managed the assembly_method in the scripts, doc, and the example templates

8 files changed, 10 insertions, 0 deletions

diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org
index c98bf27..7336cf6 100644
--- a/doc/blog/using-covid-19-pubseq-part3.org
+++ b/doc/blog/using-covid-19-pubseq-part3.org
@@ -236,6 +236,7 @@ a more elaborate example (note most fields are optional) may look like
       sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0009173,http://www.ebi.ac.uk/efo/EFO_0009173]
       alignment_protocol: Protocol used for assembly
       sequencing_coverage: [70.0, 100.0]
+      assembly_method: "http://purl.obolibrary.org/obo/GENEPIO_0001628"
       additional_technology_information: Optional free text field for additional information
 
   submitter:
diff --git a/example/esr_example.yaml b/example/esr_example.yaml
index b3e97d5..693aff3 100644
--- a/example/esr_example.yaml
+++ b/example/esr_example.yaml
@@ -25,6 +25,7 @@ virus:
 technology:
     sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632] // Nanopore MinION
     alignment_protocol: https://github.com/ESR-NZ/NZ_SARS-CoV-2_genomics
+    assembly_method: "http://purl.obolibrary.org/obo/GENEPIO_0001628"
     additional_technology_information: "Artic V3 workflow"
 
 submitter:
diff --git a/example/uthsc_example.yaml b/example/uthsc_example.yaml
index 3bdbf6f..2384114 100644
--- a/example/uthsc_example.yaml
+++ b/example/uthsc_example.yaml
@@ -25,6 +25,7 @@ virus:
 technology:
     sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632] // Nanopore MinION
     alignment_protocol: guppy
+    assembly_method: "http://purl.obolibrary.org/obo/GENEPIO_0001628"
     additional_technology_information: Optional free text field for additional information
 
 submitter:
diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py
index 2aac0e5..554aea3 100644
--- a/scripts/create_sra_metadata/create_sra_metadata.py
+++ b/scripts/create_sra_metadata/create_sra_metadata.py
@@ -227,6 +227,8 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
     taxon_id = SAMPLE.find('SAMPLE_NAME').find('TAXON_ID').text
     info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_"+taxon_id
 
+    # This script download and prepare data and metadata for samples that will be mapepd againg a referenceT
+    info_for_yaml_dict['technology']['assembly_method'] = 'http://purl.obolibrary.org/obo/GENEPIO_0002028'
 
     EXPERIMENT = EXPERIMENT_PACKAGE.find('EXPERIMENT')
     INSTRUMENT_MODEL = [x.text for x in EXPERIMENT.find('PLATFORM').iter('INSTRUMENT_MODEL')][0]
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 87b348b..9a46474 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
@@ -179,6 +179,8 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
                         else:
                             info_for_yaml_dict['submitter']['additional_submitter_information'] = GBReference_journal.text
 
+            # This script download and prepare data and metadata for assemblies samples
+            info_for_yaml_dict['technology']['assembly_method'] = 'http://purl.obolibrary.org/obo/GENEPIO_0001628'
 
             GBSeq_comment = GBSeq.find('GBSeq_comment')
             if GBSeq_comment is not None and 'Assembly-Data' in GBSeq_comment.text:
diff --git a/scripts/esr_samples/template.yaml b/scripts/esr_samples/template.yaml
index 3ca1de3..3846122 100644
--- a/scripts/esr_samples/template.yaml
+++ b/scripts/esr_samples/template.yaml
@@ -15,6 +15,7 @@ virus:
 technology:
     sample_sequencing_technology: ["http://www.ebi.ac.uk/efo/EFO_0008632"]
     alignment_protocol: "https://github.com/ESR-NZ/NZ_SARS-CoV-2_genomics"
+    assembly_method: "http://purl.obolibrary.org/obo/GENEPIO_0001628"
     additional_technology_information: "Artic V3 workflow"
 
 submitter:
diff --git a/scripts/uthsc_samples/template.yaml b/scripts/uthsc_samples/template.yaml
index c81bd28..dab8634 100644
--- a/scripts/uthsc_samples/template.yaml
+++ b/scripts/uthsc_samples/template.yaml
@@ -23,6 +23,7 @@ virus:
 technology:
     sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632]
     alignment_protocol: https://bio.tools/BWA#!
+    assembly_method: "http://purl.obolibrary.org/obo/GENEPIO_0001628"
     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 236110d..f2f190b 100644
--- a/test/data/input/TN_UT2.yaml
+++ b/test/data/input/TN_UT2.yaml
@@ -23,6 +23,7 @@ virus:
 technology:
     sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632]
     alignment_protocol: https://bio.tools/BWA#!
+    assembly_method: "http://purl.obolibrary.org/obo/GENEPIO_0001628"
     additional_technology_information: Oxford Nanopore MiniIon RNA long reads
 
 submitter: