in reply to Private Utilities
Perfect! I have been looking for just such a solution this morn and appreciate your post - here is one I just put together really quick ...
to chunk up a given fasta file (unaligned sequences) in to N files for submission of multiple smaller jobs on a cluster:
Feel free to comment or point me in the right direction where I have gone astray - this just scratched a specific itch ...#!/usr/bin/perl -w use strict; my $num_ch = $ARGV[0] or die "must pass the # of chunks $!"; open (FH,"<$ARGV[1]") or die "must pass the file name to make chunks +of $!"; my @lines = (); $/ = ">"; while (<FH>){ chomp; next if /^$/; # get rid of blank lines push @lines,">$_"; } close FH; my $num_rec = scalar(@lines); print "number of records : $num_rec\n"; #die "Chunks exceed records!!" unless ($num_rec >= $num_ch); sub write_em { my $output = shift()."_chunk.fa"; my $ar_ref = shift; open (QRTR,">$output") or die "Cannot open $output : $!"; print QRTR @$ar_ref; close (QRTR) or die "cannot close $output : $!"; } my $cnt = 0; my $rng = int($num_rec/$num_ch) + ($num_rec%$num_ch ? 1 : 0); for (1..$num_ch) { write_em($_,[@lines[$cnt..($_ == $num_ch ? $#lines : ($cnt+($r +ng-1)))]]); $cnt += $rng; }
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Re^2: Private Utilities
by thor (Priest) on Dec 01, 2005 at 20:06 UTC | |
by l3v3l (Monk) on Dec 01, 2005 at 22:36 UTC | |
by thor (Priest) on Dec 02, 2005 at 04:57 UTC | |
by l3v3l (Monk) on Dec 02, 2005 at 16:33 UTC | |
by thor (Priest) on Dec 02, 2005 at 20:22 UTC |
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