| 1 |
#!/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 $mgblast_res=$file.'.tab'; |
| 34 |
my $nomasking = $xflags=~/M/; |
| 35 |
my $gapinfo = $xflags=~/G/; |
| 36 |
my $otherDb = $xflags=~/D/; |
| 37 |
|
| 38 |
$pid=94 unless $pid>50; |
| 39 |
$minovl=40 unless $minovl; |
| 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 $toskip=($file =~ m/_\@(\d+)_v\d+\.\d+/) ? $1 : $skipped+$numpass*($slice_num-1); |
| 46 |
|
| 47 |
#= mgblast weakness - when some query seqs are entirely masked |
| 48 |
#= or what's left is just low complexity, it will abort the search |
| 49 |
#= so let's filter the input in advance |
| 50 |
unless ($nomasking) { |
| 51 |
my $renfile=$file.'_cpy'; |
| 52 |
rename($file, $renfile) || die "Cannot rename '$file' to '$renfile'!\n"; |
| 53 |
local $/="\n>"; |
| 54 |
open (INFILE, "mdust -m L < $renfile |") || die "Cannot open renamed file '$renfile'\n"; |
| 55 |
open (OUTFILE, '>'.$file) || die "Cannot create flt file '$file'\n"; |
| 56 |
open (MASKED, '>>masked.lst') || die "Cannot open masked.lst for append\n"; |
| 57 |
open (TOOSHORT, '>>tooshort.lst') || die "Cannot open tooshort.lst for append\n"; |
| 58 |
|
| 59 |
my $counter; |
| 60 |
while(<INFILE>) { |
| 61 |
s/^>//; |
| 62 |
chomp; |
| 63 |
$counter++; |
| 64 |
my ($defline, $seq)=(m/^(.+?)\n(.+)/s); |
| 65 |
my $s=$seq; |
| 66 |
$s =~ tr/\n \t//d; |
| 67 |
my $seqlen=length($s); |
| 68 |
if ($seqlen<$minovl) { |
| 69 |
print TOOSHORT $defline."\n"; |
| 70 |
next; |
| 71 |
} |
| 72 |
my @uc=($s =~ m/([A-M,O-W,Y,Z]+)/g); |
| 73 |
my $valid; |
| 74 |
foreach my $l (@uc) { |
| 75 |
if (length($l)>12) { # a valid stretch of at least 12nt would suffice |
| 76 |
$valid=1; |
| 77 |
last; |
| 78 |
} |
| 79 |
} |
| 80 |
if ($valid) { |
| 81 |
print OUTFILE '>'.$defline."\n".$seq."\n"; |
| 82 |
} |
| 83 |
else { |
| 84 |
print MASKED $defline."\n"; |
| 85 |
} |
| 86 |
} #while |
| 87 |
close(INFILE);close(OUTFILE);close(MASKED);close(TOOSHORT); |
| 88 |
die "Error: no sequence in this slice!\n" unless $counter; |
| 89 |
unlink($renfile); |
| 90 |
} |
| 91 |
|
| 92 |
my $cmd="mgblast -i $file -d $searchdb -p $pid -W12 -X12 ". |
| 93 |
" -JF -v100 -b100 -C$minovl -H$maxovh "; |
| 94 |
#$cmd.=$gapinfo ? ' -D5 ':' -D4 '; |
| 95 |
$cmd.= ' -D4 -UF -F"m D" '; #use dust filter |
| 96 |
#$cmd.= ($nomasking) ? ' -FF -UF ' : ' -UT -F "m D" '; |
| 97 |
unless ($otherDb) { |
| 98 |
$cmd.=' -KT '; |
| 99 |
$cmd.= " -k $toskip " if $toskip>0; |
| 100 |
} |
| 101 |
$cmd.=" > $mgblast_res"; |
| 102 |
my $slno=sprintf("slice:%09d",$slice_num); |
| 103 |
print STDERR ">>$slno: $cmd\n"; |
| 104 |
|
| 105 |
my $errmsg = `($cmd) 2>&1`; |
| 106 |
print STDERR "<<$slno: done.\n"; |
| 107 |
|
| 108 |
if ($? || ($errmsg=~/ERROR/i) || ($errmsg=~/Segmentation/i)) { |
| 109 |
print STDERR "!Error at:\n$cmd\n"; |
| 110 |
print STDERR "$errmsg\n"; |
| 111 |
exit(1); |
| 112 |
} |
| 113 |
$cmd="sort -k11,11g -k10,10nr -k9,9nr $mgblast_res | bzip2 -cf > $mgblast_res.bz2"; |
| 114 |
my $r=system($cmd); |
| 115 |
if ($r && ($r>>8 != 2) ) { |
| 116 |
die "Error sorting/compressing the results file '$mgblast_res'\n$cmd\n"; |
| 117 |
} |
| 118 |
|
| 119 |
unlink($file, $mgblast_res); |
| 120 |
exit 0; |
