User: A. Kozubik

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A. Kozubik0
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Posts by A. Kozubik

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Is there a Pyinstaller hook for Biopython imports? How to package a Biopython sc
... Thank you for your reply. I was afraid that indeed might be the case, since I've seen that even in the Biopython mailing list, nobody came up with any truly working solution. Setting up a VM, while it might be functional, would go against the primary intentions of why I'm trying to pack the script ...
written 9 days ago by A. Kozubik0
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Is there a Pyinstaller hook for Biopython imports? How to package a Biopython script into executable?
... I have a script written in Python 3.7.2 with following imports: from Bio import SeqIO from Bio import SearchIO from Bio import ExPASy from Bio import SwissProt from Bio.Blast import NCBIWWW and I am attempting to package it into an .exe file, which fails because of the missing ...
python pyinstaller hook biopython import written 11 days ago by A. Kozubik0
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Comment: C: Did Biopython's NCBIWWW qblast suddenly stopped supporting entrez_query paramete
... Actually, an update - after several more hours of working after the problem was fixed, it returned again. Therefore, I suspect it is not directly linked with the Biopython update, but maybe rather with the NCBI server load, which results in denying/failing a qblast request. ...
written 14 days ago by A. Kozubik0
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Comment: A: Did Biopython's NCBIWWW qblast suddenly stopped supporting entrez_query paramete
... Actually, what jrj.healey suggested might have just solved the issue - I've manually updated Biopython with all dependencies via pip, and now the qblast is working again, specifically for `entrez_query = '"Arabidopsis thaliana"[organism]'`. Thanks! ...
written 14 days ago by A. Kozubik0
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Comment: C: Did Biopython's NCBIWWW qblast suddenly stopped supporting entrez_query paramete
... I don't think so, unless my IDE (Thonny) updates the packages automatically. Checked it manually now, the Biopython package should be up to date. Other than that, the only change I've made in the code is that I've deleted some lines with imports that were not currently in use, but Bio.Blast NCBIWWW ...
written 14 days ago by A. Kozubik0
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Did Biopython's NCBIWWW qblast suddenly stopped supporting entrez_query parameter?
... I'm using Biopython 1.73 with Python 3.7.2. Until yesterday, the following code produced BLAST results as intended: entrquery = '"Arabidopsis thaliana"[organism]' result_handle = NCBIWWW.qblast(program="blastp",database="swissprot", sequence=mainfastafile.read(), entrez_query=entrquer ...
entrez_query qblast biopython blast ncbiwww written 14 days ago by A. Kozubik0 • updated 14 days ago by zx87547.3k

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