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retrodup/create_junction_library.pl
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#!/usr/bin/perl | |
# Generate exon-exon junction libraries with null model (by shifting) support | |
use warnings; | |
use strict; | |
use lib substr($0,0,rindex($0,'/')); | |
require RETRODUP; | |
my $usage = $0." [-m null_mode -g genome_dir] annotation_file\n\n"; | |
$usage .= "Null modes examples: 1-1, 2-2, 100, -1000"; | |
my $NO_ID = "__NO_GENE_ID__"; | |
my $EXTEND = 100; | |
my $gencode_file = ""; | |
my $mode = 0; | |
my ($shift_s,$shift_e) = (0,0); | |
my $genome_dir = "./"; | |
my $n_arg = scalar(@ARGV); | |
for (my $i = 0;$i < $n_arg;$i++) { | |
my $arg = $ARGV[$i]; | |
if ($arg eq "-m") { | |
if (++$i < $n_arg) { $mode = $ARGV[$i]; } | |
} elsif ($arg eq "-g") { | |
if (++$i < $n_arg) { $genome_dir = $ARGV[$i]; } | |
} else { | |
if (length($gencode_file) > 0) { | |
print STDERR "Umbiguous input.\n"; | |
print STDERR $usage,"\n"; | |
exit; | |
} | |
$gencode_file = $arg; | |
} | |
} | |
if ($mode =~ m/^(\d+)\-(\d+)$/) { | |
$shift_s = $1; | |
$shift_e = -$2; | |
} elsif ($mode =~ m/^(\-\d+)$/) { | |
$shift_s = $shift_e = $1; | |
} elsif ($mode =~ m/^(\d+)$/) { | |
$shift_s = $shift_e = $1; | |
} else { | |
print STDERR "Unrecognized mode.\n"; | |
print STDERR $usage,"\n"; | |
exit; | |
} | |
if (length($gencode_file) == 0) { | |
print STDERR "No annotation file is provided.\n"; | |
print STDERR $usage,"\n"; | |
exit; | |
} | |
my @genes = (); | |
my %gene_exons = (); | |
my $FILE = RETRODUP::openFile($gencode_file); | |
if (!$FILE) { exit; } | |
while (my $line = <$FILE>) { | |
if (substr($line,0,1) eq "#") { next; } | |
if (!($line =~ "protein_coding")) { next; } | |
my @w = split(/\t/,$line); | |
if ($w[2] eq "gene") { | |
my $id = getId($w[8]); | |
my @tmp = (getChromosome($w[0])); | |
$gene_exons{$id} = \@tmp; | |
push(@genes,$id); | |
} elsif ($w[2] eq "exon") { | |
my $id = getId($w[8]); | |
my $arr = $gene_exons{$id}; | |
if (!$arr) { next; } | |
push(@$arr,$w[3] + $shift_s); | |
push(@$arr,$w[4] + $shift_e); | |
} | |
} | |
close($FILE); | |
my @junctions = (); | |
my %junction_names = (); | |
foreach my $gene (@genes) { | |
my $arr = $gene_exons{$gene}; | |
my $n = scalar(@$arr); | |
if ($n <= 3) { next; } # if single exon, ignored | |
if (int($n/2)*2 + 1 != $n) { next; } | |
my $c = $$arr[0]; | |
my %tmp = (); | |
for (my $i = 1;$i < $n;$i += 2) { $tmp{$$arr[$i]} = 1; } | |
my @ss = sort { $a <=> $b } keys(%tmp); | |
%tmp = (); | |
for (my $i = 2;$i < $n;$i += 2) { $tmp{$$arr[$i]} = 1; } | |
my @ee = sort { $a <=> $b } keys(%tmp); | |
my ($ns,$ne) = (scalar(@ss),scalar(@ee)); | |
for (my $ie = 0;$ie < $ne;$ie++) { | |
my $s = $ee[$ie]; | |
my $prefix = $c.":".($s - $EXTEND + 1)."-".$s."|0|"; | |
for (my $is = 0;$is < $ns;$is++) { | |
my $e = $ss[$is]; | |
if ($e <= $s) { next; } | |
my $id = $prefix.$c.":".$e."-".($e + $EXTEND - 1); | |
if ($junction_names{$id}) { | |
print STDERR "Duplicate junction detected ",$id," ...\n"; | |
$junction_names{$id} .= ":".$gene; | |
} else { | |
push(@junctions,$id); | |
$junction_names{$id} = $gene; | |
} | |
} | |
} | |
} | |
my ($seq,$chrom) = ("",""); | |
foreach my $j (@junctions) { | |
my ($coor1,$ins,$coor2) = split(/\|/,$j); | |
my ($c1,$s1,$e1) = split(/[\:\-]/,$coor1); | |
my ($c2,$s2,$e2) = split(/[\:\-]/,$coor2); | |
if ($c1 ne $chrom) { | |
$chrom = $c1; | |
$seq = parseChromosome($c1); | |
} | |
my $seq1 = substr($seq,$s1 - 1,$e1 - $s1 + 1); | |
if ($c2 ne $chrom) { | |
$chrom = $c2; | |
$seq = parseChromosome($c2); | |
} | |
my $seq2 = substr($seq,$s2 - 1,$e2 - $s2 + 1); | |
print ">",$junction_names{$j},"|splj|",$j,"|0\n"; | |
print $seq1,$seq2,"\n"; | |
} | |
exit; | |
## subroutine definitions | |
sub parseChromosome # parse G1K reference | |
{ | |
my $chr = shift; | |
my $file = $genome_dir."/chr".$chr; | |
my $SEQFILE = RETRODUP::openFile($file.".fa.gz"); | |
if (!$SEQFILE) { $SEQFILE = RETRODUP::openFile($file.".fasta.gz"); } | |
if (!$SEQFILE) { $SEQFILE = RETRODUP::openFile($file.".fa"); } # exist | |
if (!$SEQFILE) { $SEQFILE = RETRODUP::openFile($file.".fasta"); } | |
if (!$SEQFILE) { return ""; } | |
my ($header,$seq) = ("",""); | |
while (my $line = <$SEQFILE>) { | |
chomp($line); | |
if (length($line) <= 0) { next; } | |
if (substr($line,0,1) eq ">") { | |
$header = substr($line,1); | |
$seq = ""; | |
} else { $seq .= $line; } | |
} | |
close($SEQFILE); | |
return $seq; | |
} | |
sub getId # return 'gene_id'_'gene_name' | |
{ | |
my $in = shift; | |
my $ret = ""; | |
if ($in =~ m/gene_id\s\"(ENSG.+)\"\;\stranscript_id/) { | |
$ret = $1; | |
} else { | |
return $NO_ID; | |
} | |
if ($in =~ m/gene_name\s\"(.+)\"\;\stranscript_type/) { | |
$ret .= "_".$1; | |
} else { | |
return $NO_ID; | |
} | |
return $ret; | |
} | |
sub getChromosome | |
{ | |
my $in = shift; | |
if (substr($in,0,3) eq "chr") { return substr($in,3); } | |
return $in; | |
} |