HGNC ROBOT template

- Update: Refactor method to do this from ShellScript / awk to Python / pandas.
- Update: Now sorts columns

General
- Update: .gitignore: Simplified ignores for files at root.
- Add: Utility function to handle < > around URIs

.github/workflows/buid_and_release.yml

@@ -40,4 +40,4 @@ jobs:
         files: |
           omim.owl
           omim.sssom.tsv
-          mondo_genes.robot.tsv
+          mondo-omim-genes.robot.tsv

.gitignore

@@ -26,12 +26,8 @@ allelicVariants.txt
 allelicVariants.tsv
 
 # Outputs
-omim.ttl
-omim.sssom.tsv
-omim.sssom.log.txt
-omim.json
-*.sssom.owl
-mondo_exactmatch_omim.sssom.tsv
-mondo_exactmatch_omimps.sssom.tsv
-omim.owl
-mondo_genes.robot.tsv
+/*.json
+/*.owl
+/*.tsv
+/*.ttl
+/*.txt

makefile

@@ -2,7 +2,7 @@
 
 
 # MAIN COMMANDS / GOALS ------------------------------------------------------------------------------------------------
-all: omim.ttl omim.sssom.tsv omim.owl mondo_genes.robot.tsv
+all: omim.ttl omim.sssom.tsv omim.owl mondo-omim-genes.robot.tsv
 
 # build: Create new omim.ttl
 omim.ttl:
@@ -35,18 +35,13 @@ omim.owl: omim.ttl mondo_exactmatch_omim.sssom.owl mondo_exactmatch_omimps.sssom
 		query --update sparql/hgnc_links.ru \
 		convert -f ofn -o $@
 
-mondo_genes.robot.tsv: omim.owl
-	# Create a TSV of relational information for gene and disease classes
-	robot query -i omim.owl --query sparql/mondo_genes.sparql $@
-	# Insert the source_code column as the second to last column
-	awk 'BEGIN {FS=OFS="\t"} {if (NR==1) {$$(NF+1)=$$(NF); $$(NF-1)="?source_code";} else {$$(NF+1)=$$(NF); $$(NF-1)="MONDO:OMIM";}} 1' $@ > temp_file && mv temp_file $@
-	# Remove the first character, a question mark (?), from each field in the header. This is an artefact of the SPARQL query.
-	awk 'BEGIN {FS=OFS="\t"} NR==1 {for (i=1; i<=NF; i++) $$i=substr($$i, 2)} {print}' $@ > temp_file && mv temp_file $@
-	# Remove < and > characters from specified columns
-	awk 'BEGIN {FS=OFS="\t"} NR>1 {gsub(/^<|>$$/, "", $$1); gsub(/^<|>$$/, "", $$2); gsub(/^<|>$$/, "", $$5)} {print}' $@ > temp_file && mv temp_file $@
-	# Insert ROBOT subheader
-	robot_subheader="ID\tSC 'has material basis in germline mutation in' some %\t>A oboInOwl:source\t>A oboInOwl:source\t" && \
-	sed 1a"$$robot_subheader" $@ > temp_file && mv temp_file $@
+# Create a TSV of relational information for gene and disease classes
+mondo-omim-genes.tsv: omim.owl
+	robot query -i omim.owl --query sparql/mondo-omim-genes.sparql $@
+
+# Create a TSV of relational information for gene and disease classes, as a ROBOT template
+mondo-omim-genes.robot.tsv: mondo-omim-genes.tsv
+	python -m omim2obo.mondo_omim_genes_robot_tsv --inpath $< --outpath $@
 
 cleanup:
 	@rm -f omim.json

omim2obo/mondo_omim_genes_robot_tsv.py

@@ -0,0 +1,64 @@
+"""Create: ROBOT template of Mondo and OMIM gene relations: relational information for gene and disease classes"""
+from argparse import ArgumentParser
+from pathlib import Path
+from typing import Dict, Union
+
+import pandas as pd
+
+from omim2obo.utils.utils import remove_angle_brackets
+
+
+ROBOT_SUBHEADER = {
+    'mondo_id': 'ID',
+    'hgnc_id': "SC 'has material basis in germline mutation in' some %",
+    'omim_disease_xref': '>A oboInOwl:source',
+    'source_code': '>A oboInOwl:source',
+    'omim_gene': '',
+}
+
+
+def mondo_omim_genes_robot_tsv(inpath: Union[Path, str], outpath: Union[Path, str]) -> pd.DataFrame:
+    """Create: ROBOT template of Mondo and OMIM gene relations"""
+    df = pd.read_csv(inpath, sep='\t')
+
+    # Remove the first character, a question mark (?), from each field in the header; an artefact of the SPARQL query.
+    df.rename(columns={col: col[1:] for col in df.columns if col.startswith('?')}, inplace=True)
+
+    # Add source_code column
+    df['source_code'] = 'MONDO:OMIM'
+
+    # Remove < and > characters from specified columns
+    uri_cols = ['mondo_id', 'hgnc_id', 'omim_gene']
+    for col in uri_cols:
+        df[col] = remove_angle_brackets(list(df[col]))
+
+    # Insert ROBOT subheader
+    df = pd.concat([pd.DataFrame([ROBOT_SUBHEADER]), df])
+
+    # Format col order
+    df = df[['mondo_id', 'hgnc_id', 'omim_disease_xref', 'source_code', 'omim_gene']]
+
+    # Sort
+    df = df.sort_values(by=['mondo_id', 'hgnc_id', 'omim_gene', 'omim_disease_xref'])
+
+    df.to_csv(outpath, sep='\t', index=False)
+    return pd.DataFrame()
+
+
+def cli():
+    """Command line interface."""
+    parser = ArgumentParser(
+        prog='mondo-genes-robot-tsv',
+        description='Create a ROBOT template TSV of relational information for gene and disease classes')
+    parser.add_argument(
+        '-i', '--inpath', required=True,
+        help='Path to file with such relational information, but not yet formatted as a ROBOT template.')
+    parser.add_argument(
+        '-o', '--outpath', required=True,
+        help='Path to save output.')
+    d: Dict = vars(parser.parse_args())
+    mondo_omim_genes_robot_tsv(**d)
+
+
+if __name__ == '__main__':
+    cli()

omim2obo/utils/utils.py

@@ -0,0 +1,16 @@
+"""Misc utilities"""
+from typing import List, Union
+
+
+# todo: also in mondo-ingest. Refactor into mondolib: https://github.com/monarch-initiative/mondolib/issues/13
+def remove_angle_brackets(uris: Union[str, List[str]]) -> Union[str, List[str]]:
+    """Remove angle brackets from URIs, e.g.:
+    <https://omim.org/entry/100050> --> https://omim.org/entry/100050"""
+    str_input = isinstance(uris, str)
+    uris = [uris] if str_input else uris
+    uris2 = []
+    for x in uris:
+        x = x[1:] if x.startswith('<') else x
+        x = x[:-1] if x.endswith('>') else x
+        uris2.append(x)
+    return uris2[0] if str_input else uris2