[Biopython] Bio.GenBank .Scanner ?
Ara Kooser
akooser at unm.edu
Mon Oct 11 22:30:04 UTC 2010
Hello all,
I found a partial answer to my question. I've download all the
GenBank files for Strep. sp. AA4. I am using SeqIO to look at the
information in the files. The documentation recommends using SeqIO. I
am searching for the tag that will only extract:
CDS 1..5256
/locus_tag="StAA4_010100030484"
/
coded_by="complement(NZ_ACEV01000078.1:25146..40916)"
/note="COG3321 Polyketide synthase modules and
related
proteins"
/transl_table=11
/db_xref="CDD:33130"
this /coded_by="complement(NZ_ACEV01000078.1:25146..40916)" line from
the GenBank files.
The api documentation on-line discusses the parse_feature which is
what I think I need. I am not sure the best way to pull out that one
line. My current code is:
from Bio import SeqIO
gb_file = "sequences.gp"
for gb_record in SeqIO.parse(open(gb_file,"r"), "genbank"):
gb_feature = gb_record.features[2]
print gb_feature
Thank you for your time and help.
Ara
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