From a73471c8e2df84fbff05760cfb7c881565e6e1ab Mon Sep 17 00:00:00 2001
From: Yuuki Galaxy <galaxy001@gmail.com>
Date: Tue, 31 Oct 2023 11:05:38 +0800
Subject: [PATCH] 	modified:   mm10.overlap.pl 	modified:   primer.pl

---
 perl/etc/justonce/mm10.overlap.pl |  1 +
 perl/etc/justonce/primer.pl       | 24 +++++++++++++++---------
 2 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/perl/etc/justonce/mm10.overlap.pl b/perl/etc/justonce/mm10.overlap.pl
index a42e8508b..4560dd4d3 100755
--- a/perl/etc/justonce/mm10.overlap.pl
+++ b/perl/etc/justonce/mm10.overlap.pl
@@ -9,6 +9,7 @@ while(<>) {
   my ($chr,undef,$type,$start,$end,undef,$strand,undef,undef,$geneid) = split;
   next if $type ne 'transcript';
   $geneid =~ s/[\";\,]//g;
+  #$geneid =~ s/(\.\d+$)//g;
   $Dat{"$chr\t$strand"}{$start}{$end} = $geneid;
   #push @{$Dat{"$chr\t$strand"}{$start}},[$end,$geneid];
 }
diff --git a/perl/etc/justonce/primer.pl b/perl/etc/justonce/primer.pl
index e3cbf1063..6c9057f71 100755
--- a/perl/etc/justonce/primer.pl
+++ b/perl/etc/justonce/primer.pl
@@ -10,10 +10,13 @@ use Galaxy::IO::FASTA qw(FastaReadNextA);
 
 open O,'>','toPCR.p3' or die "Error opening [toPCR.p3]: $!\n";
 print O <<'HEAD';
-PRIMER_MIN_SIZE=19
-PRIMER_MAX_SIZE=25
+PRIMER_MIN_SIZE=18
+PRIMER_MAX_SIZE=24
 PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/usr/local/opt/primer3/share/primer3/primer3_config/
-PRIMER_PRODUCT_SIZE_RANGE=300-500
+PRIMER_PRODUCT_SIZE_RANGE=100-600
+PRIMER_MIN_TM=56
+PRIMER_OPT_TM=58
+PRIMER_MAX_TM=60
 PRIMER_NUM_RETURN=1
 =
 HEAD
@@ -22,16 +25,17 @@ my $in = openfile('u.fa');
 while (my $ret = FastaReadNextA($in)) {
 	my ($seqname,$genome,$seqdesc) = @$ret;
 	#print $seqname," | $seqdesc\n";
-	my ($chr,$begin,$end) = split /[:-]/,$seqname;
-	my $thePos = $begin +300;
+	#my ($chr,$begin,$end) = split /[:-]/,$seqname;
+	#my $thePos = $begin +300;
 	my $seqlen = length $genome;
+	my $begin = 501;
+	my $tglen = $seqlen - 1000;
 	#print "--- $chr,$begin,$end\n";
 	print O <<"	ITEM";
-SEQUENCE_ID=${seqname}_$thePos
+SEQUENCE_ID=${seqname}_$tglen
 SEQUENCE_TEMPLATE=$genome
-SEQUENCE_TARGET=301,1
-SEQUENCE_INTERNAL_EXCLUDED_REGION=301,1
-SEQUENCE_PRIMER_PAIR_OK_REGION_LIST=251,50,, ; ,,301,50
+SEQUENCE_TARGET=501,$tglen
+SEQUENCE_INTERNAL_EXCLUDED_REGION=501,$tglen
 =
 	ITEM
 }
@@ -47,3 +51,5 @@ primer3_core < toPCR.p3.test
 
 perl -lane 'print "$F[0]:",$F[1]-300,"-",$F[1]+300' uGRCh37SNPs.txt >uGRCh37SNPs.reg
 samtools faidx Homo_sapiens_assembly19.fasta -r uGRCh37SNPs.reg >u.fa &
+
+SEQUENCE_PRIMER_PAIR_OK_REGION_LIST=251,50,, ; ,,301,50
-- 
2.11.4.GIT