diff options
| -rw-r--r-- | wqflask/utility/Plot.py | 10 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/SampleList.py | 19 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait.py | 63 |
3 files changed, 49 insertions, 43 deletions
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 372e0ac5..d60e2bb2 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -43,6 +43,8 @@ import svg import webqtlUtil from base import webqtlConfig +import utility.logger +logger = utility.logger.getLogger(__name__ ) def cformat(d, rank=0): 'custom string format' @@ -294,10 +296,10 @@ def find_outliers(vals): """ - print("xerxes vals is:", pf(vals)) + logger.debug("xerxes vals is:", pf(vals)) if vals: - #print("vals is:", pf(vals)) + #logger.debug("vals is:", pf(vals)) stats = corestats.Stats(vals) low_hinge = stats.percentile(25) up_hinge = stats.percentile(75) @@ -310,7 +312,7 @@ def find_outliers(vals): upper_bound = None lower_bound = None - print(pf(locals())) + logger.debug(pf(locals())) return upper_bound, lower_bound @@ -433,7 +435,7 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe canvas.drawCross(XCoord, plotHeight + yTopOffset - (catMean-Yll)*plotHeight/(Yur - Yll), \ color=pid.blue,size=3) - #print (catMean, catMedian, cat25per, cat75per) + #print(catMean, catMedian, cat25per, cat75per) pass XCoord += stepX diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 363b1efe..4f8f9e64 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -12,6 +12,9 @@ from pprint import pformat as pf import itertools +import utility.logger +logger = utility.logger.getLogger(__name__ ) + class SampleList(object): def __init__(self, dataset, @@ -29,7 +32,7 @@ class SampleList(object): self.sample_attribute_values = {} self.get_attributes() - print("camera: attributes are:", pf(self.attributes)) + logger.debug("camera: attributes are:", pf(self.attributes)) if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet': self.get_extra_attribute_values() @@ -41,7 +44,7 @@ class SampleList(object): try: sample = self.this_trait.data[sample_name] except KeyError: - print("No sample %s, let's create it now" % sample_name) + logger.debug("No sample %s, let's create it now" % sample_name) sample = webqtlCaseData.webqtlCaseData(sample_name) #sampleNameAdd = '' @@ -52,7 +55,7 @@ class SampleList(object): sample.extra_info['url'] = "/mouseCross.html#AXB/BXA" sample.extra_info['css_class'] = "fs12" - print(" type of sample:", type(sample)) + logger.debug(" type of sample:", type(sample)) if sample_group_type == 'primary': sample.this_id = "Primary_" + str(counter) @@ -62,17 +65,17 @@ class SampleList(object): #### For extra attribute columns; currently only used by several datasets - Zach if self.sample_attribute_values: sample.extra_attributes = self.sample_attribute_values.get(sample_name, {}) - print("sample.extra_attributes is", pf(sample.extra_attributes)) + logger.debug("sample.extra_attributes is", pf(sample.extra_attributes)) self.sample_list.append(sample) - print("self.attributes is", pf(self.attributes)) + logger.debug("self.attributes is", pf(self.attributes)) self.do_outliers() #do_outliers(the_samples) - print("*the_samples are [%i]: %s" % (len(self.sample_list), pf(self.sample_list))) + logger.debug("*the_samples are [%i]: %s" % (len(self.sample_list), pf(self.sample_list))) for sample in self.sample_list: - print("apple:", type(sample), sample) + logger.debug("apple:", type(sample), sample) #return the_samples def __repr__(self): @@ -105,7 +108,7 @@ class SampleList(object): self.attributes = {} for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name)): key, name = attr - print("radish: %s - %s" % (key, name)) + logger.debug("radish: %s - %s" % (key, name)) self.attributes[key] = Bunch() self.attributes[key].name = name self.attributes[key].distinct_values = [item.Value