Hello,
I am trying extract certain information from a gbk file I can extract the locus tag and the amino acid sequence however I am struggling to extract the gene location as it not in the same format in the file e.g.: /locus_tag="NCTC86_00002"
This is my script so far:
from Bio import GenBank
from Bio import SeqIO
gbk_filename = "HS.gb"
faa_filename = "HS_converted.faa"
input_handle = open(gbk_filename, "r")
output_handle = open(faa_filename, "w")
for seq_record in SeqIO.parse(input_handle, "genbank"):
print "Dealing with GenBank record %s" % seq_record.id
for seq_feature in seq_record.features :
if seq_feature.type=="CDS" :
assert len(seq_feature.qualifiers['translation'])==1
output_handle.write(">%s from %s\n%s\n" % (
seq_feature.qualifiers['locus_tag'][0],
seq_record.name,
seq_feature.qualifiers['translation'][0]))
output_handle.close()
input_handle.close()
print "Done"
Hi,
the SeqFeature objects have a "location" attribute that contains the start/stop position of the feature.
from Bio import SeqIO
gbk_filename = "HS.gb"
faa_filename = "HS_converted.faa"
output_handle = open(faa_filename, "w")
for seq_record in SeqIO.parse(gbk_filename, "genbank") :
print "Dealing with GenBank record %s" % seq_record.id
for seq_feature in seq_record.features :
if seq_feature.type=="CDS":
assert len(seq_feature.qualifiers['translation'])==1
output_handle.write(">%s from %s\n%s\n" % (
seq_feature.qualifiers['locus_tag'][0],
seq_record.name,
seq_feature.qualifiers['translation'][0]))
print('Start: %d, Stop: %d, Strand: %d'%(int(seq_feature.location.start),
int(seq_feature.location.end),
seq_feature.strand))
output_handle.close()
print "Done"
Hope this helps
Hi mgalactus
Thank you so much for your help. Im brand new to python and am trying to learn my best.
When I run that script I get this error:
Traceback (most recent call last):
File "gbkaafasta.py", line 18, in <module>
print('Start: %d, Stop: %d, Strand: %d'%(int(seq_feature.locations.start),
AttributeError: 'SeqFeature' object has no attribute 'locations'
Thank you so much for your help
Thank you very much, here my modified codes:
from Bio import SeqIO
gbk_filename = "N16961_Ch1.gbk"
faa_filename = "N16961_Ch1.faa"
output_handle = open(faa_filename, "w")
for seq_record in SeqIO.parse(gbk_filename, "genbank") :
print "Dealing with GenBank record %s" % seq_record.id
for seq_feature in seq_record.features :
if seq_feature.type=="CDS":
assert len(seq_feature.qualifiers['translation'])==1
output_handle.write(">%s Start: %s Stop: %s Strand: %s From %s\n" % (
seq_feature.qualifiers['locus_tag'][0],
seq_feature.location.start,
seq_feature.location.end,
seq_feature.strand,
seq_record.name))
output_handle.close()
print "Done"
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nhaituan •
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So also if I wanted to print the gene annotation, not every CDS entry contains a
/gene=""Do I need to put in a if there is no
/gene=""clause?