[Biopython-dev] [Biopython - Bug #2578] The GenBank SeqRecord parser does not record molecule type or if circular

[redmine at redmine.open-bio.org]

Issue #2578 has been updated by Mark Diekhans.


not having the molecule type is a fairly serious problem with the Genbank
parser.  The fact that it guess the type when writing the record is corrupting data.  The priority of fixing this should be increased.on top 
A the very least this should be documented in the class, since its
a huge waste of time looking for where it is store in the SeqRecord.
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Bug #2578: The GenBank SeqRecord parser does not record molecule type or if circular
https://redmine.open-bio.org/issues/2578

Author: Peter Cock
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 1.47
URL: 


Filing this bug after discussion on the mailing list, where the issue was raised by Chris Lasher:
http://lists.open-bio.org/pipermail/biopython/2008-September/004474.html
http://lists.open-bio.org/pipermail/biopython/2008-September/004475.html
http://lists.open-bio.org/pipermail/biopython/2008-September/004476.html

The LOCUS line at the start of a GenBank record can record the molecule type (DNA, RNA, mRNA, protein etc) and also if the sequence is linear or circular, e.g.

LOCUS       NC_002678            7036071 bp    DNA     circular BCT 22-JUL-2008

Currently Bio.SeqIO (and Bio.GenBank.FeatureParser if called directly) do not record these two bits of information in the SeqRecord.

Bio.SeqIO uses the Bio.GenBank.FeatureParser, which gets passed this information from the Scanner via the residue_type event.  This is a combined lump of data containing both the sequence type (DNA, RNA etc) and if it is linear or circular.  It is currently only used to determine the Seq alphabet, and has never been recorded.  So in addition to not recording if the LOCUS line said the sequence was circular, if the LOCUS line contained cDNA, mRNA, ... this fine detail is also currently lost in the SeqRecord representation.  On the other hand, the Bio.GenBank.RecordParser stores all this as the record's residue_type property (a single combined field, presumably reflecting the layout of early GenBank files).

It would be a logical improvement to record the sequence data (molecule type and if circular) in the SeqRecord's annotations dictionary - perhaps as two fields but we'd need to check if that would be straight forward for EMBL files too.  Alternatively, if Biopython included a native CircularSeq object, we could use that explicitly when the sequence is declared as circular.  This might be considered a little surprising though.


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