Mercurial > repos > romaingred > pirna_pipeline

comparison bin/piPipe.pl @ 31:241aa6141cac draft

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Uploaded
author romaingred
date Tue, 28 Nov 2017 08:54:52 -0500
parents 0a47c6cf912d
children 46d7549c1a05
comparison
equal deleted inserted replaced
30:a8a6e346893f 31:241aa6141cac
243 $pm2->wait_all_children; 243 $pm2->wait_all_children;
244 244
245 if ( $Pcheck eq 'true' ) 245 if ( $Pcheck eq 'true' )
246 { 246 {
247 my $ppp = $group_dir.'PPPartners/'; mkdir $ppp; 247 my $ppp = $group_dir.'PPPartners/'; mkdir $ppp;
248 print $report "ping_pong_partners $group_dir/bonafide_reads/TEs.sam $ppp\n"; 248 print $report "ping_pong_partners $group_dir/piRNAs/TEs.sam $ppp\n";
249 ping_pong_partners ( $group_dir.'TEs.fai', $group_dir.'bonafide_reads/bonafide_reads-TEs_sorted.bam', $ppp, $min ); 249 ping_pong_partners ( $group_dir.'TEs.fai', $group_dir.'piRNAs/piRNAs-TEs_sorted.bam', $ppp, $pi_min );
250 my $ppp_page = $dir.$fastq_n[$child].'-bonafide_reads-PPP.html'; 250 my $ppp_page = $dir.$fastq_n[$child].'-bonafide_reads-PPP.html';
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