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#!/usr/local/bin/perl -w
#
# 11/06/96 jkb
# Converts the old staden gel reading file format to an experiment file
# Usage:
#
# staden2exp [-ID name] [file]
#
# Without specifying 'file' the program acts as a filter. Specifying '-ID name'
# in either case will force outputting an ID and EN line. By default the
# filename is used or nothing is outputted when used as a filter.
#
$lseq=""; $mseq=""; $rseq=""; $file="";
# Process args
while (@ARGV) {
$arg = shift @ARGV;
if ($arg eq "-ID") {
$id = shift @ARGV;
next;
}
$file=$arg
}
if ($file) {
@ARGV=($file);
$id = $file;
} else {
@ARGV=("-");
}
if ($id) {
print "ID $id\n";
print "EN $id\n";
}
# Read the file
while (<ARGV>) {
# Title line
if (/^;[ 0-9]/) {
($type, $file) = unpack("\@19 A4 A100", $_);
print "LT $type\n";
print "LN $file\n";
next;
}
# 5' cut sequence
if (/^;<(.*)/) {
$lseq .= $1;
next;
}
# 3' cut sequence
if (/^;>(.*)/) {
$rseq .= $1;
next;
}
# tags
if (/^;;/) {
($type, $pos, $length, $anno) = unpack("\@2 A4 x A6 x A6 x A100", $_);
$pos = $pos + 0;
$end = $length + $pos - 1;
print "TG $type + $pos..$end";
$len = length($anno);
for ($i = 0; $i < $len; $i += 70) {
print "\n ", substr($anno, $i, 70);
}
print "\n";
next;
}
s/\n//;
$mseq .= $_
}
# Do QL and QR lines
$QL=length($lseq);
$QR=length($lseq)+length($mseq)+1;
$seq=$lseq . $mseq . $rseq;
$len=length($seq);
print "QL $QL\n" if ($QL != 0);
print "QR $QR\n" if ($QR != $len+1);
# Print the formatted sequence
print "SQ ";
for ($i = 0; $i < $len;) {
print "\n ";
for ($j = 0; $j < 6 && $i < $len; $j++, $i += 10) {
print substr($seq, $i, 10), " ";
}
}
print "\n//\n";
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