#!/usr/bin/perl sub nameonly { my $path = shift; $path =~ s/.*\/([^\/]+)$/$1/; return $path } $seqname = "."; $dbfile = "."; $usage .= "$0 -- convert tandem output to GFF\n"; $usage .= "\n"; $usage .= "Usage: $0 [-n seqname] [-d dbfile] [-l label] [files...]\n"; $usage .= "\n"; $usage .= "Default seqname=\"$seqname\", dbfile=\"$dbfile\" (used for labelling only)\n"; $usage .= "[group] field of GFF is used for repeat consensus\n"; $usage .= "\n"; while (@ARGV) { last unless ($ARGV[0] =~ /^-/); $arg = shift; if ($arg eq "-n") { $seqname = shift; } elsif ($arg eq "-d") { $dbfile = shift; } else { die "Unknown option $arg\n\n$usage"; } } while (<>) { ($score,$start,$end,$len,$copies,$id,$seq) = split; print "$seqname\t$dbfile\ttandem\t$start\t$end\t$score\t+\t.\t$seq\n"; }