Changeset 6


Ignore:
Timestamp:
Dec 15, 2011, 4:53:24 PM (5 years ago)
Author:
y.zhang@…
Message:

=1215.cpp, GFF, passion_pipeline

Location:
trunk
Files:
1 deleted
4 edited

Legend:

Unmodified
Added
Removed
  • trunk/compile.sh

    r2 r6  
    1 g++ ./code/PASSION0924.cpp -o PASSION -O3 -fopenmp
     1g++ ./code/PASSION1215.cpp -o PASSION -O3 -fopenmp
  • trunk/passion_pipeline.sh

    r3 r6  
    137137
    138138rm $outputfolder/tmp/deletions.*
    139 rm $outputfolder/aln*asinput*.tmp
     139
    140140rm $outputfolder/aln*asinput
    141141rm $outputfolder/deletions.*
  • trunk/userdefined_exonisland_GFF.pl

    r3 r6  
    121121  while (my $line = <USEREXONFILE>)
    122122  {
    123         if (!($line =~ /^track/ || $line =~ /^#/))
    124         {
    125           chmod $line;
    126           my @array=split("\t",$line);
    127           my ($chr,$start,$end)=($array[0],$array[3],$array[4]);
    128           $chr =~ s/chr//;
    129           for (my $i=$start;$i<=$end;$i++)
     123        chmod $line;
     124    if ($line !~ /^\s*$/)
     125        {if (!($line =~ /^track/ || $line =~ /^#/))
    130126          {
    131             $hash_user_exon{$chr}{$i}=1;
     127            my @array=split("\t",$line);
     128            my ($chr,$start,$end)=($array[0],$array[3],$array[4]);
     129            $chr =~ s/chr//;
     130            for (my $i=$start;$i<=$end;$i++)
     131            {
     132              $hash_user_exon{$chr}{$i}=1;
     133            }
     134            print $chr,"\t",$start,"\t",$end,"\n";
    132135          }
    133           print $chr,"\t",$start,"\t",$end,"\n";
    134136        }
    135137  }
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