From addbd80878cc4fedaf785c147073bb72ef8b54b4 Mon Sep 17 00:00:00 2001 From: Andrea Guarracino Date: Wed, 15 Apr 2020 15:54:26 +0200 Subject: added type id check what is not genomic DNA is removed--- scripts/from_genbank_to_fasta_and_yaml.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py index 0cc1a57..6a55b5e 100644 --- a/scripts/from_genbank_to_fasta_and_yaml.py +++ b/scripts/from_genbank_to_fasta_and_yaml.py @@ -7,7 +7,7 @@ import os path_ncbi_virus_accession = 'sequences.acc' -date = '20200414' +date = '20200415' path_seq_fasta = 'seq_from_nuccore.{}.fasta'.format(date) path_metadata_xml = 'metadata_from_nuccore.{}.xml'.format(date) @@ -19,9 +19,15 @@ for term in term_list: tmp_list = Entrez.read( Entrez.esearch(db='nuccore', term=term, idtype='acc', retmax='10000') )['IdList'] - print(term, len(tmp_list)) - + + # Remove mRNAs, ncRNAs, Proteins, and predicted models (more information here: https://en.wikipedia.org/wiki/RefSeq) + tmp_list = [x for x in tmp_list if x[:2] not in ['NM', 'NR', 'NP', 'XM', 'XR', 'XP', 'WP']] + # Remove the version in the id + tmp_list = [x.split('.')[0] for x in tmp_list] + + print(term, len(tmp_list)) + id_set.update([x.split('.')[0] for x in tmp_list]) print(term_list, len(id_set)) -- cgit v1.2.3