Mise à jour terminée. Pour connaître les apports de la version 13.8.4 par rapport à notre ancienne version vous pouvez lire les "Release Notes" suivantes :
https://about.gitlab.com/releases/2021/02/11/security-release-gitlab-13-8-4-released/
https://about.gitlab.com/releases/2021/02/05/gitlab-13-8-3-released/

Commit 24d84c96 authored by Mathieu Giraud's avatar Mathieu Giraud

germlines/{split-germlines.py,ncbi.py}: keep track of the position of retrieven up/downstreams

see #4656
parent fc6e6a51
Pipeline #206816 failed with stages
in 3 minutes and 44 seconds
......@@ -63,27 +63,34 @@ def get_updownstream_sequences(gene, start, end, additional_length):
recover. When additional_length > 0 we get the downstream
region, and conversely when additional_length < 0.
:return: A tuple whose first element is the upstream region (or empty)
and where the second element is the downstream region (or empty
and where the second element is the downstream region (or empty),
then a string carrying information
'''
info = '(%d..%d)' % (start, end)
if additional_length == 0:
return ('', '')
reversed = -1 if (end < start) else 1
if additional_length > 0:
start = end + 1 * reversed
end = end + additional_length * reversed
info = info + '..%d' % end
elif additional_length < 0:
end = start - 1 * reversed
start = max(1, start + additional_length * reversed)
info = '%d..' % start + info
updown_fasta = get_gene_sequence(gene, '', start, end, 0)
updown_raw = '\n'.join(updown_fasta.split('\n')[1:]).strip()
gene_info = "%s|%s" % (gene, info)
if additional_length > 0:
return ('', updown_raw)
return (('', updown_raw), gene_info)
else:
return (updown_raw, '')
return ((updown_raw, ''), gene_info)
# Parse output from API_GENE_ID_XML to get genomic positions of a gene
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment