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-rw-r--r--wqflask/wqflask/interval_analyst/GeneUtil.py46
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py29
2 files changed, 49 insertions, 26 deletions
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index b1cfd0ee..1f9f329b 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -5,7 +5,23 @@ from wqflask.database import database_connection
# Just return a list of dictionaries
# each dictionary contains sub-dictionary
def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
- fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd',
+ assembly_map = {
+ "mouse": "mm10",
+ "rat": "rn7"
+ }
+
+ def append_assembly(fetch_fields, species):
+ query_fields = []
+ for field in fetch_fields:
+ if field in ['Chr', 'TxStart', 'TxEnd', 'Strand']:
+ query_fields.append(field + "_" + assembly_map[species])
+ else:
+ query_fields.append(field)
+
+ return query_fields
+
+
+ fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chr', 'TxStart', 'TxEnd',
'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID',
'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd']
@@ -19,18 +35,23 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
"GROUP BY GeneList081722.SpeciesId")
results = cursor.fetchall()
for item in results:
- speciesDict[item[0]] = item[1]
+ if item[0] == "rat":
+ speciesDict[item[0]] = (item[1], "rn7")
+ else:
+ speciesDict[item[0]] = (item[1], "mm10")
# List current Species and other Species
- speciesId = speciesDict[species]
- otherSpecies = [[X, speciesDict[X]] for X in list(speciesDict.keys())]
- otherSpecies.remove([species, speciesId])
- cursor.execute(f"SELECT {', '.join(fetchFields)} FROM GeneList081722 "
+ speciesId, assembly = speciesDict[species]
+ otherSpecies = [[X, speciesDict[X][0], speciesDict[X][1]] for X in list(speciesDict.keys())]
+ otherSpecies.remove([species, speciesId, assembly])
+ query_fields = append_assembly(fetchFields, species)
+
+ cursor.execute(f"SELECT {', '.join(query_fields)} FROM GeneList081722 "
"WHERE SpeciesId = %s AND "
- "Chromosome = %s AND "
- "((TxStart > %s and TxStart <= %s) "
- "OR (TxEnd > %s and TxEnd <= %s)) "
- "ORDER BY txStart",
+ f"Chr_{assembly}" + " = %s AND "
+ f"((TxStart_{assembly}" + " > %s and " + f"TxStart_{assembly}" + " <= %s) "
+ f"OR (TxEnd_{assembly}" + " > %s and " + f"TxEnd_{assembly}" + " <= %s)) "
+ f"ORDER BY TxStart_{assembly}",
(speciesId, chrName,
startMb, endMb,
startMb, endMb))
@@ -65,10 +86,11 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
pass
# load gene from other Species by the same name
for item in otherSpecies:
- othSpec, othSpecId = item
+ othSpec, othSpecId, othSpecAssembly = item
newdict2 = {}
+ query_fields = append_assembly(fetchFields, othSpec)
cursor.execute(
- f"SELECT {', '.join(fetchFields)} FROM GeneList081722 WHERE "
+ f"SELECT {', '.join(query_fields)} FROM GeneList081722 WHERE "
"SpeciesId = %s AND "
"geneSymbol= %s LIMIT 1",
(othSpecId,
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 1d59c694..baae95e0 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -1341,9 +1341,10 @@ class DisplayMappingResults:
tenPercentLength = geneLength * 0.0001
SNPdensity = theGO["snpCount"] / geneLength
- exonStarts = list(
- map(float, theGO['exonStarts'].split(",")[:-1]))
- exonEnds = list(map(float, theGO['exonEnds'].split(",")[:-1]))
+ if theGO['exonStarts']:
+ exonStarts = list(
+ map(float, theGO['exonStarts'].split(",")[:-1]))
+ exonEnds = list(map(float, theGO['exonEnds'].split(",")[:-1]))
cdsStart = theGO['cdsStart']
cdsEnd = theGO['cdsEnd']
accession = theGO['NM_ID']
@@ -2993,7 +2994,7 @@ class DisplayMappingResults:
if theGO["snpCount"]:
snpString = HT.Link(
(f"http://genenetwork.org/webqtl/main.py?FormID=snpBrowser&"
- f"chr={theGO['Chromosome']}&"
+ f"chr={theGO['Chr']}&"
f"start={theGO['TxStart']}&"
f"end={theGO['TxEnd']}&"
f"geneName={theGO['GeneSymbol']}&"
@@ -3006,17 +3007,17 @@ class DisplayMappingResults:
snpString = 0
mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm10&position=chr" + \
- theGO["Chromosome"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0)) + "-" + str(
+ theGO["Chr"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0)) + "-" + str(
int(theGO["TxEnd"] * 1000000.0)) + "&pix=620&Submit=submit"
# the chromosomes for human 1 are 1qXX.XX
- if theGO['humanGene']:
+ if 'humanGene' in theGO:
if theGO['humanGene']["TxStart"] == '':
humanStartDisplay = ""
else:
humanStartDisplay = "%0.6f" % theGO['humanGene']["TxStart"]
- humanChr = theGO['humanGene']["Chromosome"]
+ humanChr = theGO['humanGene']["Chr"]
humanTxStart = theGO['humanGene']["TxStart"]
humanStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg17&position=chr%s:%d-%d" % (
@@ -3040,10 +3041,10 @@ class DisplayMappingResults:
avgExpr = "%0.6f" % avgExpr
# If we have a referenceGene then we will show the Literature Correlation
- if theGO["Chromosome"] == "X":
+ if theGO["Chr"] == "X":
chr_as_int = 19
else:
- chr_as_int = int(theGO["Chromosome"]) - 1
+ chr_as_int = int(theGO["Chr"]) - 1
if refGene:
literatureCorrelationString = str(self.getLiteratureCorrelation(
self.cursor, refGene, theGO['GeneID']) or "N/A")
@@ -3122,13 +3123,13 @@ class DisplayMappingResults:
else:
geneSymbolNCBI = theGO["GeneSymbol"]
- if theGO["Chromosome"] == "X":
+ if theGO["Chr"] == "X":
chr_as_int = 20
else:
- chr_as_int = int(theGO["Chromosome"]) - 1
+ chr_as_int = int(theGO["Chr"]) - 1
geneLength = (float(theGO["TxEnd"]) - float(theGO["TxStart"]))
- geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float(
+ geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chr"], float(
theGO["TxStart"]) - (geneLength * 0.1), float(theGO["TxEnd"]) + (geneLength * 0.1))
avgExprVal = []
@@ -3139,14 +3140,14 @@ class DisplayMappingResults:
# Mouse Gene
if theGO['mouseGene']:
- mouseChr = theGO['mouseGene']["Chromosome"]
+ mouseChr = theGO['mouseGene']["Chr"]
mouseTxStart = "%0.6f" % theGO['mouseGene']["TxStart"]
else:
mouseChr = mouseTxStart = ""
# the chromosomes for human 1 are 1qXX.XX
if theGO['humanGene']:
- humanChr = theGO['humanGene']["Chromosome"]
+ humanChr = theGO['humanGene']["Chr"]
humanTxStart = "%0.6f" % theGO['humanGene']["TxStart"]
else:
humanChr = humanTxStart = ""
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-23 00:23:14 +0000