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Changeset 16:4155dba0d57a (2018-01-26)

Previous changeset 15:6d9f127da28f (2018-01-26) Next changeset 17:18171b884c3a (2018-01-26)

Commit message:
Uploaded

modified:
bin/subgroups.pm

diff -r 6d9f127da28f -r 4155dba0d57a bin/subgroups.pm
--- a/bin/subgroups.pm Fri Jan 26 08:08:42 2018 -0500
+++ b/bin/subgroups.pm Fri Jan 26 08:08:57 2018 -0500

[

@@ -7,6 +7,7 @@
our @EXPORT_OK = qw( &subgroups );

use POSIX;
+use File::Copy;
use FindBin;
use lib $FindBin::Bin;
use align qw ( get_hash_alignment );
@@ -27,30 +28,54 @@
my $reject_miRNAs = $dir.'miRNAs_rejected.fastq';
my $sam_miRNAs = $dir.'miRNAs.sam';
my @tmp = get_hash_alignment($miRNAs, $mis, 1, 1, $accept_miRNas, $reject_miRNAs, $fin, $proc, 'miRNAs',$sam_miRNAs, $report);
- my $mi = $tmp[0];
+ my $mi = $tmp[0]; my $sam = '';
$repartition{'miRNAs'} = $mi;

- my $sam = new String::Random;
- $sam = $sam->randpattern("CCcccccc");
+
my $reject_rRNAs = $dir.'rRNAs_rejected.fastq';
- @tmp = get_hash_alignment($rRNAs, $mis, 0, 1, 'NA', $reject_rRNAs, $reject_miRNAs, $proc, 'rRNAs', $sam, $report);
- $repartition{'rRNAs'} = $tmp[0];
- unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
+ if ( $rRNAs eq 'None')
+ {
+ move($reject_miRNAs,$reject_rRNAs);
+ }
+ else
+ {
+ $sam = new String::Random;
+ $sam = $sam->randpattern("CCcccccc");
+ @tmp = get_hash_alignment($rRNAs, $mis, 0, 1, 'NA', $reject_rRNAs, $reject_miRNAs, $proc, 'rRNAs', $sam, $report);
+ $repartition{'rRNAs'} = $tmp[0];
+ unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
+ }

- $sam = new String::Random;
- $sam = $sam->randpattern("CCcccccc");
- my $reject_tRNAs = $dir.'tRNAs_rejected.fastq';
- @tmp = get_hash_alignment($tRNAs, $mis, 0, 1, 'NA', $reject_tRNAs, $reject_rRNAs, $proc, 'tRNAs', $sam, $report);
- $repartition{'tRNAs'} = $tmp[0];
- unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
+ my $reject_tRNAs = $dir.'rRNAs_rejected.fastq';
+ if ( $rRNAs eq 'None')
+ {
+ move($reject_rRNAs,$reject_tRNAs);
+ }
+ else
+ {
+ $sam = new String::Random;
+ $sam = $sam->randpattern("CCcccccc");
+ @tmp = get_hash_alignment($tRNAs, $mis, 0, 1, 'NA', $reject_tRNAs, $reject_rRNAs, $proc, 'tRNAs', $sam, $report);
+ $repartition{'tRNAs'} = $tmp[0];
+ unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
+ }
+

- $sam = new String::Random;
- $sam = $sam->randpattern("CCcccccc");
my $bonafide = $dir.'bonafide_reads.fastq';
- @tmp = get_hash_alignment($snRNAs, $mis, 0, 1, 'NA', $bonafide, $reject_tRNAs, $proc, 'snRNAs', $sam, $report);
- $repartition{'snRNAs'} = $tmp[0];
+ if ( $rRNAs eq 'None')
+ {
+ move($reject_tRNAs,$bonafide);
+ }
+ else
+ {
+ $sam = new String::Random;
+ $sam = $sam->randpattern("CCcccccc");
+ @tmp = get_hash_alignment($snRNAs, $mis, 0, 1, 'NA', $bonafide, $reject_tRNAs, $proc, 'snRNAs', $sam, $report);
+ $repartition{'snRNAs'} = $tmp[0];
+
+ unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
+ }
my $bo = $tmp[1];
- unlink $sam, $sam.'_aln.err', $sam.'_samse.err';

my $sam_transcripts = $dir.'transcripts.sam';
my $reject_transcripts = $dir.'rejected_transcripts.fastq';