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-rwxr-xr-xscripts/maintenance/readProbeSetMean_v7.py20
-rwxr-xr-xscripts/maintenance/readProbeSetSE_v7.py14
-rw-r--r--wqflask/base/data_set.py2
-rw-r--r--wqflask/base/trait.py14
-rw-r--r--wqflask/utility/webqtlUtil.py4
-rw-r--r--wqflask/wqflask/external_tools/send_to_geneweaver.py2
-rw-r--r--wqflask/wqflask/external_tools/send_to_webgestalt.py2
-rw-r--r--wqflask/wqflask/interval_analyst/GeneUtil.py4
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py2
-rw-r--r--wqflask/wqflask/marker_regression/plink_mapping.py6
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py4
-rw-r--r--wqflask/wqflask/snp_browser/snp_browser.py12
12 files changed, 43 insertions, 43 deletions
diff --git a/scripts/maintenance/readProbeSetMean_v7.py b/scripts/maintenance/readProbeSetMean_v7.py
index a540796a..43f084f4 100755
--- a/scripts/maintenance/readProbeSetMean_v7.py
+++ b/scripts/maintenance/readProbeSetMean_v7.py
@@ -60,15 +60,15 @@ print('Checking if each line have same number of members')
GeneList = []
isCont = 1
header = fp.readline()
-header = string.split(string.strip(header), '\t')
-header = list(map(string.strip, header))
+header = header.strip().split('\t')
+header = [x.strip() for x in header]
nfield = len(header)
line = fp.readline()
kj = 0
while line:
- line2 = string.split(string.strip(line), '\t')
- line2 = list(map(string.strip, line2))
+ line2 = line.strip().split('\t')
+ line2 = [x.strip() for x in line2]
if len(line2) != nfield:
print(("Error : " + line))
isCont = 0
@@ -98,8 +98,8 @@ print('Checking if each strain exist in database')
isCont = 1
fp.seek(0)
header = fp.readline()
-header = string.split(string.strip(header), '\t')
-header = list(map(string.strip, header))
+header = header.strip().split('\t')
+header = [x.strip() for x in header]
header = list(map(translateAlias, header))
header = header[dataStart:]
Ids = []
@@ -126,8 +126,8 @@ print('Check if each ProbeSet exist in database')
##---- find PID is name or target ----##
line = fp.readline()
line = fp.readline()
-line2 = string.split(string.strip(line), '\t')
-line2 = list(map(string.strip, line2))
+line2 = line.strip().split('\t')
+line2 = [x.strip() for x in line2]
PId = line2[0]
db.execute('select Id from ProbeSet where Name="%s" and ChipId=%d' %
@@ -222,8 +222,8 @@ kj = 0
values1 = []
values2 = []
while line:
- line2 = string.split(string.strip(line), '\t')
- line2 = list(map(string.strip, line2))
+ line2 = line.strip().split('\t')
+ line2 = [x.strip() for x in line2]
PId = line2[0]
recordId = NameIds[PId]
diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py
index 20a846a4..edd9e7b0 100755
--- a/scripts/maintenance/readProbeSetSE_v7.py
+++ b/scripts/maintenance/readProbeSetSE_v7.py
@@ -71,14 +71,14 @@ print('Checking if each line have same number of members')
GeneList = []
isCont = 1
header = fp.readline()
-header = string.split(string.strip(header), '\t')
+header = header.strip().split('\t')
header = list(map(string.strip, header))
nfield = len(header)
line = fp.readline()
kj = 0
while line:
- line2 = string.split(string.strip(line), '\t')
+ line2 = line.strip().split('\t')
line2 = list(map(string.strip, line2))
if len(line2) != nfield:
isCont = 0
@@ -109,7 +109,7 @@ print('Checking if each strain exist in database')
isCont = 1
fp.seek(0)
header = fp.readline()
-header = string.split(string.strip(header), '\t')
+header = header.strip().split('\t')
header = list(map(string.strip, header))
header = list(map(translateAlias, header))
header = header[dataStart:]
@@ -137,8 +137,8 @@ print('Check if each ProbeSet exist in database')
##---- find PID is name or target ----##
line = fp.readline()
line = fp.readline()
-line2 = string.split(string.strip(line), '\t')
-line2 = list(map(string.strip, line2))
+line2 = line.strip().split('\t')
+line2 = [x.strip() for x in line2]
PId = line2[0]
db.execute('select Id from ProbeSet where Name="%s" and ChipId=%d' %
@@ -217,8 +217,8 @@ line = fp.readline()
kj = 0
while line:
- line2 = string.split(string.strip(line), '\t')
- line2 = list(map(string.strip, line2))
+ line2 = line.strip().split('\t')
+ line2 = [x.strip() for x in line2]
CellId = line2[0]
if CellId not in ProbeNameId:
