Mercurial > repos > romaingred > pirna_pipeline
comparison bin/piPipe.pl @ 37:af4ee65eaffb draft
Uploaded
| author | romaingred |
|---|---|
| date | Tue, 28 Nov 2017 10:05:52 -0500 |
| parents | 67edc34cf0ef |
| children | 0be8011b3d98 |
comparison
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| 36:dfe259eb1e6b | 37:af4ee65eaffb |
|---|---|
| 201 extract_sam ( $type_sequence_hashP, $sam_TEs, $type_sam_TEs, $type_sam_uni_TEs, $type_TEs_fastq, $type_uni_TEs_fastq ); | 201 extract_sam ( $type_sequence_hashP, $sam_TEs, $type_sam_TEs, $type_sam_uni_TEs, $type_TEs_fastq, $type_uni_TEs_fastq ); |
| 202 extract_sam ( $type_sequence_hashP, $sam_transcripts, $type_sam_transcripts, $type_sam_uni_transcripts, $type_transcripts_fastq, $type_uni_transcripts_fastq ); | 202 extract_sam ( $type_sequence_hashP, $sam_transcripts, $type_sam_transcripts, $type_sam_uni_transcripts, $type_transcripts_fastq, $type_uni_transcripts_fastq ); |
| 203 extract_sam ( $type_sequence_hashP, $sam_genome, $type_sam_genome, $type_sam_uni_genome, $type_genome_fastq, $type_uni_genome_fastq ); | 203 extract_sam ( $type_sequence_hashP, $sam_genome, $type_sam_genome, $type_sam_uni_genome, $type_genome_fastq, $type_uni_genome_fastq ); |
| 204 } | 204 } |
| 205 | 205 |
| 206 my $ex_count_file = $type_dir.'transcripts_reads_counts.txt'; | 206 my $ex_count_file = $type_dir.$type_prefix.'transcripts_reads_counts.txt'; |
| 207 my ( $ex_count, $ex_ref_size ) = sam_count ( $type_sam_transcripts ); | 207 my ( $ex_count, $ex_ref_size ) = sam_count ( $type_sam_transcripts ); |
| 208 rpms_rpkm( $ex_count, $ex_ref_size, $ma, $ex_count_file, $pi, $mi, $bo ); | 208 rpms_rpkm( $ex_count, $ex_ref_size, $ma, $ex_count_file, $pi, $mi, $bo ); |
| 209 | 209 |
| 210 my ( $TEs_count, $TEs_ref_size, $TEs_count_NoM, $TEs_count_M ) = sam_count_mis ( $type_sam_TEs ); | 210 my ( $TEs_count, $TEs_ref_size, $TEs_count_NoM, $TEs_count_M ) = sam_count_mis ( $type_sam_TEs ); |
| 211 my $TEs_count_file = $type_dir.$type_prefix.'TEs_reads_counts.txt'; | 211 my $TEs_count_file = $type_dir.$type_prefix.'TEs_reads_counts.txt'; |
| 251 ppp_page ( $group_dir, $ppp_page, \@fastq_n, $fastq_n[$child], $ppp, $dir ); | 251 ppp_page ( $group_dir, $ppp_page, \@fastq_n, $fastq_n[$child], $ppp, $dir ); |
| 252 } | 252 } |
| 253 | 253 |
| 254 #HTML Main Webpage | 254 #HTML Main Webpage |
| 255 my $index_page = $dir.$fastq_n[$child].'.html'; | 255 my $index_page = $dir.$fastq_n[$child].'.html'; |
| 256 main_page ( $gen_dir, $index_page, \@fastq_n, $fastq_n[$child], $ma, $ma_uni, $dir ); | 256 main_page ( $gen_dir, $index_page, \@fastq_n, $fastq_n[$child], $ma, $ma_uni, $dir ); |
| 257 copy ($index_page, $html_out) if $child == 0; | 257 copy ($index_page, $html_out) if $child == 0; |
| 258 #HTML Menu | 258 #HTML Menu |
| 259 my $menu_page = $dir.$fastq_n[$child].'-sub.html'; | 259 my $menu_page = $dir.$fastq_n[$child].'-sub.html'; |
| 260 menu_page ( $group_dir, $menu_page, \@fastq_n, $fastq_n[$child], $min, $max, $si_min, $si_max, $pi_min, $pi_max, $dir ); | 260 menu_page ( $group_dir, $menu_page, \@fastq_n, $fastq_n[$child], $min, $max, $si_min, $si_max, $pi_min, $pi_max, $dir ); |
| 261 unlink glob "$group_dir*.sam"; unlink glob "$group_dir*.fastq"; | 261 unlink glob "$group_dir*.sam"; unlink glob "$group_dir*.fastq"; |