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-rwxr-xr-xscripts/maintenance/QTL_Reaper_v6.py2
-rwxr-xr-xscripts/maintenance/readProbeSetMean_v7.py16
-rwxr-xr-xscripts/maintenance/readProbeSetSE_v7.py16
-rw-r--r--test/requests/link_checker.py3
-rw-r--r--wqflask/utility/webqtlUtil.py2
-rw-r--r--wqflask/wqflask/api/router.py2
-rw-r--r--wqflask/wqflask/correlation_matrix/show_corr_matrix.py4
-rw-r--r--wqflask/wqflask/export_traits.py2
-rw-r--r--wqflask/wqflask/interval_analyst/GeneUtil.py2
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py10
-rw-r--r--wqflask/wqflask/marker_regression/plink_mapping.py4
-rw-r--r--wqflask/wqflask/pbkdf2.py2
-rw-r--r--wqflask/wqflask/snp_browser/snp_browser.py6
13 files changed, 35 insertions, 36 deletions
diff --git a/scripts/maintenance/QTL_Reaper_v6.py b/scripts/maintenance/QTL_Reaper_v6.py
index 7fb56eca..2fbeb53b 100755
--- a/scripts/maintenance/QTL_Reaper_v6.py
+++ b/scripts/maintenance/QTL_Reaper_v6.py
@@ -23,7 +23,7 @@ for item in results:
ProbeSetFreezeIds=sys.argv[1:]
if ProbeSetFreezeIds:
#####convert the Ids to integer
- ProbeSetFreezeIds=map(int, ProbeSetFreezeIds)
+ ProbeSetFreezeIds=list(map(int, ProbeSetFreezeIds))
else:
#####get all of the dataset that need be updated
diff --git a/scripts/maintenance/readProbeSetMean_v7.py b/scripts/maintenance/readProbeSetMean_v7.py
index fea26731..97767715 100755
--- a/scripts/maintenance/readProbeSetMean_v7.py
+++ b/scripts/maintenance/readProbeSetMean_v7.py
@@ -61,14 +61,14 @@ GeneList = []
isCont = 1
header = fp.readline()
header = string.split(string.strip(header),'\t')
-header = map(string.strip, header)
+header = list(map(string.strip, header))
nfield = len(header)
line = fp.readline()
kj=0
while line:
line2 = string.split(string.strip(line),'\t')
- line2 = map(string.strip, line2)
+ line2 = list(map(string.strip, line2))
if len(line2) != nfield:
print(("Error : " + line))
isCont = 0
@@ -80,7 +80,7 @@ while line:
if kj%100000 == 0:
print(('checked ',kj,' lines'))
-GeneList = map(string.lower, GeneList)
+GeneList = list(map(string.lower, GeneList))
GeneList.sort()
if isCont==0:
@@ -100,8 +100,8 @@ isCont = 1
fp.seek(0)
header = fp.readline()
header = string.split(string.strip(header),'\t')
-header = map(string.strip, header)
-header = map(translateAlias, header)
+header = list(map(string.strip, header))
+header = list(map(translateAlias, header))
header = header[dataStart:]
Ids = []
for item in header:
@@ -128,7 +128,7 @@ print('Check if each ProbeSet exist in database')
line = fp.readline()
line = fp.readline()
line2 = string.split(string.strip(line),'\t')
-line2 = map(string.strip, line2)
+line2 = list(map(string.strip, line2))
PId = line2[0]
db.execute('select Id from ProbeSet where Name="%s" and ChipId=%d' % (PId, GeneChipId) )
@@ -148,7 +148,7 @@ for item in results:
print(Names)
-Names = map(string.lower, Names)
+Names = list(map(string.lower, Names))
Names.sort() # -- Fixed the lower case problem of ProbeSets affx-mur_b2_at doesn't exist --#
@@ -223,7 +223,7 @@ values1 = []
values2 = []
while line:
line2 = string.split(string.strip(line),'\t')
- line2 = map(string.strip, line2)
+ line2 = list(map(string.strip, line2))
PId = line2[0]
recordId = NameIds[PId]
diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py
index 79ed455f..7b2fee87 100755
--- a/scripts/maintenance/readProbeSetSE_v7.py
+++ b/scripts/maintenance/readProbeSetSE_v7.py
@@ -72,14 +72,14 @@ GeneList = []
isCont = 1
header = fp.readline()
header = string.split(string.strip(header), '\t')
-header = map(string.strip, header)
+header = list(map(string.strip, header))
nfield = len(header)
line = fp.readline()
kj = 0
while line:
line2 = string.split(string.strip(line), '\t')
- line2 = map(string.strip, line2)
+ line2 = list(map(string.strip, line2))
if len(line2) != nfield:
isCont = 0
print(("Error : " + line))
@@ -91,7 +91,7 @@ while line:
if kj % 100000 == 0:
print(('checked ', kj, ' lines'))
-GeneList = map(string.lower, GeneList)
