geneclicker
New User
Sep 27, 2012, 10:55 PM
Post #1 of 7
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Help with DNA sequence software
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Hello everyone. I'm new to perl. I work on manual curation projects on alphabet based content.
I have a perl program which reads a text file and breaks it up in contiguous chunks according to input provided by the user.
My problem is can get the program to run but it gives me error messages. It says command not found.
The original coder has moved on to better projects.
Can someone please help?
I work on a mac in case this is important to know.
Thank you much.
G clicker
The code in perl
#!/usr/bin/perl
use strict;
use warnings;
my @params = ();
while ( my $param = shift ) {
push @params, $param;
}
unless ( scalar @params == 4 ) {
print "$0 <input fasta file> <block size> <block label> <output file>\n";
exit;
}
my ( $inputFile, $blockSize, $blockLabel, $outputFile ) = @params;
print "Input seems to be valid. Now I will try reading the contents of $inputFile...";
open INPUT, '<', $inputFile or die $!;
open OUTPUT, '>', $outputFile or die $!;
my $sequence = '';
while ( <INPUT> ) {
chomp;
next if ( /^\s*$/ );
next if ( /^>/ );
$sequence .= $_;
}
print "done.\n";
my $pos = 0;
my $index = 0;
print "The sequence has ", length($sequence), " bases. Now I will try breaking it into segments, each of size $blockSize bases.\n";
while ( $pos < length($sequence) ) {
$index++;
print OUTPUT ">$blockLabel$index\n";
print OUTPUT substr($sequence, $pos, $blockSize) . "\n";
$pos += $blockSize;
}
close OUTPUT;
close INPUT;
print "Successfully generated $outputFile.\n";
end of code.
the target file looks like this, the extension on the file is .fa
GCGTCCGCGGAGGGGGCGGCGGGCCTGGGCGACCCTGCACCTCTGGGCCG
TGGGGACTGTGGGGTGGGGCGGGGGCCGATGCGGCAGGGGTGAGGCCTGG
GGCCGGCGGGGTGACGGGGACCCGGCCCTGCGTGGGGAAGCCTCGGGGGG
ACAAGCAGAGACGCAGCCTGCTGGGAGCGGCCCAAGCTCTGCACCGGCCC
GCGGCGGGAGCACAGCAGCCCCCTCCCGCCCCTCCTCCCGGGGGCTCCGA
GGGGTGGTTATGGGGCGAGGGTCCTTGCGGGGCCCGGGCAGTGAAGGGCC
TGGAGGCCCCAGAGTCTGTGCCAGGTCTGAGCCGCGGGGCGTGGGGGGAG
GAGGGGCCTCGGCCGGGGCCCAGGAGACCCAGGACAGGTGGGCCTGGGGC
CAGGTCCCTACGGAGAGGTGGCCGGGCCGGGCTCTGGCTTGCCGGGGTAG
GGGCTCCGCTAGGGGCTGGAGTCCGTCCCTTCGCCAGCGCAGAGCCCCTC
GGCCCGCATCTGCCAAGTGACTGAGGATCGAGCGACAGCGTAGTGGGGCG
GAGGGGCTGGAGGCACGGCCGGAAAGGGTGAGCGGCGCCGTGGCTCCCCC
GCTATTTATTTGGCCCCGCCACGCGCGGAGAGGGAGGAAATTCTCAGGCT
GCGGCTGCAGCTAGGGGAGGCCCAGGTGGGCCTGGAATGGGCCCAGAGAG
GGCTTCCTGGGTCAGACGTGTAGATCCAGTGGACGTGAAAACCGGGTGAG
TGTCCCGGTGGGACCCAGAGCGCGGGGAGGCTTGGAGGCAGGGGCATGGG
CTGAGGACCCTCAAGGCACCCTCCTCGCGACCTGTCAGAGCTCCGAGGGG
TGGGGGTGTCCTGTGTGTGGCTGTGGGGATCCTGGGCGGCGGGTGCTGGG
Please see attached files.
(This post was edited by geneclicker on Sep 27, 2012, 11:12 PM)
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splitFasta.pl
IGK_2.fa