comparison tools/rdock/bin/sdsort @ 0:bc03dbb6eb37 draft

planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty

0:bc03dbb6eb37

#!/usr/bin/perl
# Sorts SD records by given data field
use lib "$ENV{'RBT_ROOT'}/lib";

use SDRecord;

my $SDSORTKEY; # sort key
my $SDSORTASCEND = 1;# 1 = ascending, 0 = descending
my $SDSORTTEXT = 1;# 1 = text sort, 0 = numeric sort

my $FASTFORMAT = 0;
my $FASTKEY = "_TITLE1";

#Print help if no command line arguments
printHelpAndExit() if (scalar(@ARGV) == 0);

#Parse command line arguments
my @files;
while (scalar(@ARGV)) {
  $arg = shift @ARGV;
  printHelpAndExit() if ($arg eq '-h');
  if ($arg eq '-r') {
    $SDSORTASCEND = 0;#descending sort requested
  }
  elsif ($arg eq '-n') {
    $SDSORTTEXT = 0;;#numeric sort requested
  }
  elsif (index($arg,'-s')==0) {
    $FASTFORMAT = 1;
  }
  elsif (index($arg,'-id')==0) {
    $FASTKEY = substr($arg,3);
  }
  elsif (index($arg,'-f')==0) {
    $SDSORTKEY = substr($arg,2);#sort key
  }
  else {
    push @files,$arg;#must be a filename
  }
}
push @ARGV,@files;#put the filenames back in the arg list

#read records
my $sdRec = new SDRecord;
my @records;
my $nRec=0;

my $lastid="";
while ($sdRec->readRec('DATA'=>1,'LINES'=>1)) {
  $sdRec->addData('_REC' => ++$nRec);#add record# as temp data field
  if ($FASTFORMAT) {
    my $id = $sdRec->{'DATA'}->{$FASTKEY};
    if (($lastid ne "") && ($lastid ne $id)) {
      foreach $rec (sort sortSD @records) {
	$rec->writeRec();
      }
      @records = ();#clear the list
    }
    $lastid = $id;
  }
  push(@records,$sdRec->copy('DATA'=>1,'LINES'=>1));
}

#write sorted records
foreach $rec (sort sortSD @records) {
  $rec->writeRec();
}

#######################################################
# sort function to sort SD records by given field
# handles text/numeric and ascending/descending sort
sub sortSD {
  if ($SDSORTTEXT) {
    return $a->{'DATA'}->{$SDSORTKEY} cmp $b->{'DATA'}->{$SDSORTKEY} if ($SDSORTASCEND);
    return $b->{'DATA'}->{$SDSORTKEY} cmp $a->{'DATA'}->{$SDSORTKEY};
  }
  else {
    return $a->{'DATA'}->{$SDSORTKEY} <=> $b->{'DATA'}->{$SDSORTKEY} if ($SDSORTASCEND);
    return $b->{'DATA'}->{$SDSORTKEY} <=> $a->{'DATA'}->{$SDSORTKEY};
  }
}

#######################################################################
sub printHelpAndExit {
  print "\nSorts SD records by given data field\n";
  print "\nUsage:\tsdsort [-n] [-r] [-f<DataField>] [sdFiles]\n\n";
  print "\t-n\t\tnumeric sort (default is text sort)\n";
  print "\t-r\t\tdescending sort (default is ascending sort)\n";
  print "\t-f<DataField>\tspecifies sort field\n";
  print "\t-s\t\tfast mode. Sorts the records for each named compound independently (must be consecutive)\n";
  print "\t-id<NameField>\tspecifies compound name field (default = 1st title line)\n\n";
  print "Note:\t_REC (record #) is provided as a pseudo-data field\n";
  print "\n\tIf SD file list not given, reads from standard input\n";
  print "\tOutput is to standard output\n";
  print "\tFast mode can be safely used for partial sorting of huge SD files of raw docking hits\n";
  print "\twithout running into memory problems.\n\n"; 
  exit;
}