+GeneList = list(map(string.lower, GeneList))
GeneList.sort()
if isCont == 0:
@@ -111,8 +111,8 @@ isCont = 1
fp.seek(0)
header = fp.readline()
header = string.split(string.strip(header), '\t')
-header = map(string.strip, header)
-header = map(translateAlias, header)
+header = list(map(string.strip, header))
+header = list(map(translateAlias, header))
header = header[dataStart:]
Ids = []
for item in header:
@@ -139,7 +139,7 @@ print('Check if each ProbeSet exist in database')
line = fp.readline()
line = fp.readline()
line2 = string.split(string.strip(line), '\t')
-line2 = map(string.strip, line2)
+line2 = list(map(string.strip, line2))
PId = line2[0]
db.execute('select Id from ProbeSet where Name="%s" and ChipId=%d' %
@@ -158,7 +158,7 @@ results = db.fetchall()
Names = []
for item in results:
Names.append(item[0])
- Names = map(string.lower, Names)
+ Names = list(map(string.lower, Names))
Names.sort() # -- Fixed the lower case problem of ProbeSets affx-mur_b2_at doesn't exist --#
##---- compare genelist with names ----##
@@ -220,7 +220,7 @@ line = fp.readline()
kj = 0
while line:
line2 = string.split(string.strip(line), '\t')
- line2 = map(string.strip, line2)
+ line2 = list(map(string.strip, line2))
CellId = line2[0]
if not ProbeNameId.has_key(CellId):
diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 715f330c..df4d32d8 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -27,8 +27,7 @@ def get_links(doc):
lambda x: not (
is_root_link(x)
or is_mailto_link(x))
- , map(lambda y: y.get("href")
- , doc.cssselect("a")))
+ , [y.get("href") for y in doc.cssselect("a")])
def verify_link(link):
if link[0] == "#":
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 53661ae4..79991149 100644
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -107,7 +107,7 @@ def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users)
if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']:
access_to_confidential_phenotype_trait = 1
else:
- AuthorizedUsersList=map(string.strip, string.split(authorized_users, ','))
+ AuthorizedUsersList=list(map(string.strip, string.split(authorized_users, ',')))
if AuthorizedUsersList.__contains__(userName):
access_to_confidential_phenotype_trait = 1
return access_to_confidential_phenotype_trait \ No newline at end of file
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index 6324cabe..3fa1d5ba 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -517,7 +517,7 @@ def all_sample_data(dataset_name, file_format = "csv"):
line_list.append("x")
results_list.append(line_list)
- results_list = map(list, zip(*results_list))
+ results_list = list(map(list, zip(*results_list)))
si = StringIO.StringIO()
csv_writer = csv.writer(si)
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 0ac94139..a912344f 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -278,7 +278,7 @@ def zScore(trait_data_array):
stdev = math.sqrt(var/(N-1))
if stdev == 0:
stdev = 1e-100
- data2 = map(lambda x:(x-mean)/stdev,data)
+ data2 = [(x-mean)/stdev for x in data]
trait_data_array[i] = data2
i += 1
return trait_data_array
@@ -299,7 +299,7 @@ def sortEigenVectors(vector):
A.append(item[0])
B.append(item[1])
sum = reduce(lambda x,y: x+y, A, 0.0)
- A = map(lambda x:x*100.0/sum, A)
+ A = [x*100.0/sum for x in A]
return [A, B]
except:
return [] \ No newline at end of file
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index 3272c03d..6646cc36 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -122,7 +122,7 @@ def export_search_results_csv(targs):
csv_rows.append(row_contents)
- csv_rows = map(list, itertools.izip_longest(*[row for row in csv_rows]))
+ csv_rows = list(map(list, itertools.izip_longest(*[row for row in csv_rows])))
writer.writerows(csv_rows)
csv_data = buff.getvalue()
buff.close()
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index 2c60dd70..273168a8 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -24,7 +24,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
##List current Species and other Species
