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-rw-r--r--wqflask/base/species.py83
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py81
-rw-r--r--wqflask/wqflask/views.py11
3 files changed, 119 insertions, 56 deletions
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 85f076ca..9d4cac4c 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -6,14 +6,17 @@ from flask import Flask, g
#from MySQLdb import escape_string as escape
+from utility import Bunch
+
from pprint import pformat as pf
class TheSpecies(object):
def __init__(self, dataset):
self.dataset = dataset
print("self.dataset is:", pf(self.dataset.__dict__))
- self.chromosomes = Chromosomes(self.dataset.group.name)
- self.genome_length = self.chromosomes.get_genome_length()
+ self.chromosomes = Chromosomes(self.dataset)
+ self.genome_mb_length = self.chromosomes.get_genome_mb_length()
+
#@property
#def chromosomes(self):
@@ -27,10 +30,22 @@ class TheSpecies(object):
#
# return chromosomes
+class IndChromosome(object):
+ def __init__(self, length):
+ self.length = length
+
+ @property
+ def mb_length(self):
+ """Chromosome length in megabases"""
+ return self.length / 1000000
+
+ def set_cm_length(self, genofile_chr):
+ self.cm_length = genofile_chr[-1].cM - genofile_chr[0].cM
class Chromosomes(object):
- def __init__(self, group_name):
+ def __init__(self, dataset):
+ self.dataset = dataset
self.chromosomes = collections.OrderedDict()
results = g.db.execute("""
@@ -40,27 +55,63 @@ class Chromosomes(object):
Chr_Length.SpeciesId = InbredSet.SpeciesId AND
InbredSet.Name = %s
Order by OrderId
- """, group_name).fetchall()
+ """, self.dataset.group.name).fetchall()
print("bike:", results)
for item in results:
- self.chromosomes[item.Name] = item.Length
+ self.chromosomes[item.Name] = IndChromosome(item.Length)
+
+ self.set_mb_graph_interval()
+ self.get_cm_length_list()
+
+
+ def set_mb_graph_interval(self):
+ """Empirical megabase interval"""
+
+ #if self.chromosomes:
+ assert self.chromosomes, "Have to add some code back in apparently to set it to 1"
+ self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12)
+ #else:
+ #self.mb_graph_interval = 1
- print("self.chromosomes:", self.chromosomes)
+ def get_genome_mb_length(self):
+ """Gets the sum of each chromosome's length in megabases"""
- def get_mb_length(self):
- """Gets the chromosome length in megabases"""
+ return sum([ind_chromosome.mb_length for ind_chromosome in self.chromosomes.values()])
- mb_lengths = chr_length/1000000.0 for name, chr_length in self.chromosomes
- return mb_lengths
+ def get_genome_cm_length(self):
+ """Gets the sum of each chromosome's length in centimorgans"""
- def get_genome_length(self):
- """Gets the sum of each chromosome's length"""
+ return sum([ind_chromosome.cm_length for ind_chromosome in self.chromosomes.values()])
- genome_length = 0
- for name, value in self.chromosomes.items():
- genome_length += value
+ def get_cm_length_list(self):
+ """Chromosome length in centimorgans
+
+ Calculates the length in centimorgans by subtracting the centimorgan position
+ of the last marker in a chromosome by the position of the first marker
+
+ """
+
+ self.dataset.group.read_genotype_file()
+
+ self.cm_length_list = []
+
+ for chromosome in self.dataset.group.genotype:
+ self.cm_length_list.append(chromosome[-1].cM - chromosome[0].cM)
+
+ print("self.cm_length_list:", pf(self.cm_length_list))
+
+ assert len(self.cm_length_list) == len(self.chromosomes), "Uh-oh lengths should be equal!"
+ for counter, chromosome in enumerate(self.chromosomes.values()):
+ chromosome.cm_length = self.cm_length_list[counter]
+ #self.chromosomes[counter].cm_length = item
+
+ for key, value in self.chromosomes.items():
+ print("bread - %s: %s" % (key, pf(vars(value))))
+
- return genome_length \ No newline at end of file
+# Testing
+#if __name__ == '__main__':
+# foo = dict(bar=dict(length)) \ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 0aad4e54..73f1246f 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -256,54 +256,58 @@ class MarkerRegression(object):
#for i, indChr in enumerate(self.genotype):
# self.ChrList.append((indChr.name, i))
- self.cursor.execute("""
- Select
- Length from Chr_Length, InbredSet
- where
- Chr_Length.SpeciesId = InbredSet.SpeciesId AND
- InbredSet.Name = '%s' AND
- Chr_Length.Name in (%s)
- Order by
- OrderId
- """ % (fd.RISet, string.join(map(lambda X: "'%s'" % X[0], self.ChrList[1:]), ", ")))
-
- self.ChrLengthMbList = self.cursor.fetchall()
- self.ChrLengthMbList = map(lambda x: x[0]/1000000.0, self.ChrLengthMbList)
- self.ChrLengthMbSum = reduce(lambda x, y:x+y, self.ChrLengthMbList, 0.0)
- if self.ChrLengthMbList:
- self.MbGraphInterval = self.ChrLengthMbSum/(len(self.ChrLengthMbList)*12) #Empirical Mb interval
- else:
- self.MbGraphInterval = 1
-
- self.ChrLengthCMList = []
- for i, _chr in enumerate(self.genotype):
- self.ChrLengthCMList.append(_chr[-1].cM - _chr[0].cM)
- self.ChrLengthCMSum = reduce(lambda x, y:x+y, self.ChrLengthCMList, 0.0)# used for calculate plot scale
