perl/etc/justonce/toPCR.pl

   1 #!/usr/bin/env perl
   2 =pod
   3 Author: Hu Xuesong @ BGI <huxuesong@genomics.org.cn>
   4 Version: 1.0.0 @ 20170612
   5 =cut
   6 use strict;
   7 use warnings;
   8 use Galaxy::IO;
   9 use Galaxy::IO::FASTA qw(FastaReadNextA);
  10
  11 open O,'>','toPCR.p3' or die "Error opening [toPCR.p3]: $!\n";
  12 print O <<'HEAD';
  13 PRIMER_MIN_SIZE=19
  14 PRIMER_MAX_SIZE=25
  15 PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/usr/local/opt/primer3/share/primer3/primer3_config/
  16 PRIMER_PRODUCT_SIZE_RANGE=30-401
  17 PRIMER_NUM_RETURN=1
  18 =
  19 HEAD
  20
  21 my $in = openfile('toPCR.fa.gz');
  22 while (my $ret = FastaReadNextA($in)) {
  23         my ($seqname,$genome,$seqdesc) = @$ret;
  24         #print $seqname," | $seqdesc\n";
  25         $seqdesc = (split / /,$seqdesc)[0];
  26         $seqdesc = (split /:/,$seqdesc)[1];
  27         my ($begin,$end) = split /-/,$seqdesc;
  28         my $thePos = (split /_/,$seqname)[-1];
  29         $begin -= $thePos;
  30         $end -= $thePos;
  31         my $seqlen = length $genome;
  32         if( $begin > -20 or $end < 20 or $seqlen < 55) {
  33                 print "\n>$seqname $thePos-($begin,$end)->Skipped.\n";
  34                 next;
  35         } else {
  36                 print '.';
  37         }
  38         #print "$thePos, $begin,$end\n";
  39         # Position starts from 0.
  40         my $targetPos = - $begin;
  41         my $left = -55 - $begin;
  42         $left = 0 if $begin < 0;
  43         my $right = 20 - $begin;
  44         my $maxL = $seqlen - $right;
  45         $maxL = 55 if $maxL > 55;
  46         #$end = $seqlen -1 if $end >= $seqlen;
  47         print O <<"     ITEM";
  48 SEQUENCE_ID=$seqname
  49 SEQUENCE_TEMPLATE=$genome
  50 SEQUENCE_TARGET=$targetPos,1
  51 SEQUENCE_INTERNAL_EXCLUDED_REGION=$targetPos,1
  52 SEQUENCE_PRIMER_PAIR_OK_REGION_LIST=$left,55,, ; ,,$right,$maxL
  53 =
  54         ITEM
  55 }
  56 print "\n";
  57 close $in;
  58 close O;
  59 print "Run [primer3_core < toPCR.p3 > toPCR.out] now.\n";
  60 __END__
  61 primer3_core -format_output < toPCR.p3.test
  62 primer3_core < toPCR.p3.test