def bxd_probesets_locus(locus, inbredsetid):
#
file = open('probesets_%s.txt' % (locus), 'w+')
file.write("GN Dataset ID\t")
file.write("Dataset Full Name\t")
file.write("ProbeSet Name\t")
file.write("Symbol\t")
file.write("ProbeSet Description\t")
file.write("Probe Target Description\t")
file.write("ProbeSet Chr\t")
file.write("ProbeSet Mb\t")
file.write("Mean\t")
file.write("LRS\t")
file.write("Geno Chr\t")
file.write("Geno Mb\t")
file.write("\n")
file.flush()
#
results = probesets.get_normalized_probeset(locus=locus, inbredsetid=inbredsetid)
for row in results:
file.write("%s\t" % (row[0]))
file.write("%s\t" % (utilities.clearspaces(row[2], default='')))
file.write("%s\t" % (utilities.clearspaces(row[3], default='')))
file.write("%s\t" % (utilities.clearspaces(row[4], default='')))
file.write("%s\t" % (utilities.clearspaces(row[5], default='')))
file.write("%s\t" % (utilities.clearspaces(row[6], default='')))
file.write("%s\t" % (utilities.clearspaces(row[7], default='')))
file.write("%s\t" % (row[8]))
file.write("%s\t" % (row[9]))
file.write("%s\t" % (row[10]))
file.write("%s\t" % (utilities.clearspaces(row[11], default='')))
file.write("%s\t" % (row[12]))
file.write('\n')
file.flush()
file.close()
def fetch(inbredsetid, filename):
# parameters
phenotypesfile = open(filename, 'w+')
#
phenotypesfile.write("id\tAuthors\tOriginal_description\tPre_publication_description\tPost_publication_description\t")
# open db
cursor, con = utilities.get_cursor()
# get strain list
strains = []
sql = """
SELECT Strain.`Name`
FROM StrainXRef, Strain
WHERE StrainXRef.`StrainId`=Strain.`Id`
AND StrainXRef.`InbredSetId`=%s
ORDER BY StrainXRef.`OrderId`
"""
cursor.execute(sql, (inbredsetid))
results = cursor.fetchall()
for row in results:
strain = row[0]
strain = strain.lower()
strains.append(strain)
print "get %d strains: %s" % (len(strains), strains)
phenotypesfile.write('\t'.join([strain.upper() for strain in strains]))
phenotypesfile.write('\n')
phenotypesfile.flush()
# phenotypes
sql = """
SELECT PublishXRef.`Id`, Publication.`Authors`, Phenotype.`Original_description`, Phenotype.`Pre_publication_description`, Phenotype.`Post_publication_description`
FROM (PublishXRef, Phenotype, Publication)
WHERE PublishXRef.`InbredSetId`=%s
AND PublishXRef.`PhenotypeId`=Phenotype.`Id`
AND PublishXRef.`PublicationId`=Publication.`Id`
"""
cursor.execute(sql, (inbredsetid))
results = cursor.fetchall()
print "get %d phenotypes" % (len(results))
for phenotyperow in results:
publishxrefid = phenotyperow[0]
authors = utilities.clearspaces(phenotyperow[1])
original_description = utilities.clearspaces(phenotyperow[2])
pre_publication_description = utilities.clearspaces(phenotyperow[3])
post_publication_description = utilities.clearspaces(phenotyperow[4])
phenotypesfile.write("%s\t%s\t%s\t%s\t%s\t" % (publishxrefid, authors, original_description, pre_publication_description, post_publication_description))
sql = """
SELECT Strain.Name, PublishData.value
FROM (PublishXRef, PublishData, Strain)
WHERE PublishXRef.`InbredSetId`=%s
AND PublishXRef.Id=%s
AND PublishXRef.DataId=PublishData.Id
AND PublishData.StrainId=Strain.Id
"""
cursor.execute(sql, (inbredsetid, publishxrefid))
results = cursor.fetchall()
print "get %d values" % (len(results))
strainvaluedic = {}
for strainvalue in results:
strainname = strainvalue[0]
strainname = strainname.lower()
value = strainvalue[1]
strainvaluedic[strainname] = value
for strain in strains:
if strain in strainvaluedic:
phenotypesfile.write(str(strainvaluedic[strain]))
else:
phenotypesfile.write('x')
phenotypesfile.write('\t')
phenotypesfile.write('\n')
phenotypesfile.flush()
# release
phenotypesfile.close()
