Question: BLAST using Biopython
0
gravatar for a.lathifbt
4 weeks ago by
a.lathifbt0
Chennai, India
a.lathifbt0 wrote:

Hello.I am new to biopython and I am trying to do BLAST search for a single query sequence. This is the script I wrote:

""" BLAST OVER INTERNET """
from Bio.Blast import NCBIWWW
file_name=input("enter the file name:")
filename = open(file_name).read()
result=NCBIWWW.qblast("blastn", "nt", "filename")
from Bio.Blast import NCBIXML
blast_record = NCBIXML.read(result)
print(len(blast_record.alignments))
evalue = 0.01
for alignment in blast_record.alignments:
   for hsp in alignment.hsps:
     if hsp.expect < evalue:
       print("****Alignment****")
       print("sequence:", alignment.title)
       print("length:", alignment.length)
       print("e value:", hsp.expect)
       print(hsp.query[0:75] + "...")
       print(hsp.match[0:75] + "...")
       print(hsp.sbjct[0:75] + "...")

So the issue I am getting is, no result is being generated. The length of the "blast_record_allignments" returns 0 value. Can anyone please help me with it? Thanks in advance

alignment gene • 111 views
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by a.lathifbt0

Please use 101010 button to format the code. Could you provide a samples fasta sequence you're using for this script?

ADD REPLYlink written 4 weeks ago by Sej Modha4.2k
2
gravatar for massa.kassa.sc3na
4 weeks ago by
massa.kassa.sc3na40 wrote:

few problems: You pass the STRING "filename" to the NCBIWWW.qblast call instead of variable.

If the file from input should be FASTA file, then you need to pass file_name variable (without quotes) and the open(..).read() is not necessary.

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by massa.kassa.sc3na40

Thank you so much! rectified the issue and it's working now.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by a.lathifbt0

Great. I’ve moved the comment to an answer, so if you’re happy with the resolution to the thread, please go ahead and toggle the Tick to accept the answer as a solution.

ADD REPLYlink written 4 weeks ago by jrj.healey13k
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