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authorzsloan2022-10-18 22:00:32 +0000
committerzsloan2022-10-18 22:00:32 +0000
commit060c50532161cfdbd61096ef02cdee614b886fbb (patch)
tree5877f9b2475f16d3706ca902574863babecbbedf
parentd8309bdbbbdca875fa042ee9bcd7dc6b40e2e9a7 (diff)
downloadgenenetwork2-060c50532161cfdbd61096ef02cdee614b886fbb.tar.gz
Change logic in retrieve_trait_info to account for situations where a marker doesn't have a position in the DB
-rw-r--r--wqflask/base/trait.py11
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: