Mercurial > repos > big-tiandm > sirna_plant

comparison siRNA.pl @ 18:22d79320085c draft

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Uploaded
author big-tiandm
date Thu, 30 Oct 2014 21:31:55 -0400
parents a0222bdfe2ac
children e0884a4b996b
comparison
equal deleted inserted replaced
17:b75750b21aa4 18:22d79320085c
141 my $deg_dir; 141 my $deg_dir;
142 my %id; 142 my %id;
143 for (my $i=0;$i<@mark ;$i++) { 143 for (my $i=0;$i<@mark ;$i++) {
144 $id{$mark[$i]}=$i+4; 144 $id{$mark[$i]}=$i+4;
145 } 145 }
146
147
146 group_and_filter(); #collapse reads to tags 148 group_and_filter(); #collapse reads to tags
147 149
148 rfam(); 150 rfam();
149 151
150 my @map_read; 152 my @map_read;
421 } 423 }
422 $pm->wait_all_children; 424 $pm->wait_all_children;
423 } 425 }
424 426
425 sub dec_pel{ 427 sub dec_pel{
426 print "start:\n"; 428 print "\n******************\nstart:\n";
427 Time(); 429 Time();
428 my $sample=shift(@_); 430 my $sample=shift(@_);
429 my @each=split/\s+/,$sample; 431 my @each=split/\s+/,$sample;
430 print "$each[0]\t$each[1]\n"; 432 print "$each[0]\t$each[1]\n";
431 my $deg_sample_dir=$deg_dir."$each[0]_VS_$each[1]\/"; 433 my $deg_sample_dir=$deg_dir."$each[0]_VS_$each[1]\/";
432 mkdir ("$deg_sample_dir"); 434 mkdir ("$deg_sample_dir");
435 print "read: $read\n";
436 print "deg_sample_dir: $deg_sample_dir\n";
437 print "$id{$each[0]}\t$each[0]\n";
438 print "$id{$each[1]}\t$each[1]\n";
433 my $deg=`perl $path\/DEGseq_2.pl -i $read -outdir $deg_sample_dir -column1 $id{$each[0]} -mark1 $each[0] -column2 $id{$each[1]} -mark2 $each[1]`; #-depth1 -depth2 439 my $deg=`perl $path\/DEGseq_2.pl -i $read -outdir $deg_sample_dir -column1 $id{$each[0]} -mark1 $each[0] -column2 $id{$each[1]} -mark2 $each[1]`; #-depth1 -depth2
434 my $time2=time(); 440 my $time2=time();
435 print "end:\n"; 441 print "end:\n*************************\n";
436 Time(); 442 Time();
437 sleep 1; 443 sleep 1;
438 } 444 }
439 445
440 sub infor_merge{ 446 sub infor_merge{