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| author | Andrea Guarracino | 2020-04-15 15:54:26 +0200 |
|---|---|---|
| committer | GitHub | 2020-04-15 15:54:26 +0200 |
| commit | addbd80878cc4fedaf785c147073bb72ef8b54b4 (patch) | |
| tree | 9641c33fdb2f9169d7cf6cc55f276e8945a56dd1 /scripts | |
| parent | 7cf44a7aed6dd190e16ac94958aefcf7bffed6a0 (diff) | |
| download | bh20-seq-resource-addbd80878cc4fedaf785c147073bb72ef8b54b4.tar.gz bh20-seq-resource-addbd80878cc4fedaf785c147073bb72ef8b54b4.tar.lz bh20-seq-resource-addbd80878cc4fedaf785c147073bb72ef8b54b4.zip | |
added type id check
what is not genomic DNA is removed
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/from_genbank_to_fasta_and_yaml.py | 12 |
1 files 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)) |