Deparse an ABI file...

#!/usr/bin/perl -w

use strict;

my $stadenApp = "~/staden-linux-1-6-0/linux-bin/getABIfield";

for my $inputFile (@ARGV){

unless($inputFile =~ /\/(KN654-BAC(\d\d)-(\d\d)_([A-H]\d\d)-(FP|RP))\.ab[1i]$/){

warn "ignoring $inputFile\n";

next;

}

my $fileName = $1;

my $wellId = $4;

open APP, "-|", "$stadenApp -a -t $inputFile"

or die "failed to exec $stadenApp : $!\n";

my %data;

while(){

## Skip some 'data rows' that we can ignore for now.

next unless

/^$inputFile (\S{4}) (\d+) (.*)$/;

chomp;

$data{"$1 $2"} .= $3;

}

if (keys %data == 0){

die "wha? \n"

}

print

join("\t",

$fileName,

$data{"SMPL 1"}, # Trace name (unique id)

$data{"RunN 1"}, # Run name

$wellId,

$data{"TUBE 1"}, # Well id

$data{"GTyp 1"}, # Polymer name

$data{"MCHN 1"}, # Instrument name

$data{"MODL 1"}, # Instrument model

$data{"PDMF 1"}, # Mobility file

$data{"CMNT 1"}, # Comment

## Signal to noise ratio for the 4 dyes

split(/ /, $data{"S/N% 1"}),

## Times of the various 'events'

$data{"RUND 1"}. " ". $data{"RUNT 1"},

$data{"RUND 2"}. " ". $data{"RUNT 2"},

$data{"RUND 3"}. " ". $data{"RUNT 3"},

$data{"RUND 4"}. " ". $data{"RUNT 4"},

## More...

$data{"APrV 1"}, # Analysis protocol version number

$data{"CTNM 1"}, # Plate Name

$data{"CTID 1"}, # Plate barcode

$data{"ASPt 1"}, # Basecall start scan

$data{"AEPt 1"}, # Basecall stop scan

$data{"SPAC 1"}, # Base spaceing

), "\n";

}