Mercurial > repos > romaingred > pirna_pipeline
changeset 29:0a47c6cf912d draft
Uploaded
| author | romaingred |
|---|---|
| date | Thu, 09 Nov 2017 05:28:50 -0500 |
| parents | aea6ed0da85b |
| children | a8a6e346893f |
| files | bin/piPipe.pl |
| diffstat | 1 files changed, 4 insertions(+), 5 deletions(-) [+] |
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--- a/bin/piPipe.pl Tue Oct 24 05:23:42 2017 -0400 +++ b/bin/piPipe.pl Thu Nov 09 05:28:50 2017 -0500 @@ -16,7 +16,7 @@ use html qw ( main_page details_pages menu_page ppp_page ); use File::Copy; -my ( @fastq, @fastq_n, $dir, $min, $max, $mis, $misTE, $help, $Pcheck, $Dcheck, $mapnumf, $html_out); +my ( @fastq, @fastq_n, $dir, $min, $max, $mis, $misTE, $help, $Pcheck, $mapnumf, $html_out); my ( $ref, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $exons, $TE ); my ( $si_min, $si_max, $pi_min, $pi_max ); my ( $build_index, $build_tRNAs, $build_rRNAs, $build_snRNAs, $build_miRNAs, $build_exons, $build_TE ); @@ -40,7 +40,6 @@ "misTE:i" => \$misTE, "html:s" => \$html_out, "PPPon:s" => \$Pcheck, - "Dison:s" => \$Dcheck, "help" => \$help, "ref:s" => \$ref, "tRNAs:s" => \$tRNAs, @@ -213,8 +212,8 @@ my $TEs_count_file_M = $type_dir.$type_prefix.'TEs_reads_counts_mismatches.txt'; my $TEs_count_file_noM = $type_dir.$type_prefix.'TEs_reads_counts_nomismatches.txt'; rpms_rpkm( $TEs_count, $TEs_ref_size, $ma, $TEs_count_file, $pi, $mi, $bo ); - rpms_rpkm( $TEs_count_NoM, $TEs_ref_size, $ma, $TEs_count_file_M, $pi, $mi, $bo ); - rpms_rpkm( $TEs_count_M, $TEs_ref_size, $ma, $TEs_count_file_noM, $pi, $mi, $bo ); + rpms_rpkm( $TEs_count_NoM, $TEs_ref_size, $ma, $TEs_count_file_noM, $pi, $mi, $bo ); + rpms_rpkm( $TEs_count_M, $TEs_ref_size, $ma, $TEs_count_file_M, $pi, $mi, $bo ); sam_to_bam_bg ( $type_sam_TEs, $scale, $grand_child ); sam_sorted_bam ( $type_sam_exons, $grand_child ); sam_sorted_bam ( $type_sam_uni_exons, $grand_child ); @@ -237,7 +236,7 @@ #HTML Details my $prefix_details_pages = $dir.$fastq_n[$child].'-'.$types_names[$grand_child]; - details_pages ( $type_dir, $prefix_details_pages, \@fastq_n, $fastq_n[$child], $misTE, $dir ); + details_pages ( $type_dir, $prefix_details_pages, \@fastq_n, $fastq_n[$child], $misTE, $dir, $Pcheck ); $pm2->finish(); }