Just to note, as others have indicated putting the code here that generated that stack trace does help to trace the problem down. Looks like the problem arises when you are creating a new Bio::Seq::Quality, on line 165 of the code you submitted.

According to the Bio::Seq::Quality you are using the wrong named attribute for the quality information:

my $new_qual = Bio::Seq::Quality->new(-seq => $qual_string, -id => $seq->id(), -desc => $seq->desc);

That should be:

my $new_qual = Bio::Seq::Quality->new(-qual => $qual_string, -id => $seq->id(), -desc => $seq->desc);

This class also accepts sequence data to go with those scores; not sure if it requires it, though.

In reply to Re^3: .qual File Writing Complication by cjfields
in thread .qual File Writing Complication by twaddlac

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.