diff options
| -rw-r--r-- | scripts/download_genbank_data/.guix-run | 5 | ||||
| -rwxr-xr-x | scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py | 32 |
2 files changed, 34 insertions, 3 deletions
diff --git a/scripts/download_genbank_data/.guix-run b/scripts/download_genbank_data/.guix-run new file mode 100644 index 0000000..1403c69 --- /dev/null +++ b/scripts/download_genbank_data/.guix-run @@ -0,0 +1,5 @@ +#!/bin/sh +# Runner + +echo python3 from_genbank_to_fasta_and_yaml.py +guix environment guix --ad-hoc python python-biopython python-requests python-dateutil 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 788f7e9..9b2c9eb 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 @@ -1,4 +1,9 @@ #!/usr/bin/env python3 +# +# - bulk download genbank data and matadata, preparing the FASTA and +# the YAML files +# +# See .guix-run python3 from_genbank_to_fasta_and_yaml.py import argparse parser = argparse.ArgumentParser() @@ -61,21 +66,34 @@ if args.ids_to_ignore: print('There are {} accessions to ignore.'.format(len(accession_to_ignore_set))) +# ---------------------------------------------------------------------- +""" +With --only-missing-ids only download accessions that we do not yet have! +""" accession_already_downloaded_set = set() if os.path.exists(dir_fasta_and_yaml): + """ + If the fasta_and_yaml directory exists and --only-missing-ids was set + we make a list of all downloaded accessions: + """ print("The directory '{}' already exists.".format(dir_fasta_and_yaml)) if not args.only_missing_ids: print("To start the download, delete the directory '{}' or specify --only-missing-ids.".format(dir_fasta_and_yaml)) sys.exit(-1) + """ + Fetch all YAML filenames and load `accession_already_downloaded_set` + """ accession_already_downloaded_set = set([x.split('.yaml')[0].split('.')[0] for x in os.listdir(dir_fasta_and_yaml) if x.endswith('.yaml')]) print('There are {} accessions already downloaded.'.format(len(accession_already_downloaded_set))) - accession_to_ignore_set.update(accession_already_downloaded_set) - +# ---------------------------------------------------------------------- +""" +Check for --ids-to-consider +""" accession_to_consider_set = set() if args.ids_to_consider: @@ -89,6 +107,10 @@ if args.ids_to_consider: if len(accession_to_consider_set) > 0: print('There are {} accessions to consider.'.format(len(accession_to_consider_set))) +# ---------------------------------------------------------------------- +""" +Download section for genbank XML +""" if not os.path.exists(dir_metadata): # Take all the ids @@ -143,11 +165,15 @@ if not os.path.exists(dir_metadata): Entrez.efetch(db='nuccore', id=id_x_list, retmode='xml').read() ) +# ---------------------------------------------------------------------- +""" +Generate metadata (YAML) and FASTA files for each accession +""" + if not os.path.exists(dir_fasta_and_yaml): os.makedirs(dir_fasta_and_yaml) - min_len_to_count = 15000 num_seq_with_len_ge_X_bp = 0 |