diff options
| -rw-r--r-- | .guix-deploy | 2 | ||||
| -rw-r--r-- | doc/INSTALL.md | 2 | ||||
| -rwxr-xr-x | scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py | 19 |
3 files changed, 11 insertions, 12 deletions
diff --git a/.guix-deploy b/.guix-deploy index e978e23..570ae10 100644 --- a/.guix-deploy +++ b/.guix-deploy @@ -6,5 +6,5 @@ export GUILE_LOAD_COMPILED_PATH=$GUIX_PROFILE/share/guile/site/3.0/ ls $GUILE_LOAD_PATH -env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-bioinformatics/ $GUIX_PROFILE/bin/guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs python-pyshex python-pyyaml --network openssl python-pyshex python-pyshexc clustalw python-schema-salad python-arvados-python-client --share=/export/tmp -- env TMPDIR=/export/tmp FLASK_ENV=development FLASK_RUN_PORT=5067 FLASK_APP=bh20simplewebuploader/main.py flask run +env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-bioinformatics/ $GUIX_PROFILE/bin/guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs python-pyshex python-pyyaml --network openssl python-pyshex python-pyshexc minimap2 python-schema-salad python-arvados-python-client --share=/export/tmp -- env TMPDIR=/export/tmp FLASK_ENV=development FLASK_RUN_PORT=5067 FLASK_APP=bh20simplewebuploader/main.py flask run diff --git a/doc/INSTALL.md b/doc/INSTALL.md index 3b270dd..e31b7d7 100644 --- a/doc/INSTALL.md +++ b/doc/INSTALL.md @@ -59,7 +59,7 @@ WIP: add gunicorn container Currently the full webserver container deploy command looks like ``` -penguin2:~/iwrk/opensource/code/vg/bh20-seq-resource$ env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-oinformatics/ ~/iwrk/opensource/guix/guix/pre-inst-env guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs python-pyshex python-pyyaml --network openssl python-pyshex python-pyshexc clustalw python-schema-salad python-arvados-python-client --share=/export/tmp -- env TMPDIR=/export/tmp FLASK_ENV=development FLASK_APP=bh20simplewebuploader/main.py flask run +penguin2:~/iwrk/opensource/code/vg/bh20-seq-resource$ env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-oinformatics/ ~/iwrk/opensource/guix/guix/pre-inst-env guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs python-pyshex python-pyyaml --network openssl python-pyshex python-pyshexc minimap2 python-schema-salad python-arvados-python-client --share=/export/tmp -- env TMPDIR=/export/tmp FLASK_ENV=development FLASK_APP=bh20simplewebuploader/main.py flask run ``` Note: see above on GUIX_PACKAGE_PATH. 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 272b5ba..8ef76e1 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 @@ -145,7 +145,7 @@ for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_x if not os.path.exists(dir_fasta_and_yaml): os.makedirs(dir_fasta_and_yaml) -min_len_to_count = 27500 +min_len_to_count = 15000 num_seq_with_len_ge_X_bp = 0 missing_value_list = [] @@ -411,18 +411,17 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) not_created_accession_dict[accession_version] = [] not_created_accession_dict[accession_version].append('host_species not found') - if accession_version in not_created_accession_dict: - continue - - with open(os.path.join(dir_fasta_and_yaml, '{}.fasta'.format(accession_version)), 'w') as fw: - fw.write('>{}\n{}'.format(accession_version, GBSeq_sequence.text.upper())) + if len(GBSeq_sequence.text) < min_len_to_count: + not_created_accession_dict[accession_version].append('sequence shorter than {} bp'.format(min_len_to_count)) - with open(os.path.join(dir_fasta_and_yaml, '{}.yaml'.format(accession_version)), 'w') as fw: - json.dump(info_for_yaml_dict, fw, indent=2) + if accession_version not in not_created_accession_dict: + num_seq_with_len_ge_X_bp += 1 + with open(os.path.join(dir_fasta_and_yaml, '{}.fasta'.format(accession_version)), 'w') as fw: + fw.write('>{}\n{}'.format(accession_version, GBSeq_sequence.text.upper())) - if(len(GBSeq_sequence.text) >= min_len_to_count): - num_seq_with_len_ge_X_bp += 1 + with open(os.path.join(dir_fasta_and_yaml, '{}.yaml'.format(accession_version)), 'w') as fw: + json.dump(info_for_yaml_dict, fw, indent=2) except: print("Unexpected error for the ID {}: {}".format(accession_version, sys.exc_info()[0])) accession_with_errors_list.append(accession_version) |