From 87440554e57d5c5ed846e98a3b3ec428330e15e8 Mon Sep 17 00:00:00 2001 From: AndreaGuarracino Date: Thu, 12 Nov 2020 18:35:00 +0100 Subject: updated alignment_protocol field in the script, doc, and the example templates --- doc/blog/using-covid-19-pubseq-part3.html | 2 +- doc/blog/using-covid-19-pubseq-part3.org | 2 +- example/esr_example.yaml | 2 +- example/maximum_metadata_example.yaml | 2 +- example/uthsc_example.yaml | 2 +- scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py | 2 +- scripts/esr_samples/template.yaml | 2 +- scripts/uthsc_samples/template.yaml | 2 +- test/data/input/TN_UT2.yaml | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) diff --git a/doc/blog/using-covid-19-pubseq-part3.html b/doc/blog/using-covid-19-pubseq-part3.html index b49830b..aea74ad 100644 --- a/doc/blog/using-covid-19-pubseq-part3.html +++ b/doc/blog/using-covid-19-pubseq-part3.html @@ -589,7 +589,7 @@ virus: technology: sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0009173,http://www.ebi.ac.uk/efo/EFO_0009173] - sequence_assembly_method: Protocol used for assembly + alignment_protocol: Protocol used for assembly sequencing_coverage: [70.0, 100.0] additional_technology_information: Optional free text field for additional information diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org index d0d6c7f..c98bf27 100644 --- a/doc/blog/using-covid-19-pubseq-part3.org +++ b/doc/blog/using-covid-19-pubseq-part3.org @@ -234,7 +234,7 @@ a more elaborate example (note most fields are optional) may look like technology: sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0009173,http://www.ebi.ac.uk/efo/EFO_0009173] - sequence_assembly_method: Protocol used for assembly + alignment_protocol: Protocol used for assembly sequencing_coverage: [70.0, 100.0] additional_technology_information: Optional free text field for additional information diff --git a/example/esr_example.yaml b/example/esr_example.yaml index 48b11e4..b3e97d5 100644 --- a/example/esr_example.yaml +++ b/example/esr_example.yaml @@ -24,7 +24,7 @@ virus: technology: sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632] // Nanopore MinION - 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/example/maximum_metadata_example.yaml b/example/maximum_metadata_example.yaml index 54736f8..cd8890d 100644 --- a/example/maximum_metadata_example.yaml +++ b/example/maximum_metadata_example.yaml @@ -35,7 +35,7 @@ virus: technology: sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0009173,http://www.ebi.ac.uk/efo/EFO_0009173] - sequence_assembly_method: Protocol used for assembly + alignment_protocol: Protocol used for assembly sequencing_coverage: [70.0, 100.0] additional_technology_information: Optional free text field for additional information diff --git a/example/uthsc_example.yaml b/example/uthsc_example.yaml index 956faf1..3bdbf6f 100644 --- a/example/uthsc_example.yaml +++ b/example/uthsc_example.yaml @@ -24,7 +24,7 @@ virus: technology: sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632] // Nanopore MinION - sequence_assembly_method: guppy + alignment_protocol: guppy additional_technology_information: Optional free text field for additional information submitter: 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: diff --git a/test/data/input/TN_UT2.yaml b/test/data/input/TN_UT2.yaml index 9c4370d..236110d 100644 --- a/test/data/input/TN_UT2.yaml +++ b/test/data/input/TN_UT2.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: -- cgit v1.2.3