for item in values] diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 73acde22..a8ff0fdf 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -26,6 +26,9 @@ from pprint import pformat as pf from utility.tools import flat_files MAPPING_PATH = flat_files("mapping") +from utility.logger import getLogger +logger = getLogger(__name__ ) + ############################################### # # Todo: Put in security to ensure that user has permission to access confidential data sets @@ -36,7 +39,7 @@ MAPPING_PATH = flat_files("mapping") class ShowTrait(object): def __init__(self, kw): - print("in ShowTrait, kw are:", kw) + logger.debug("in ShowTrait, kw are:", kw) if kw['trait_id'] != None: self.temp_trait = False @@ -97,7 +100,7 @@ class ShowTrait(object): #Get nearest marker for composite mapping - print("self.dataset.type:", self.dataset.type) + logger.debug("self.dataset.type:", self.dataset.type) if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish": self.nearest_marker = get_nearest_marker(self.this_trait, self.dataset) #self.nearest_marker1 = get_nearest_marker(self.this_trait, self.dataset)[0] @@ -143,7 +146,7 @@ class ShowTrait(object): else: self.sample_group_types['samples_primary'] = self.dataset.group.name sample_lists = [group.sample_list for group in self.sample_groups] - print("sample_lists is:", pf(sample_lists)) + logger.debug("sample_lists is:", pf(sample_lists)) self.get_mapping_methods() @@ -204,7 +207,7 @@ class ShowTrait(object): except ValueError: return None - print("bottle samplelist is:", samplelist) + logger.debug("bottle samplelist is:", samplelist) if traitfiledata: tt = traitfiledata.split() values = map(webqtlUtil.StringAsFloat, tt) @@ -212,17 +215,17 @@ class ShowTrait(object): tt = traitpastedata.split() values = map(webqtlUtil.StringAsFloat, tt) else: - print("mapping formdataasfloat") + logger.debug("mapping formdataasfloat") #values = map(self.FormDataAsFloat, samplelist) values = [to_float(getattr(self, key)) for key in samplelist] - print("rocket values is:", values) + logger.debug("rocket values is:", values) if len(values) < len(samplelist): values += [None] * (len(samplelist) - len(values)) elif len(values) > len(samplelist): values = values[:len(samplelist)] - print("now values is:", values) + logger.debug("now values is:", values) if variancefiledata: @@ -253,7 +256,7 @@ class ShowTrait(object): if values[i] != None: self.allTraitData[_sample] = webqtlCaseData( _sample, values[i], variances[i], nsamples[i]) - print("allTraitData is:", pf(self.allTraitData)) + logger.debug("allTraitData is:", pf(self.allTraitData)) def dispTraitInformation(self, args, title1Body, hddn, this_trait): @@ -504,7 +507,7 @@ class ShowTrait(object): txst = int(txst*1000000) txen = int(txen*1000000) if self.species_name == "mouse": - print("this_trait.symbol:", this_trait.symbol) + logger.debug("this_trait.symbol:", this_trait.symbol) result = g.db.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = %s", (this_trait.symbol)).fetchone() if result != None: this_chr, txst, txen = result[0], result[1], result[2] @@ -752,14 +755,14 @@ class ShowTrait(object): primary_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_samples #XZ: note that fd.f1list and fd.parlist are added. all_samples = primary_samples + other_samples other_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + other_samples #XZ: note that fd.f1list and fd.parlist are added. - print("ac1") # This is the one used for first sall3 + logger.debug("ac1") # This is the one used for first sall3 self.MDP_menu.append(('All Cases','0')) self.MDP_menu.append(('%s Only' % fd.group, '1')) self.MDP_menu.append(('Non-%s Only' % fd.group, '2')) else: if (len(other_samples) > 0) and (len(primary_samples) + len(other_samples) > 3): - print("ac2") + logger.debug("ac2") self.MDP_menu.append(('All