[Biopython-dev] [Biopython - Bug #2351] Make Seq more like a string, even subclass string?

[redmine at redmine.open-bio.org]

Issue #2351 has been updated by Michiel de Hoon.


Same code, now readable:

<pre>
>>> from Bio import SeqIO
>>> genome = SeqIO.read('chrY.fa', 'fasta')
>>> output = open("sequences.txt", 'w')
>>> output.write(genome.seq)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: argument 1 must be string or read-only character buffer, not Seq
>>>
</pre>
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Bug #2351: Make Seq more like a string, even subclass string?
https://redmine.open-bio.org/issues/2351

Author: Peter Cock
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: Not Applicable
URL: 


We've started talking on the mailing list about making the SeqRecord class a subclass of the Seq object, and making that a subclass of the Python string.

This bug is for holding patches - I suspect a lot of the discussion will continueon the mailing lists rather than here.

I explicitly have left the "assign to" field pointing at the dev mailinglist.


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