[Biopython-dev] [Bug 2826] New: when creating a de-novo SeqRecord, the dbxrefs are not written by SeqIO.write

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2826

           Summary: when creating a de-novo SeqRecord, the dbxrefs are not
                    written by SeqIO.write
           Product: Biopython
           Version: 1.49
          Platform: All
        OS/Version: Linux
            Status: NEW
          Severity: minor
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: david.wyllie at ndm.ox.ac.uk


Hi

when creating a SeqRecord de novo, the dbxrefs are not written by SeqIO.write.
Is this the intended behaviour?

here is an example:

# example script
from Bio.Seq import Seq
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import generic_protein

# list to hold output records
outlist=[]

# ofh is the output file handle
ofh = open("/home/dwyllie/temporary.gbk","w")

# example of de novo creation of SeqRecord object from url:
# http://biopython.org/DIST/docs/api/Bio.SeqRecord.SeqRecord-class.html
rec = SeqRecord(Seq("MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKAT",
generic_protein),  \
                                id="NP_418483.1", name="b4059",  
description="ssDNA-binding protein", \
                                dbxrefs=["ASAP:13298", "GI:16131885",
"GeneID:948570"])

print rec

outlist.append(rec)
count = SeqIO.write(outlist, ofh, "genbank")
ofh.close()

# end of script

OUTPUT:
ID: NP_418483.1
Name: b4059
Description: ssDNA-binding protein
Database cross-references: ASAP:13298, GI:16131885, GeneID:948570
Number of features: 0
Seq('MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKAT', ProteinAlphabet())

Contents of temporary.gbk:
LOCUS       b4059                     46 bp                     UNK 01-JAN-1980
DEFINITION  ssDNA-binding protein
ACCESSION   NP_418483
VERSION     NP_418483.1
KEYWORDS    .
SOURCE      .
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
ORIGIN
        1 MASRGVNKVI LVGNLGQDPE VRYMPNGGAV ANITLATSES WRDKAT
//


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