[med-svn] [Git][med-team/epcr][master] Refactor the fetching script to fetch all the data

[Saira Hussain]

Saira Hussain pushed to branch master at Debian Med / epcr


Commits:
bf488007 by Saira Hussain at 2019-06-27T09:45:07Z
Refactor the fetching script to fetch all the data

Rename and refactor the fasta fetching script in order to fetch
all the data and save them in the right directore

- - - - -


1 changed file:

- − debian/tests/fetch_fasta.py


Changes:

=====================================
debian/tests/fetch_fasta.py deleted
=====================================
@@ -1,25 +0,0 @@
-#!/usr/bin/python3
-
-from Bio import Entrez
-
-Entrez.email = 'unknown at debian.org'
-database = 'nucleotide'
-fn = 'data/gingo.fasta'
-
-query = [
-    '((chloroplast OR plastid) AND "complete genome" AND Embryophyta NOT (mi- tochondrion OR mitochondrial)) AND "Ginkgo biloba"'
-]
-
-# Fetch the query IDs
-handle = Entrez.esearch(db=database, term=query)
-record = Entrez.read(handle)
-ids = record['IdList']
-handle.close()
-
-# Fetch the first result
-ff = open(fn, 'w')
-
-handle_fasta = Entrez.efetch(db=database, id=ids[0], rettype='fasta', retmode='text')
-ff.write(handle_fasta.read().rstrip('\n'))
-
-handle_fasta.close()



View it on GitLab: https://salsa.debian.org/med-team/epcr/commit/bf488007d0ef797e1bac0bbf228025ca4c9167bd

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View it on GitLab: https://salsa.debian.org/med-team/epcr/commit/bf488007d0ef797e1bac0bbf228025ca4c9167bd
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