diff options
| author | AndreaGuarracino | 2020-11-12 18:35:00 +0100 |
|---|---|---|
| committer | AndreaGuarracino | 2020-11-12 18:35:00 +0100 |
| commit | 87440554e57d5c5ed846e98a3b3ec428330e15e8 (patch) | |
| tree | f5c02264faac820a91cbe92974f279f5bec10c48 /scripts | |
| parent | 0bfe144ca40b4dfc1d75e195f3cfae7a8af94dc0 (diff) | |
| download | bh20-seq-resource-87440554e57d5c5ed846e98a3b3ec428330e15e8.tar.gz bh20-seq-resource-87440554e57d5c5ed846e98a3b3ec428330e15e8.tar.lz bh20-seq-resource-87440554e57d5c5ed846e98a3b3ec428330e15e8.zip | |
updated alignment_protocol field in the script, doc, and the example templates
Diffstat (limited to 'scripts')
| -rwxr-xr-x | scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py | 2 | ||||
| -rw-r--r-- | scripts/esr_samples/template.yaml | 2 | ||||
| -rw-r--r-- | scripts/uthsc_samples/template.yaml | 2 |
3 files changed, 3 insertions, 3 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 364090e..87b348b 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 @@ -190,7 +190,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) for info_to_check, field_in_yaml in zip( ['Assembly Method', 'Coverage', 'Sequencing Technology'], - ['sequence_assembly_method', 'sequencing_coverage', 'sample_sequencing_technology'] + ['alignment_protocol', 'sequencing_coverage', 'sample_sequencing_technology'] ): if info_to_check in GBSeq_comment_text: tech_info_to_parse = GBSeq_comment_text.split('{} :: '.format(info_to_check))[1].split(' ;')[0] diff --git a/scripts/esr_samples/template.yaml b/scripts/esr_samples/template.yaml index 98f08a6..3ca1de3 100644 --- a/scripts/esr_samples/template.yaml +++ b/scripts/esr_samples/template.yaml @@ -14,7 +14,7 @@ virus: technology: sample_sequencing_technology: ["http://www.ebi.ac.uk/efo/EFO_0008632"] - sequence_assembly_method: "https://github.com/ESR-NZ/NZ_SARS-CoV-2_genomics" + alignment_protocol: "https://github.com/ESR-NZ/NZ_SARS-CoV-2_genomics" additional_technology_information: "Artic V3 workflow" submitter: diff --git a/scripts/uthsc_samples/template.yaml b/scripts/uthsc_samples/template.yaml index 07e0828..c81bd28 100644 --- a/scripts/uthsc_samples/template.yaml +++ b/scripts/uthsc_samples/template.yaml @@ -22,7 +22,7 @@ virus: technology: sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632] - sequence_assembly_method: https://bio.tools/BWA#! + alignment_protocol: https://bio.tools/BWA#! additional_technology_information: "Oxford Nanopore MiniIon RNA long reads" submitter: |