How do I make my code go through all through my list in my file.
1
0
Entering edit mode
3.1 years ago
hello = open("humanSeq.txt", "r")

l = []

for line in hello:

    fields = line.split()

    l.append(fields[0])

import Bio
from Bio import Entrez
Entrez.email = "trejomarco@test.edu"
handle = Bio.Entrez.efetch(db="nucleotide", id="NC_001643.1",rettype="gb",retmode="text")
gb_file_contents = handle.read()
handle.close()
from Bio import SeqIO
with open("NC_001643.1", "w") as out_handle:    
   out_handle.write(gb_file_contents)
with open("NC_001643.1", "r") as in_handle:   
   record = SeqIO.read(in_handle, format="gb")
print(record.seq[0:])

In my text file, I have a list of ids and I want to know how do I make my code input in all of my ids and record them all into a fasta file.

sequence • 619 views
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2
Entering edit mode
3.1 years ago

The following code would be an option:

from Bio import Entrez
from Bio import SeqIO

Entrez.email = "trejomarco@test.edu"

fh = open("humanSeq.txt")
oh = open("humanSeq.fasta", "w")
for line in fh:
    seq_id = line.strip()
    try:
        handle = Entrez.efetch(db="nucleotide", id=seq_id, rettype="fasta", retmode="text")
        fasta_str = handle.read()
        handle.close()
        oh.write(fasta_str)
    except:
        continue
oh.close()
fh.close()
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