perl/etc/justonce/primer.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=18
  14 PRIMER_MAX_SIZE=24
  15 PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/usr/local/opt/primer3/share/primer3/primer3_config/
  16 PRIMER_PRODUCT_SIZE_RANGE=100-600
  17 PRIMER_MIN_TM=56
  18 PRIMER_OPT_TM=58
  19 PRIMER_MAX_TM=60
  20 PRIMER_NUM_RETURN=1
  21 =
  22 HEAD
  23
  24 my $in = openfile('u.fa');
  25 while (my $ret = FastaReadNextA($in)) {
  26         my ($seqname,$genome,$seqdesc) = @$ret;
  27         #print $seqname," | $seqdesc\n";
  28         #my ($chr,$begin,$end) = split /[:-]/,$seqname;
  29         #my $thePos = $begin +300;
  30         my $seqlen = length $genome;
  31         my $begin = 501;
  32         my $tglen = $seqlen - 1000;
  33         #print "--- $chr,$begin,$end\n";
  34         print O <<"     ITEM";
  35 SEQUENCE_ID=${seqname}_$tglen
  36 SEQUENCE_TEMPLATE=$genome
  37 SEQUENCE_TARGET=501,$tglen
  38 SEQUENCE_INTERNAL_EXCLUDED_REGION=501,$tglen
  39 =
  40         ITEM
  41 }
  42 print "\n";
  43 close $in;
  44 close O;
  45 print "Run [primer3_core < toPCR.p3 > toPCR.out] now.\n";
  46 __END__
  47 primer3_core -format_output < toPCR.p3.test
  48 primer3_core < toPCR.p3.test
  49
  50 其中一端的引物距离目标位点少于50bp
  51
  52 perl -lane 'print "$F[0]:",$F[1]-300,"-",$F[1]+300' uGRCh37SNPs.txt >uGRCh37SNPs.reg
  53 samtools faidx Homo_sapiens_assembly19.fasta -r uGRCh37SNPs.reg >u.fa &
  54
  55 SEQUENCE_PRIMER_PAIR_OK_REGION_LIST=251,50,, ; ,,301,50