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| author | zsloan | 2022-10-18 22:00:32 +0000 |
|---|---|---|
| committer | zsloan | 2022-10-18 22:00:32 +0000 |
| commit | 060c50532161cfdbd61096ef02cdee614b886fbb (patch) | |
| tree | 5877f9b2475f16d3706ca902574863babecbbedf /wqflask/base/trait.py | |
| parent | d8309bdbbbdca875fa042ee9bcd7dc6b40e2e9a7 (diff) | |
| download | genenetwork2-060c50532161cfdbd61096ef02cdee614b886fbb.tar.gz | |
Change logic in retrieve_trait_info to account for situations where a marker doesn't have a position in the DB
Diffstat (limited to 'wqflask/base/trait.py')
| -rw-r--r-- | wqflask/base/trait.py | 11 |
1 files changed, 6 insertions, 5 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 781abf7a..6e835b45 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -550,7 +550,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): (trait.name, dataset.id,) ) trait_qtl = cursor.fetchone() - if trait_qtl: + if any(trait_qtl): trait.locus, trait.lrs, trait.pvalue, trait.mean, trait.additive = trait_qtl if trait.locus: cursor.execute( @@ -565,7 +565,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait.locus_chr = result[0] trait.locus_mb = result[1] else: - trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = "" + trait.locus_chr = trait.locus_mb = "" else: trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = "" @@ -597,9 +597,10 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = "" else: trait.locus = trait.lrs = trait.additive = "" - if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and str(trait.locus_chr or "") != "" and str(trait.locus_mb or "") != "": - trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % ( - trait.locus_chr, float(trait.locus_mb)) + if (dataset.type == 'Publish' or dataset.type == "ProbeSet"): + if str(trait.locus_chr or "") != "" and str(trait.locus_mb or "") != "": + trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % ( + trait.locus_chr, float(trait.locus_mb)) if str(trait.lrs or "") != "": trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs else: |