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Convert (possibly stranded) BED to sequence via samtools faidx-indexed compressed or uncompressed FASTA files
#!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long;
#
# bed2faidxsta.pl
# --
# Reads BED data from standard input, writes FASTA to standard output.
#
# Dependent on samtools and indexed FASTA data files located in $fastaDir
# variable. Set --fastaDir=dir to set custom directory containing a source
# of per-build, bgzip-compressed FASTA and associated index (fa.gz.fai)
# files, or leave unset to use data in current working directory. Use the
# --fastaIsUncompressed option if the FASTA files are not compressed.
#
# test if samtools is available
`samtools --version` || die "Error: The samtools application is required to run this script. Try 'module add samtools' or install a local copy of samtools.\n";
# default FASTA input is current working directory
my $fastaDir = `pwd`; chomp $fastaDir;
# default is to assume input coordinates use zero-based index scheme
my $oneBased;
# default is to leave IDs alone
my $useIDPrefixAsStrand;
# default is to assume FASTA files are bgzip-compressed
my $fastaIsUncompressed;
GetOptions ('fastaDir=s' => \$fastaDir, 'oneBased' => \$oneBased, 'useIDPrefixAsStrand' => \$useIDPrefixAsStrand, 'fastaIsUncompressed' => \$fastaIsUncompressed);
if (! -d $fastaDir) { die "Error: FASTA directory does not exist\n"; }
while (<STDIN>) {
chomp;
my ($chr, $start, $stop, $id, $score, $strand) = split("\t", $_);
if (!defined($chr) || !defined($start) || !defined($stop)) { die "Error: No chromosome name, start or stop position defined\n"; }
if (!defined($id)) { $id = "."; }
if (!defined($score)) { $score = "."; }
if (!defined($strand)) { $strand = "+"; } else { $strand = substr($strand, 0, 1); }
# adjust coordinates to one-based index, if necessary
my ($queryChr, $queryStart, $queryStop) = ($chr, $start, $stop);
if (!$oneBased) {
$queryStart++;
}
# adjust strand if required
if ($useIDPrefixAsStrand) {
$strand = substr($id, 0, 1);
}
# lookup
my $queryFn = "$fastaDir/$chr.fa.gz";
if ($fastaIsUncompressed) {
$queryFn = "$fastaDir/$chr.fa";
}
my $queryKey = "$queryChr:$queryStart-$queryStop";
my $queryResult = `samtools faidx $queryFn $queryKey`; chomp $queryResult;
# linearize result
my @lines = split("\n", $queryResult);
my @seqs = @lines[1..(scalar @lines - 1)];
my $seq = join("", @seqs);
# handle reverse-stranded elements
if ($strand eq "-") {
$seq = rc_sequence($seq);
}
# print to standard output
my $header = ">".join(":",($chr, $start, $stop, $id, $score, $strand));
print STDOUT $header."\n".$seq."\n";
}
sub rc_sequence {
my $seq = shift @_;
my $reverse_complement = reverse($seq);
$reverse_complement =~ tr/ACGTacgt/TGCAtgca/;
return $reverse_complement;
}
@alexpreynolds

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alexpreynolds commented Feb 27, 2017

Example usage:

$ bed2faidxsta.pl < in.bed > out.fa
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