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 8ac7a279..ce017fb4 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -697,7 +697,7 @@ class DataSet(object):
else:
query = "SELECT {}.Name,".format(escape(dataset_type))
data_start_pos = 1
- query += string.join(temp, ', ')
+ query += ', '.join(temp)
query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type,
self.type,
self.type))
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index b20efd2a..2fd5d725 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -150,8 +150,8 @@ class GeneralTrait(object):
alias = 'Not available'
if getattr(self, "alias", None):
- alias = string.replace(self.alias, ";", " ")
- alias = string.join(string.split(alias), ", ")
+ alias = self.alias.replace(";", " ")
+ alias = ", ".join(alias.split())
return alias
@@ -437,7 +437,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
#XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
# to avoid the problem of same marker name from different species.
elif dataset.type == 'Geno':
- display_fields_string = string.join(dataset.display_fields, ',Geno.')
+ display_fields_string = ',Geno.'.join(dataset.display_fields)
display_fields_string = 'Geno.' + display_fields_string
query = """
SELECT %s
@@ -456,8 +456,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
query = """SELECT %s FROM %s WHERE Name = %s"""
logger.sql(query)
trait_info = g.db.execute(query,
- (string.join(dataset.display_fields, ','),
- dataset.type, trait.name)).fetchone()
+ ','.join(dataset.display_fields),
+ dataset.type, trait.name).fetchone()
if trait_info:
trait.haveinfo = True
@@ -501,8 +501,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id
if dataset.type == 'ProbeSet' and dataset.group:
- description_string = str(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8')
- target_string = str(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
+ description_string = trait.description
+ target_string = trait.probe_target_description
if len(description_string) > 1 and description_string != 'None':
description_display = description_string
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index d4979011..5681fadf 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=list(map(string.strip, string.split(authorized_users, ',')))
- if AuthorizedUsersList.__contains__(userName):
+ AuthorizedUsersList=[x.strip() for x in authorized_users.split(',')]
+ if userName in AuthorizedUsersList:
access_to_confidential_phenotype_trait = 1
return access_to_confidential_phenotype_trait
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py
index 93164233..4c958a88 100644
--- a/wqflask/wqflask/external_tools/send_to_geneweaver.py
+++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py
@@ -55,7 +55,7 @@ class SendToGeneWeaver(object):
'client': "genenetwork",
'species': species_name,
'idtype': self.chip_name,
- 'list': string.join(trait_name_list, ","),
+ 'list': ",".join(trait_name_list),
}
def get_trait_name_list(trait_list):
diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py
index b255ba95..2f068792 100644
--- a/wqflask/wqflask/external_tools/send_to_webgestalt.py
+++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py
@@ -47,7 +47,7 @@ class SendToWebGestalt(object):
id_type = "entrezgene"
self.hidden_vars = {
- 'gene_list' : string.join(gene_id_list, "\n"),
+ 'gene_list' : "\n".join(gene_id_list),
'id_type' : "entrezgene",
'ref_set' : "genome",
'enriched_database_category' : "geneontology",
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index 17c8ccbf..d0dd7aea 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -31,7 +31,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
Chromosome = '%s' AND
((TxStart > %f and TxStart <= %f) OR (TxEnd > %f and TxEnd <= %f))
ORDER BY txStart
- """ % (string.join(fetchFields, ", "),
+ """ % (", ".join(fetchFields),
speciesId, chrName,
startMb, endMb,
startMb, endMb)).fetchall()
@@ -66,7 +66,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
othSpec, othSpecId = item
newdict2 = {}
- resultsOther = g.db.execute("SELECT %s FROM GeneList WHERE SpeciesId = %d AND geneSymbol= '%s' LIMIT 1" % (string.join(fetchFields, ", "),
+ resultsOther = g.db.execute("SELECT %s FROM GeneList WHERE SpeciesId = %d AND geneSymbol= '%s' LIMIT 1" % (", ".join(fetchFields),
