Yes - that's the built-in documentation also available within Python with:
from Bio import SeqIO
help(SeqIO)
Or I would suggest http://biopython.org/wiki/SeqIO or the main Biopython Tutorial, http://biopython.org/DIST/docs/tutorial/Tutorial.html
Is Biopython unable to read draft genomes (having multiple contigs)?
I want to extract specific CDS from a gbk file into another gbk file. Apparently it is not so trivial.
I can read here how to slice a genbank so I do the following:
record = SeqIO.read("SpeciesA.gbk", "genbank")
sub_record=(record[25500:33500])
SeqIO.write(sub_record, "test.gbk", "genbank")
This seems to work quite well, but I have problem to read draft genomes were I have multiple contigs.
When I try to import them I get:
record = SeqIO.read("SpeciesB.gbk", "genbank")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python2.7/dist-packages/Bio/SeqIO/__init__.py", line 656, in read
raise ValueError("More than one record found in handle")
ValueError: More than one record found in handle
I did not manage to find a way around it, any idea how to fix this?
1 answer
May be you should check this page?
Use the Bio.SeqIO.parse(handle, format) function if you want to read multiple records from the handle
• 0 views
•
link
updated
by
Ram
•
written
by
GouthamAtla
•
written
by
GouthamAtla
Log in to answer this question.
More posts like this
-
Non-standard Genbank format
written by mrmrwinter •
-
Failure to extract CDS from embl file using BioPython
written by rjqmantaring •
-
error to install varsimlab
written by joselu
-
Problem with Parse SeqIO SOLVED - link to cross-reference
written by felipelira3 •
-
Change sequence in SEQIO
written by grant.hovhannisyan
-
PubMed connection error
written by agata88
-
Biopython error when reading UTRdb swissprot formatted file
written by themantalope •
-
Error extracting faa sequences from multifasta using faidx
written by dago
-
How To Parse 'Embl' Annotation File
written by fm271 •
-
Parsing List Of Sequences In Embl Format
written by Pappu