Cases','0')) self.MDP_menu.append(('%s Only' % fd.group,'1')) self.MDP_menu.append(('Non-%s Only' % fd.group,'2')) @@ -768,7 +771,7 @@ class ShowTrait(object): all_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + all_samples primary_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_samples else: - print("ac3") + logger.debug("ac3") all_samples = samplelist other_samples.sort(key=webqtlUtil.natsort_key) @@ -785,18 +788,18 @@ class ShowTrait(object): for sampleNameOrig in all_samples: sampleName = sampleNameOrig.replace("_2nd_", "") - print("* type of this_trait:", type(this_trait)) - print(" name:", this_trait.__class__.__name__) - print(" this_trait:", this_trait) - print(" type of this_trait.data[sampleName]:", type(this_trait.data[sampleName])) - print(" name:", this_trait.data[sampleName].__class__.__name__) - print(" this_trait.data[sampleName]:", this_trait.data[sampleName]) + logger.debug("* type of this_trait:", type(this_trait)) + logger.debug(" name:", this_trait.__class__.__name__) + logger.debug(" this_trait:", this_trait) + logger.debug(" type of this_trait.data[sampleName]:", type(this_trait.data[sampleName])) + logger.debug(" name:", this_trait.data[sampleName].__class__.__name__) + logger.debug(" this_trait.data[sampleName]:", this_trait.data[sampleName]) thisval = this_trait.data[sampleName].value - print(" thisval:", thisval) + logger.debug(" thisval:", thisval) thisvar = this_trait.data[sampleName].variance - print(" thisvar:", thisvar) + logger.debug(" thisvar:", thisvar) thisValFull = [sampleName, thisval, thisvar] - print(" thisValFull:", thisValFull) + logger.debug(" thisValFull:", thisValFull) vals1.append(thisValFull) @@ -1202,9 +1205,9 @@ class ShowTrait(object): this_trait=this_trait, sample_group_type='primary', header="%s Only" % (self.dataset.group.name)) - print("primary_samples is: ", pf(primary_samples)) + logger.debug("primary_samples is: ", pf(primary_samples)) - print("other_sample_names2:", other_sample_names) + logger.debug("other_sample_names2:", other_sample_names) if other_sample_names and self.dataset.group.species != "human": parent_f1_samples = None if self.dataset.group.parlist and self.dataset.group.f1list: @@ -1214,7 +1217,7 @@ class ShowTrait(object): if parent_f1_samples: other_sample_names = parent_f1_samples + other_sample_names - print("other_sample_names:", other_sample_names) + logger.debug("other_sample_names:", other_sample_names) other_samples = SampleList(dataset=self.dataset, sample_names=other_sample_names, @@ -1229,14 +1232,14 @@ class ShowTrait(object): #TODO: Figure out why this if statement is written this way - Zach #if (other_sample_names or (fd.f1list and this_trait.data.has_key(fd.f1list[0])) # or (fd.f1list and this_trait.data.has_key(fd.f1list[1]))): - # print("hjs") + # logger.debug("hjs") self.dataset.group.allsamples = all_samples_ordered def get_nearest_marker(this_trait, this_db): this_chr = this_trait.locus_chr - print("this_chr:", this_chr) + logger.debug("this_chr:", this_chr) this_mb = this_trait.locus_mb - print("this_mb:", this_mb) + logger.debug("this_mb:", this_mb) #One option is to take flanking markers, another is to take the two (or one) closest query = """SELECT Geno.Name FROM Geno, GenoXRef, GenoFreeze @@ -1245,10 +1248,10 @@ def get_nearest_marker(this_trait, this_db): GenoFreeze.Id = GenoXRef.GenoFreezeId AND GenoFreeze.Name = '{}' ORDER BY ABS( Geno.Mb - {}) LIMIT 1""".format(this_chr, this_db.group.name+"Geno", this_mb) - print("query:", query) + logger.debug("query:", query) result = g.db.execute(query).fetchall() - print("result:", result) + logger.debug("result:", result) if result == []: return "" @@ -1267,5 +1270,3 @@ def get_trait_table_width(sample_groups): table_width += len(sample_groups[0].attributes)*10 return table_width - - |