othSpecId,
newdict["GeneSymbol"])).fetchone()
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index ccdafa14..dfaa1562 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -454,7 +454,7 @@ class DisplayMappingResults(object):
Chr_Length.Name in (%s)
Order by
Chr_Length.OrderId
- """ % (self.dataset.group.name, string.join(["'%s'" % X[0] for X in self.ChrList[1:]], ", ")))
+ """ % (self.dataset.group.name, ", ".join(["'%s'" % X[0] for X in self.ChrList[1:]])))
self.ChrLengthMbList = [x[0]/1000000.0 for x in self.ChrLengthMbList]
self.ChrLengthMbSum = reduce(lambda x, y:x+y, self.ChrLengthMbList, 0.0)
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index 2f282adc..6c38c34f 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -83,7 +83,7 @@ def get_samples_from_ped_file(dataset):
sample_list=[]
while line:
- lineList = string.split(string.strip(line), '\t')
+ lineList = line.strip().split('\t')
lineList = list(map(string.strip, lineList))
sample_name = lineList[0]
@@ -155,8 +155,8 @@ def parse_plink_output(output_filename, species):
# output: lineList list
#######################################################
def build_line_list(line=None):
- line_list = string.split(string.strip(line), ' ')# irregular number of whitespaces between columns
+ line_list = line.strip().split(' ')# irregular number of whitespaces between columns
line_list = [item for item in line_list if item !='']
line_list = list(map(string.strip, line_list))
- return line_list \ No newline at end of file
+ return line_list
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index e93b0289..88cd7dca 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -229,8 +229,8 @@ class ShowTrait(object):
hddn = OrderedDict()
if self.dataset.group.allsamples:
- hddn['allsamples'] = string.join(self.dataset.group.allsamples, ' ')
- hddn['primary_samples'] = string.join(self.primary_sample_names, ',')
+ hddn['allsamples'] = ''.join(self.dataset.group.allsamples)
+ hddn['primary_samples'] = ''.join(self.primary_sample_names)
hddn['trait_id'] = self.trait_id
hddn['trait_display_name'] = self.this_trait.display_name
hddn['dataset'] = self.dataset.name
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 0db7e1fe..2df71b12 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -456,7 +456,7 @@ class SnpBrowser(object):
function_list = []
if function_details:
- function_list = string.split(string.strip(function_details), ",")
+ function_list = function_details.strip().split(",")
function_list = list(map(string.strip, function_list))
function_list[0] = function_list[0].title()
function_details = ", ".join(item for item in function_list)
@@ -722,11 +722,11 @@ def get_effect_details_by_category(effect_name = None, effect_value = None):
new_codon_group_list = ['Start Gained']
codon_effect_group_list = ['Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous']
- effect_detail_list = string.split(string.strip(effect_value), '|')
+ effect_detail_list = effect_value.strip().split('|')
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 = item.strip().split(',')
item_list = list(map(string.strip, item_list))
gene_id = item_list[0]
@@ -746,13 +746,13 @@ def get_effect_details_by_category(effect_name = None, effect_value = None):
if effect_name in new_codon_group_list:
new_codon = item_list[6]
tmp_list = [biotype, new_codon]
- function_detail_list.append(string.join(tmp_list, ", "))
+ function_detail_list.append(", ".join(tmp_list))
elif effect_name in codon_effect_group_list:
old_new_AA = item_list[6]
old_new_codon = item_list[7]
codon_num = item_list[8]
tmp_list = [biotype, old_new_AA, old_new_codon, codon_num]
- function_detail_list.append(string.join(tmp_list, ", "))
+ function_detail_list.append(", ".join(tmp_list))
else:
function_detail_list.append(biotype)
@@ -852,7 +852,7 @@ def get_gene_id_name_dict(species_id, gene_name_list):
if len(gene_name_list) == 0:
return ""
gene_name_str_list = ["'" + gene_name + "'" for gene_name in gene_name_list]
- gene_name_str = string.join(gene_name_str_list, ",")
+ gene_name_str = ",".join(gene_name_str_list)
query = """
SELECT
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 14:44:35 +0000