diff options
| -rw-r--r-- | wqflask/wqflask/interval_analyst/GeneUtil.py | 46 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 29 |
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 = "" |