[Biopython-dev] [Bug 1944] New: Align.Generic adding iterator and more

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=1944

           Summary: Align.Generic adding iterator and more
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: mcolosimo at mitre.org


I thought it would be nice to be able to directly iterate over the SeqRecords
in an alignment. So, I wrote it up and tested it with Bio.Clustalw. I also
added the ability to fill in other fields of the SeqRecord (similar to
Fasta.SequenceParser)

Diff below:

Index: Generic.py
===================================================================
RCS file: /home/repository/biopython/biopython/Bio/Align/Generic.py,v
retrieving revision 1.5
diff -r1.5 Generic.py
32c32
<         # hold everything at a list of seq record objects
---
>         # hold everything as a list of SeqRecord objects
33a34
>         self._iter_pos = 0
34a36,51
>     def __iter__(self):
>         self.__iter_pos = 0
>         return iter(self.next, None)
>         
>     def next(self):
>         """Returns one sequence record at a time.
>         
>         @return: a SeqRecord or None if end of iteration.
>         """
>         if self._iter_pos >= len(self._records):
>             return None
>             
>         rec = self._records[self._iter_pos]
>         self._iter_pos += 1
>         return rec
>         
38c55,56
<         The return value is a list of SeqRecord objects.
---
>         @return: a list of the sequences.
>         @rtype: SeqRecord
45,49c63,66
<         Returns:
<         o A Seq object for the requested sequence.
< 
<         Raises:
<         o IndexError - If the specified number is out of range.
---
>         @param number: the number of the sequence in the consensus.
>         @return: the requested sequence.
>         @rtype: SeqRecord.
>         @raise IndexError: If the specified number is out of range.
69c86
<                      weight = 1.0):
---
>                      weight = 1.0, description2ids = None):
86a104,107
>         o descriptor2id - A function that, when given the descriptor,
>         will return the id, name, and description (in that order)
>         for the record. If this is not given, then the entire descriptor
>         line will be used as the description.
89c110,117
<         new_record = SeqRecord(new_seq, description = descriptor)
---
>         rec = SeqRecord(new_seq)
>         if title2ids:
>             seq_id, name, descr = title2ids(descriptor)
>             rec.id = seq_id
>             rec.name = name
>             rec.description = descr
>         else:
>             rec.description = descriptor
99c127
<             new_record.annotations['start'] = start
---
>             rec.annotations['start'] = start
101c129
<             new_record.annotations['end'] = end
---
>             rec.annotations['end'] = end
104c132
<         new_record.annotations['weight'] = weight
---
>         rec.annotations['weight'] = weight
106c134,147
<         self._records.append(new_record)
---
>         # what happens if we're iterating?
>         self._records.append(rec)
> 
>         
>     def addSeqRecord(self, seqRec):
>         """Add a Sequence Record to the Alignment
> 
>         @param seqRec: a sequence record (SeqRecord) to add.
>         """
>         if isinstance(seqRec, SeqRecord):
>             self._records.append(seqRec)
>         else:
>             raise TypeError("sequence is NOT a SeqRecord Object")
>




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