aboutsummaryrefslogtreecommitdiff
path: root/scripts/download_genbank_data
diff options
context:
space:
mode:
authorAndreaGuarracino2020-09-04 11:13:25 +0200
committerAndreaGuarracino2020-09-04 11:13:25 +0200
commit327b6db4e7c9ceda190617f2a793e6a646bb30cc (patch)
treea4e4750c85dcd4352bce415091a084fe9e64b707 /scripts/download_genbank_data
parent1430c62ff9245bfecb1d41cc87bbafafcfc81ca3 (diff)
downloadbh20-seq-resource-327b6db4e7c9ceda190617f2a793e6a646bb30cc.tar.gz
bh20-seq-resource-327b6db4e7c9ceda190617f2a793e6a646bb30cc.tar.lz
bh20-seq-resource-327b6db4e7c9ceda190617f2a793e6a646bb30cc.zip
added in the sra script an option to include only a subset of ids
Diffstat (limited to 'scripts/download_genbank_data')
-rwxr-xr-xscripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py3
1 files changed, 2 insertions, 1 deletions
diff --git a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
index 7251819..52aee4e 100755
--- a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
@@ -58,7 +58,8 @@ if args.ids_to_ignore:
with open(args.ids_to_ignore) as f:
accession_to_ignore_set.update(set([x.split('.')[0] for x in f.read().strip('\n').split('\n')]))
- print('There are {} accessions to ignore.'.format(len(accession_to_ignore_set)))
+
+ print('There are {} accessions to ignore.'.format(len(accession_to_ignore_set)))
accession_already_downloaded_set = set()