[Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO

Abhishek Pratap abhishek.vit at gmail.com
Fri Jul 9 11:02:09 EDT 2010


Hi (Chris)

I feel I might be hitting a bug or missing something. I am trying to convert
a raw FASTQ from ASCII-64 to ASCII-33.  I am copying the actual code and IO
for more clarity. I think the quality line is missing and the read is
breaking into two lines.

Any obvious mistakes ?

Thanks!
-Abhi




## Reading the FASTQ ASCII-64 file
     my $in = Bio::SeqIO->new( -format    => 'fastq',
 -variant   => 'illumina',
                             -file      => "<$in_fastq_file",
                             );

## File Handle for writing ASCII-33 (sanger) standard format
   my $out = Bio::SeqIO->new ( -format   => 'fastq',
   -variant  => 'sanger',
   -file     => ">$out_fastq_file",
      );

while (my $oneread = $in->next_seq){
$out->write_seq($oneread);
}



Output:
>HWI-EAS397_0006:6:1:1023:19461#0/1
ATGTGCTGCTGGCTTCGGTTTGCCAGTATTTTATTGAGGATTTTTGCATCAATGTCATCA
AGGATATTGGTCTAA

Input:
@HWI-EAS397_0006:6:1:1023:19461#0/1
ATGTGCTGCTGGCTTCGGTTTGCCAGTATTTTATTGAGGATTTTTGCATCAATGTCATCAAGGATATTGGTCTAA
+HWI-EAS397_0006:6:1:1023:19461#0/1
^aYa^\a^aaaa\]a^^^^^]]]^L^Y]]]aa\`YZ^a]]a[a^^^^^`I^^^`]aaaa]]^]R`W^``^BBBBB


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