<div dir="ltr">If you store your list of identifiers in a file given by the variable 'file_path', with one identifier per line, you can use:<div><br></div><div>ids_to_fetch = ",".join(open(file_path))</div><div><br></div><div>This code will open the file, and use the default iteration behavior for file objects to yield a line at a time to the join method of the string ",". This will create a long string of comma-separated identifiers to use in your efetch call.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jul 8, 2015 at 9:12 PM, Zach Gayk <span dir="ltr"><<a href="mailto:zgayk@nmu.edu" target="_blank">zgayk@nmu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello,<br>
<br>
I would like to use the following code from the biopython tutorial to<br>
retrieve gi numbers for a number of sequences that matched to scaffolds on<br>
a genome assembly:<br>
<br>
import os<br>
os.chdir('/Users/zachgayk/Desktop/GAVIABioinformatics/')<br>
from Bio import Entrez # this is the most likely script modified<br>
from Bio import SeqIO<br>
Entrez.email = "<a href="mailto:zgayk@nmu.edu">zgayk@nmu.edu</a>"<br>
handle = Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", \<br>
id="gi|50254217|gb|`, gi|50254217|gb|AY567890.1|,<br>
gi|559028|gb|L33375.1|GVSMTDGI,<br>
gi|559028|gb|L33375.1|GVSMTDGI")<br>
for seq_record in SeqIO.parse(handle, "gb"):<br>
print seq_record.description[:100] + "..." # the :100 specifies no.<br>
characters and "..." says this comes after specified character limit<br>
handle.close()<br>
<br>
The problem, however, is that there are a large number of gi numbers I<br>
wish to retrieve, and so there are simply too many to manually enter into<br>
the id ="" field. What I would like to do is specify a file containing all<br>
of the needed gi numbers in a list and then have the code parse all of<br>
them. I haven't been able to figure out how to do this yet, and if anyone<br>
has any ideas they would be very much appreciated.<br>
<br>
Thank you,<br>
Zach Gayk<br>
<br>
<br>
<br>
<br>
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</blockquote></div><br></div>