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authorzsloan2022-12-21 18:56:43 +0000
committerzsloan2022-12-21 13:04:07 -0600
commit6bdbab327ac9a26517ef81a105c0ba5a8b0c360d (patch)
tree2d772a9a848ef19f441554b649d4cc99de298b4b
parente98e9aee54034bc2c3ab349fdda38ff6138ab09e (diff)
downloadgenenetwork2-6bdbab327ac9a26517ef81a105c0ba5a8b0c360d.tar.gz
Replace hard-coded homology source file
Remove limitation on when to show homology track
-rw-r--r--wqflask/wqflask/interval_analyst/GeneUtil.py6
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py7
2 files changed, 6 insertions, 7 deletions
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index 633cc9bf..5b28f458 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -2,11 +2,9 @@ import string
from wqflask.database import database_connection
-mm10_to_hg38_file = "/home/zas1024/gn2-zach/mm10_hg38_homology/mm10ToHg38_chain_only_sorted.csv"
-
-def load_homology(chr_name, start_mb, end_mb):
+def load_homology(chr_name, start_mb, end_mb, source_file):
homology_list = []
- with open(mm10_to_hg38_file) as h_file:
+ with open(source_file) as h_file:
current_chr = 0
for line in h_file:
line_items = line.split()
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 44067a5d..16eaee24 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -544,7 +544,8 @@ class DisplayMappingResults:
chrName = self.selectedChr
self.geneCol = GeneUtil.loadGenes(
str(chrName), self.diffCol, self.startMb, self.endMb, "mouse")
- self.homology = GeneUtil.load_homology(str(chrName), self.startMb, self.endMb)
+ self.homology = GeneUtil.load_homology(str(chrName), self.startMb, self.endMb, "mouse_to_human.csv")
+
elif self.dataset.group.species == "rat":
if self.selectedChr == 21:
chrName = "X"
@@ -586,7 +587,7 @@ class DisplayMappingResults:
(self.NR_INDIVIDUALS + 10) * self.EACH_GENE_HEIGHT
# END HaplotypeAnalyst
- if self.homologyChecked and self.homology and (self.endMb - self.startMb < 2) and self.geneChecked and self.geneCol:
+ if self.homologyChecked and self.homology and self.geneChecked and self.geneCol:
self.graphHeight = self.graphHeight + (self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT
if self.geneChecked and self.geneCol:
self.graphHeight = self.graphHeight + (self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT
@@ -739,7 +740,7 @@ class DisplayMappingResults:
if self.geneChecked and self.geneCol:
self.drawGeneBand(canvas, gifmap, plotXScale, offset=newoffset,
zoom=zoom, startMb=startMb, endMb=endMb)
- if self.homologyChecked and self.homology and (endMb - startMb < 2):
+ if self.homologyChecked and self.homology:
if self.geneChecked and self.geneCol:
yTopOffset = newoffset[3] + self.NUM_GENE_ROWS * \
self.EACH_GENE_HEIGHT + 3 * self.BAND_SPACING + 10