|
|
$ENV{BLASTMAT}='/fs/sz-user-supported/Linux-i686/packages/wu-blast/matrix' unless $ENV{BLASTMAT}; |
| 47 |
|
|
my $cmd = "blastp $searchdb $file E=1e-10 B=30 V=30 -noseqs -notes -warnings -novalidctxok -cpus=1 -topcomboN 1 "; |
| 48 |
|
|
$cmd.= " -dbrecmin $toskip " if $toskip>0 && $otherDb==0; |
| 49 |
|
|
# $cmd.= "| blastflt PID=25 | bzip2 -cf > $blast_res.bz2"; |
| 50 |
|
|
$cmd.= "| blast2btab PID=30 | bzip2 -f > $blast_res.bz2" ; |
| 51 |
|
|
# $cmd.=$gapinfo ? ' -D5 ':' -D4 '; |
| 52 |
|
|
# $cmd.= ($nomasking) ? ' -FF -UF ' : ' -UT -F "m D" '; |
| 53 |
|
|
# unless ($otherDb) { |
| 54 |
|
|
# $cmd.=' -KT '; |
| 55 |
|
|
# $cmd.= " -k $toskip " if $toskip>0; |
| 56 |
|
|
# } |
| 57 |
|
|
#$cmd.=" > $blast_res"; |
| 58 |
|
|
my $slno=sprintf("slice:%09d",$slice_num); |
| 59 |
|
|
print STDERR ">>$slno: $cmd\n"; |
| 60 |
|
|
|
| 61 |
|
|
my $errmsg = `($cmd) 2>&1`; |
| 62 |
|
|
my $r=$?; |
| 63 |
|
|
print STDERR "<<$slno: done.\n"; |
| 64 |
|
|
|
| 65 |
|
|
if ($r || ($errmsg=~/ERROR/is) || ($errmsg=~/Segmentation/is)) { |
| 66 |
|
|
print STDERR "!Error at:\n$cmd\n"; |
| 67 |
|
|
print STDERR "$errmsg\n"; |
| 68 |
|
|
exit(1); |
| 69 |
|
|
} |
| 70 |
|
|
#------- sorting of results not needed for blastn |
| 71 |
|
|
# $cmd="sort -k11,11g -k10,10nr -k9,9nr $blast_res | bzip2 -cf > $mgblast_res.bz2"; |
| 72 |
|
|
# $errmsg=`($cmd) 2>&1`; |
| 73 |
|
|
#$r=$?; |
| 74 |
|
|
#if (($r && ($r>>8 != 2)) || $errmsg=~m/memory/is) { |
| 75 |
|
|
# die "Error sorting/compressing the results file '$mgblast_res'\n$cmd\n"; |
| 76 |
|
|
# } |
| 77 |
|
|
# unlink($file, $mgblast_res); |
| 78 |
|
|
unlink($file); |
| 79 |
|
|
exit 0; |
