Where in the source code for SeqIO.write() does the function write the IDs and annotations to a new genbank file?
1
0
Entering edit mode
8.8 years ago
Tom ▴ 20

When I write custom annotations to my working genbank object in the form of

genbankObject.annoations["new key"]= "new value"

I can't get it to print out when I go to write it. SeqIO.write(genbankObject, outfile, genbank) just refuses to put in those new fields. It works when I switch it to "accession" of "source", but I need to add information like "reference" bases, and there's just no instance of that in the source code anywhere.

I want to dive into the source code to figure out why.

python seqio biopython • 2.5k views
ADD COMMENT
0
Entering edit mode
ADD COMMENT
0
Entering edit mode

I've tried. Where is it specifically?

ADD REPLY
0
Entering edit mode

I can't find any instance of "annotation" "accession", or "reference" anywhere. Am I looking at the wrong code?

ADD REPLY
0
Entering edit mode

The SeqIO code (if it's anything like bioperl) iteratively returns a sequence record object (SeqRecord). May want to look for that?

ADD REPLY
0
Entering edit mode

I'm not sure if I'm looking at it correctly. I've skimmed through it. No luck, I'm not good enough at parsing the source to know what I'm looking for, hence why I'm asking for help

ADD REPLY

Login before adding your answer.

Traffic: 1285 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6