save sequences from NCBI in fasta format using a list of IDs in excel - parsing

Question

I am fairly new using python and I love it. However I am stuck with this problem and I hope you could give me a hind about what I am missing.
I have a list of gene IDs in an excel file and I am trying to use xrld and biopython to retrieve sequences and save (in fasta format) my results in to a text document. so far, my code allow me to see the results in the shell but it only save the last sequence in a document.
this is my code:
import xlrd
import re
book = xlrd.open_workbook('ids.xls')
sh = book.sheet_by_index(0)
for rx in range(sh.nrows):
if sh.row(rx)[0].value:
from Bio import Entrez
from Bio import SeqIO
Entrez.email = "mail#xxx.com"
in_handle = Entrez.efetch(db="nucleotide", rettype="fasta", id=sh.row(rx)[0].value)
record = SeqIO.parse(in_handle, "fasta")
for record in SeqIO.parse(in_handle, "fasta"):
print record.format("fasta")
out_handle = open("example.txt", "w")
SeqIO.write(record, out_handle, "fasta")
in_handle.close()
out_handle.close()
As I mentioned, the file "example.txt", only have the last sequence (in fasta format) that shows the shell.
could anyone please help me how to get al the sequences I retrieve from NCBI in the same document?
Thank you very much
Antonio

Answer 1

I am also fairly new to python and also love it! this is my first attempt at answering a question, but maybe it is because of your loop structure and the 'w' mode? perhaps try changing ("example.txt", "w") to append mode ("example.txt", "a") as below?
import xlrd
import re
book = xlrd.open_workbook('ids.xls')
sh = book.sheet_by_index(0)
for rx in range(sh.nrows):
if sh.row(rx)[0].value:
from Bio import Entrez
from Bio import SeqIO
Entrez.email = "mail#xxx.com"
in_handle = Entrez.efetch(db="nucleotide", rettype="fasta", id=sh.row(rx)[0].value)
record = SeqIO.parse(in_handle, "fasta")
for record in SeqIO.parse(in_handle, "fasta"):
print record.format("fasta")
out_handle = open("example.txt", "a")
SeqIO.write(record, out_handle, "fasta")
in_handle.close()
out_handle.close()

Answer 2

Nearly there my friends!
The main problem is that your For loop keeps closing the file each loop. I also fixed some minor issues that should just speed up the code (e.g. you kept importing Bio each loop).
Use this new code:
out_handle = open("example.txt", "w")
import xlrd
import re
from Bio import Entrez
from Bio import SeqIO
book = xlrd.open_workbook('ids.xls')
sh = book.sheet_by_index(0)
for rx in range(sh.nrows):
if sh.row(rx)[0].value:
Entrez.email = "mail#xxx.com"
in_handle = Entrez.efetch(db="nucleotide", rettype="fasta", id=rx)
record = SeqIO.parse(in_handle, "fasta")
SeqIO.write(record, out_handle, "fasta")
in_handle.close()
out_handle.close()
If it still errors, It must be a problem in your excel file. Send this to me if the error still persists and I will help :)