Entering edit mode
14.1 years ago
Ahmed
▴
10
I have a DNA sequence from macrogen and file. How can i convert this data to SCF or ABI format
I have a DNA sequence from macrogen and file. How can i convert this data to SCF or ABI format
Assuming you have BioPerl with the iolib
modules compiled in:
my $seq_in = Bio::SeqIO->new('-file' => "<$infile",
'-format' => 'fasta');
my $seq_out = Bio::SeqIO->new('-file' => ">$outfile",
'-format' => 'scf'); ## or 'abi'
# write each entry in the input file to the output file
while (my $inseq = $seq_in->next_seq) {
$seq_out->write_seq($inseq);
}
exit;
The above does not work... I get the following error:
Reference found where even-sized list expected at /usr/share/perl5/Bio/SeqIO/scf.pm line 610, <GEN0> line 5.
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: You must pass a Bio::Seq::Quality or a Bio::Seq::SequenceTrace object to write_seq as a parameter named "target"
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:486
STACK: Bio::SeqIO::scf::write_seq /usr/share/perl5/Bio/SeqIO/scf.pm:625
STACK: fastq2scf.pl:14
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Which format (file extension) do you have?