Goci 2607 tw remove bkgd trait links #3
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DSuveges
reviewed
May 3, 2019
| for line in file_data: | ||
| formatted_line = line.split('\t') | ||
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| study_accession = formatted_line[2].strip() |
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This line assumes this script will only be run on already published studies with accession IDs. If this assumption is correct there's nothing to do.
DSuveges
reviewed
May 3, 2019
| if delimiter in background_column: | ||
| background_column = background_column.split(delimiter) | ||
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| for background_trait in background_column: |
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I think this is unnecessary code duplication. You don't need to check if the delimiter is in the string or not.
string = 'acute graft vs. host disease || donor genotype effect measurement'
delimiter = '||'
for trait in string.split(delimiter):
print("Trait: {}".format(trait.strip()))
# Trait: acute graft vs. host disease
# Trait: donor genotype effect measurement
delimiter = '&&'
for trait in string.split(delimiter):
print("Trait: {}".format(trait.strip()))
# Trait: acute graft vs. host disease || donor genotype effect measurement Works both cases.
DSuveges
reviewed
May 3, 2019
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| for background_trait in background_column: | ||
| # Get the EFO_ID | ||
| background_trait_id = efo_map[background_trait.strip().lower()] |
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Just a suggestion: given the file is (more or less) manually created, I would add a test to check if the trait name is in the hash. But that's not particularly important.
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The script is written to remove rows from the STUDY_EFO_TRAIT table for traits the curators have marked as "background traits" in the provided data file (study_background_traits-ALL.txt).
This is to address: https://www.ebi.ac.uk/panda/jira/browse/GOCI-2607