[med-svn] [Git][med-team/epcr][master] 2 commits: Add script to fetch the required data for testing

[Saira Hussain]

Saira Hussain pushed to branch master at Debian Med / epcr


Commits:
92b00bb3 by Saira Hussain at 2019-06-24T13:16:06Z
Add script to fetch the required data for testing

Python script to fetch the required data from NCBI
database in order to be used for the testing of the package.

- - - - -
12e555ff by Saira Hussain at 2019-06-24T13:17:00Z
Merge branch 'master' of salsa.debian.org:med-team/epcr

- - - - -


2 changed files:

- + debian/tests/data/gingo.fasta
- + debian/tests/fetch_fasta.py


Changes:

=====================================
debian/tests/data/gingo.fasta
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/tests/fetch_fasta.py
=====================================
@@ -0,0 +1,23 @@
+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/compare/bfe1a449e2ceb32b5736010cd81c39790625efe8...12e555ff37609d3d9d2a6a6b6b82182fae387094

-- 
View it on GitLab: https://salsa.debian.org/med-team/epcr/compare/bfe1a449e2ceb32b5736010cd81c39790625efe8...12e555ff37609d3d9d2a6a6b6b82182fae387094
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