#WatsonStudio and #Biopython and #fasta file saved on #S3 #Objectstorage

Question

I need to read a fasta file uploaded on Cloud Object storage using Biopython. I've anotebook in Python 2.7 in Watson Studio. Does anyone have tried this?

Answer 1

Download the sample dataset from biopython :- http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc49

Drag and drop the file to Cloud Object Storage.

Click Down arrow next to that file and click InsertStreamingBody object

This will insert a streamingBody object(ex. streaming_body_1), Please run that cell.

Next read that in a bytes Object

fastareadbytes = streaming_body_1.read()

Now we need to decode the bytes to string and then convert it to StringIO so that we can use it in SeqIO.parse() to read it

from io import StringIO
from Bio import SeqIO
for seq_record in SeqIO.parse(StringIO(fastareadbytes.decode('utf-8')), "fasta"):
    print(seq_record.id)
    print(repr(seq_record.seq))
    print(len(seq_record))

You will see response like this:-