| Previous changeset 42:cb33c7d521c4 (2017-12-01) Next changeset 44:bd4b30bff219 (2017-12-01) |
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Commit message:
Uploaded |
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modified:
bin/piPipe.pl |
| b |
| diff -r cb33c7d521c4 -r 0be8011b3d98 bin/piPipe.pl --- a/bin/piPipe.pl Fri Dec 01 05:35:14 2017 -0500 +++ b/bin/piPipe.pl Fri Dec 01 08:01:45 2017 -0500 |
| [ |
| @@ -107,7 +107,7 @@ $pm->start($fastq[$child]) and next; - my $dir_fq = $dir.$name.'/'; + my $dir_fq = $dir.$fastq_n[$child].'/'; mkdir $dir_fq; my $gen_dir = $dir_fq.'genome/'; @@ -119,12 +119,12 @@ my $fastq_resized = $dir_fq.$name.'_'.$min.'-'.$max.'.fastq'; size_distribution ( $fastq[$child], $fastq_resized, $size_dir, $min, $max ); - my $sam_genome = $gen_dir.$name.'_'.$min.'-'.$max.'_'.$ref_name.'.sam'; - my $sam_genome_unique = $gen_dir.$name.'_'.$min.'-'.$max.'_'.$ref_name.'_unique.sam'; - my $fastq_prefix = $gen_dir.$name.'_'.$min.'-'.$max.'_'.$ref_name; + my $sam_genome = $gen_dir.$fastq_n[$child].'_'.$min.'-'.$max.'_'.$ref_name.'.sam'; + my $sam_genome_unique = $gen_dir.$fastq_n[$child].'_'.$min.'-'.$max.'_'.$ref_name.'_unique.sam'; + my $fastq_prefix = $gen_dir.$fastq_n[$child].'_'.$min.'-'.$max; BWA_call ( $ref, $fastq_resized, $sam_genome, $mis, $proc_child, $report ); - my ( $fai_ref_hashP, $ma, $ma_uni ) = get_unique ( $sam_genome, $sam_genome_unique, $gen_dir, 1, $report ); + my ( $fai_ref_hashP, $ma, $ma_uni ) = get_unique ( $sam_genome, $sam_genome_unique, $gen_dir, $fq_collection.$fastq_n[$child], 1, $report ); my $scale = 1000000 / $ma; sam_to_bam_bg ( $sam_genome_unique, $scale, $proc_child ); @@ -148,8 +148,8 @@ bg_to_png ( $fai_file, $fastq_prefix.'_plus.bedgraph', $fastq_prefix.'_minus.bedgraph', $Gviz_dir_rand, 'Mb' ); my $group_dir = $dir_fq.'subgroups/'; - my $fastq_uni = $gen_dir.'unique.fastq'; - my $fastq_all = $gen_dir.'all.fastq'; + my $fastq_uni = $fq_collection.$fastq_n[$child].'unique_mappers.fastq'; + my $fastq_all = $fq_collection.$fastq_n[$child].'all_mappers.fastq'; my ($bo, $mi, $pi) = subgroups ( $fastq_all, $group_dir, $mis, $misTE, $proc_child, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $transcripts, $TE, $si_min, $si_max, $pi_min, $pi_max, $report); pie_chart($group_dir); @@ -183,8 +183,8 @@ $pm2->start($types[$grand_child]) and next; my ( $type_sam_genome, $type_sam_TEs, $type_sam_transcripts ) = ( $type_dir.$type_prefix.'genome.sam', $type_dir.$type_prefix.'TEs.sam', $type_dir.$type_prefix.'transcripts.sam' ); my ( $type_sam_uni_genome, $type_sam_uni_TEs, $type_sam_uni_transcripts ) = ( $type_dir.$type_prefix.'genome_unique.sam', $type_dir.$type_prefix.'TEs_unique.sam', $type_dir.$type_prefix.'transcripts_unique.sam' ); - my ( $type_uni_genome_fastq, $type_uni_TEs_fastq, $type_uni_transcripts_fastq ) = ( $fq_collection.$type_prefix.'genome_uni.fastq', $fq_collection.$type_prefix.'TEs_uni.fastq', $fq_collection.$type_prefix.'transcripts_uni.fastq'); - my ( $type_genome_fastq, $type_TEs_fastq, $type_transcripts_fastq ) = ( $fq_collection.$type_prefix.'genome.fastq', $fq_collection.$type_prefix.'TEs.fastq', $fq_collection.$type_prefix.'transcripts.fastq'); + my ( $type_uni_genome_fastq, $type_uni_TEs_fastq, $type_uni_transcripts_fastq ) = ( $fq_collection.$fastq_n[$child].$type_prefix.'genome_uni.fastq', $fq_collection.$fastq_n[$child].$type_prefix.'TEs_uni.fastq', $fq_collection.$fastq_n[$child].$type_prefix.'transcripts_uni.fastq'); + my ( $type_genome_fastq, $type_TEs_fastq, $type_transcripts_fastq ) = ( $fq_collection.$fastq_n[$child].$type_prefix.'genome.fastq', $fq_collection.$fastq_n[$child].$type_prefix.'TEs.fastq', $fq_collection.$fastq_n[$child].$type_prefix.'transcripts.fastq'); my $type_sequence_hashP = get_fastq_seq ( $types[$grand_child] ); if ( $grand_child == 1 ) |