[Biopython-dev] SeqIO and qual: Question about reading and writing qual files

[Sebastian Bassi]

I have a .fasta file and its corresponding .qual file.
I run seqclean on the fasta file and I got a shorter .fasta file as
output (that is expected).
Using the .cln file from seqclean, I want to "trim" the .qual file the
same way my new fasta is trimmed.
I can read the cln and parse the information of "where to trim".
For example, in one original sequence of 1000 bp, I may need to trim
from 150 to 800.
The problem is that I can't modify qual values using the new SeqIO
qual parser (at least the size of the list can't be modified). I read
the example in the doc, where it is cut doing something like:
sub_rec = fullrec[150:800]
But, this works only when there is a sequence (so, when read it as
"fastq"), but it doesn't work when the sequence is read as "qual"
(because there is no sequence and in this case I can't modify the
length of the list in letter_annotations['phred_quality'], it is true
that I can modify qual values in the list, but I want to modify list
size).
Here is the error:
Traceback (most recent call last):
  File "/home/sbassi/bioinfo/INTA/qualparser.py", line 18, in <module>
    s.letter_annotations['phred_quality'] = [0,0,0,0,10,1]
  File "/home/sbassi/test/virtualenv-1.3.2/t6/lib/python2.5/site-packages/biopython-1.49-py2.5-linux-i686.egg/Bio/SeqRecord.py",
line 33, in __setitem__
    "strings) of length %i." % self._length)
TypeError: We only allow python sequences (lists, tuples or strings)
of length 5.


(Note: 5 was the size of the original qual record, when I tried to set
it to [0,0,0,0,10,1], I get this).

So my question is: Does it make sense to allow the user to modify the
size of the list in letter_annotations['phred_quality'] in qual
sequences? I think this is a nice feature for qual SeqIO.parse. If I
can modify the list size, then I can save the modified version with
SeqIO.write(x,fh,"qual") and have a qual file with a new size.

I am using 1.49 with new files from CVS.



-- 
Sebastián Bassi. Diplomado en Ciencia y Tecnología.

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