speciesId = speciesDict[species]
- otherSpecies = map(lambda X: [X, speciesDict[X]], speciesDict.keys())
+ otherSpecies = [[X, speciesDict[X]] for X in speciesDict.keys()]
otherSpecies.remove([species, speciesId])
results = g.db.execute("""
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index bda899fb..7b6e70d2 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -389,9 +389,9 @@ class DisplayMappingResults(object):
Chr_Length.Name in (%s)
Order by
Chr_Length.OrderId
- """ % (self.dataset.group.name, string.join(map(lambda X: "'%s'" % X[0], self.ChrList[1:]), ", ")))
+ """ % (self.dataset.group.name, string.join(["'%s'" % X[0] for X in self.ChrList[1:]], ", ")))
- self.ChrLengthMbList = map(lambda x: x[0]/1000000.0, self.ChrLengthMbList)
+ self.ChrLengthMbList = [x[0]/1000000.0 for x in 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
@@ -1147,8 +1147,8 @@ class DisplayMappingResults(object):
tenPercentLength = geneLength*0.0001
SNPdensity = theGO["snpCount"]/geneLength
- exonStarts = map(float, theGO['exonStarts'].split(",")[:-1])
- exonEnds = map(float, theGO['exonEnds'].split(",")[:-1])
+ 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']
@@ -2145,7 +2145,7 @@ class DisplayMappingResults(object):
lrsEdgeWidth = 1
else:
if self.additiveChecked:
- additiveMax = max(map(lambda X : abs(X['additive']), self.qtlresults))
+ additiveMax = max([abs(X['additive']) for X in self.qtlresults])
lrsEdgeWidth = 3
if zoom == 2:
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index 2f327faf..9571015e 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -84,7 +84,7 @@ def get_samples_from_ped_file(dataset):
while line:
lineList = string.split(string.strip(line), '\t')
- lineList = map(string.strip, lineList)
+ lineList = list(map(string.strip, lineList))
sample_name = lineList[0]
sample_list.append(sample_name)
@@ -157,6 +157,6 @@ def parse_plink_output(output_filename, species):
def build_line_list(line=None):
line_list = string.split(string.strip(line),' ')# irregular number of whitespaces between columns
line_list = [item for item in line_list if item <>'']
- line_list = map(string.strip, line_list)
+ line_list = list(map(string.strip, line_list))
return line_list \ No newline at end of file
diff --git a/wqflask/wqflask/pbkdf2.py b/wqflask/wqflask/pbkdf2.py
index 811c83b0..731c8843 100644
--- a/wqflask/wqflask/pbkdf2.py
+++ b/wqflask/wqflask/pbkdf2.py
@@ -66,7 +66,7 @@ def pbkdf2_bin(data, salt, iterations=1000, keylen=24, hashfunc=None):
def _pseudorandom(x, mac=mac):
h = mac.copy()
h.update(x)
- return map(ord, h.digest())
+ return list(map(ord, h.digest()))
buf = []
for block in xrange(1, -(-keylen // mac.digest_size) + 1):
rv = u = _pseudorandom(salt + _pack_int(block))
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 1d28d76a..b18bfc62 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -459,7 +459,7 @@ class SnpBrowser(object):
function_list = []
if function_details:
function_list = string.split(string.strip(function_details), ",")
- function_list = map(string.strip, function_list)
+ function_list = list(map(string.strip, function_list))
function_list[0] = function_list[0].title()
function_details = ", ".join(item for item in function_list)
function_details = function_details.replace("_", " ")
@@ -725,11 +725,11 @@ def get_effect_details_by_category(effect_name = None, effect_value = None):
codon_effect_group_list = ['Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous']
effect_detail_list = string.split(string.strip(effect_value), '|')
- effect_detail_list = map(string.strip, effect_detail_list)
+ effect_detail_list = list(map(string.strip, effect_detail_list))
for index, item in enumerate(effect_detail_list):
item_list = string.split(string.strip(item), ',')
- item_list = map(string.strip, item_list)
+ item_list = list(map(string.strip, item_list))
gene_id = item_list[0]
gene_name = item_list[1]
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 09:47:40 +0000