+ #self.cursor.execute("""
+ # Select
+ # Length from Chr_Length, InbredSet
+ # where
+ # Chr_Length.SpeciesId = InbredSet.SpeciesId AND
+ # InbredSet.Name = '%s' AND
+ # Chr_Length.Name in (%s)
+ # Order by
+ # OrderId
+ # """ % (fd.RISet, string.join(map(lambda X: "'%s'" % X[0], self.ChrList[1:]), ", ")))
+ #
+ #self.ChrLengthMbList = self.cursor.fetchall()
+ #self.ChrLengthMbList = map(lambda x: x[0]/1000000.0, self.ChrLengthMbList)
+ #self.ChrLengthMbSum = reduce(lambda x, y:x+y, self.ChrLengthMbList, 0.0)
+ #if self.ChrLengthMbList:
+ # self.MbGraphInterval = self.ChrLengthMbSum/(len(self.ChrLengthMbList)*12) #Empirical Mb interval
+ #else:
+ # self.MbGraphInterval = 1
+ #
+ #self.ChrLengthCMList = []
+ #for i, _chr in enumerate(self.genotype):
+ # self.ChrLengthCMList.append(_chr[-1].cM - _chr[0].cM)
+ #self.ChrLengthCMSum = reduce(lambda x, y:x+y, self.ChrLengthCMList, 0.0)# used for calculate plot scale
- self.GraphInterval = self.MbGraphInterval #Mb
+ #self.GraphInterval = self.MbGraphInterval #Mb
# begin: common part with human data
- intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight))
- gifmap = self.plotIntMapping(fd, intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= "")
- filename= webqtlUtil.genRandStr("Itvl_")
- intCanvas.save(os.path.join(webqtlConfig.IMGDIR, filename), format='png')
- intImg=HT.Image('/image/'+filename+'.png', border=0, usemap='#WebQTLImageMap')
+ #intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight))
+ #gifmap = self.plotIntMapping(fd, intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= "")
+ #filename= webqtlUtil.genRandStr("Itvl_")
+ #intCanvas.save(os.path.join(webqtlConfig.IMGDIR, filename), format='png')
+ #intImg=HT.Image('/image/'+filename+'.png', border=0, usemap='#WebQTLImageMap')
################################################################
# footnote goes here
################################################################
- btminfo = HT.Paragraph(Id="smallsize") #Small('More information about this graph is available here.')
-
- if (self.additiveChecked):
- btminfo.append(HT.BR(), 'A positive additive coefficient (', HT.Font('green', color='green'), ' line) indicates that %s alleles increase trait values. In contrast, a negative additive coefficient (' % fd.ppolar, HT.Font('red', color='red'), ' line) indicates that %s alleles increase trait values.' % fd.mpolar)
+ #btminfo = HT.Paragraph(Id="smallsize") #Small('More information about this graph is available here.')
+ #if (self.additiveChecked):
+ # btminfo.append(HT.BR(), 'A positive additive coefficient (', HT.Font('green', color='green'), ' line) indicates that %s alleles increase trait values. In contrast, a negative additive coefficient (' % fd.ppolar, HT.Font('red', color='red'), ' line) indicates that %s alleles increase trait values.' % fd.mpolar)
- TD_LR = HT.TR(HT.TD(HT.Blockquote(gifmap,intImg, HT.P()), bgColor='#eeeeee', height = 200))
- self.dict['body'] = str(datadiv)+str(TD_LR)+str(resultstable)+str(HT.TR(HT.TD(descriptionTable)))
+ #TD_LR = HT.TR(HT.TD(HT.Blockquote(gifmap,intImg, HT.P()), bgColor='#eeeeee', height = 200))
+ #
+ #self.dict['body'] = str(datadiv)+str(TD_LR)+str(resultstable)+str(HT.TR(HT.TD(descriptionTable)))
# end: common part with human data
-
+
+ self.js_data = dict(
+ qtl_results = self.pure_qtl_results,
+ #lrs_array = vars(self.lrs_array),
+ )
@@ -467,7 +471,12 @@ class MarkerRegression(object):
filtered_results = self.qtl_results
else:
suggestive_results = []
+ self.pure_qtl_results = []
for result in self.qtl_results:
+ self.pure_qtl_results.append(dict(locus=dict(cM=result.locus.cM,
+ chromosome=result.locus.chr),
+ lrs=result.lrs,
+ additive=result.additive))
if result.lrs > self.lrs_thresholds.suggestive:
suggestive_results.append(result)
filtered_results = suggestive_results
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index f6c0dfb0..fc628d77 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -151,10 +151,10 @@ def show_trait_page():
def marker_regression_page():
template_vars = marker_regression.MarkerRegression(request.form)
#print("js_data before dump:", template_vars.js_data)
- #template_vars.js_data = json.dumps(template_vars.js_data,
- # default=json_default_handler,
- # indent=" ")
- #print("js_data after dump:", template_vars.js_data)
+ template_vars.js_data = json.dumps(template_vars.js_data,
+ default=json_default_handler,
+ indent=" ")
+ print("[dub] js_data after dump:", template_vars.js_data)
print("marker_regression template_vars:", pf(template_vars.__dict__))
return render_template("marker_regression.html", **template_vars.__dict__)
@@ -190,6 +190,9 @@ def json_default_handler(obj):
# Handle custom objects
if hasattr(obj, '__dict__'):
return obj.__dict__
+ #elif type(obj) == "Dataset":
+ # print("Not going to serialize Dataset")
+ # return None
else:
raise TypeError, 'Object of type %s with value of %s is not JSON serializable' % (
type(obj), repr(obj))