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-rwxr-xr-xscripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py2
-rw-r--r--scripts/esr_samples/template.yaml2
-rw-r--r--scripts/uthsc_samples/template.yaml2
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: