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Extract sequence from UCSC
By Jit 3103 days ago
#!/usr/bin/env perl
use strict;
use warnings;
use LWP::Simple;
use XML::XPath;
use XML::XPath::XMLParser;
# Use DAS of UCSC to fetch specific sequence by its given chromosome position
# From here: https://www.biostars.org/p/6156/
my $chr = shift;
my $pos = shift;
my $size = shift;
my $usage = "Example: perl extract_seq_from_ucsc.pl 14 482780 1000\n";
if (! $size) {
die "ERROR: You must pass three arguments: chr. num., position, and size.\n$usage";
}
chomp $size;
my $start = $pos - ($size/2);
my $end = $pos + ($size/2);
# Figure out URL for the DAS server. Example:
# http://genome.ucsc.edu/cgi-bin/das/calJac3/dna?segment=chr14:482280,483280
my $URL_gene ="http://genome.ucsc.edu/cgi-bin/das/papAnu2/dna?segment=chr";
$URL_gene .= $chr . ":" . $start . "," . $end;
my $xml = get($URL_gene);
my $xp = XML::XPath->new(xml=>$xml);
my $nodeset = $xp->find('/DASDNA/SEQUENCE/DNA/text()'); # find all sequences
# there should be only one node, anyway:
foreach my $node ($nodeset->get_nodelist) {
my $seq = $node->getValue;
$seq =~ s/\s//g; # remove white spaces
print ">papAnu2_chr" . $chr . ":" . $start . "-" . $end . "\n";
print $seq, "\n";
}
