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-rw-r--r--wqflask/maintenance/convert_geno_to_bimbam.py3
-rw-r--r--wqflask/maintenance/geno_to_json.py3
-rw-r--r--wqflask/utility/Plot.py2
-rw-r--r--wqflask/utility/tools.py3
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py25
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py66
-rw-r--r--wqflask/wqflask/snp_browser/snp_browser.py4
-rw-r--r--wqflask/wqflask/user_manager.py4
8 files changed, 59 insertions, 51 deletions
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index a1712500..a2ede1f9 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -21,7 +21,8 @@ import simplejson as json
from pprint import pformat as pf
-class EmptyConfigurations(Exception): pass
+class EmptyConfigurations(Exception):
+ pass
class Marker:
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index 7bdf2b53..76a0fc98 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -26,7 +26,8 @@ from pprint import pformat as pf
#from utility.tools import flat_files
-class EmptyConfigurations(Exception): pass
+class EmptyConfigurations(Exception):
+ pass
class Marker:
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 4f5691c1..00658d10 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -319,7 +319,7 @@ def colorSpectrum(n=100):
ImageColor.getrgb("rgb(0%,100%,0%)"),
ImageColor.getrgb("rgb(0%,0%,100%)")]
N = n * multiple
- out = [None] * N;
+ out = [None] * N
for i in range(N):
x = float(i) / N
out[i] = ImageColor.getrgb("rgb({}%,{}%,{}%".format(
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 263c3948..d82e478d 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -198,7 +198,8 @@ def locate(name, subdir=None):
return lookfor
else:
raise Exception("Can not locate " + lookfor)
- if subdir: sys.stderr.write(subdir)
+ if subdir:
+ sys.stderr.write(subdir)
raise Exception("Can not locate " + name + " in " + base)
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index cde822e8..8d0134d8 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -1343,13 +1343,13 @@ class DisplayMappingResults:
(float(txEnd) - startMb) # at least one pixel
if (geneEndPix < xLeftOffset):
- return; # this gene is not on the screen
+ return # this gene is not on the screen
elif (geneEndPix > xLeftOffset + plotWidth):
- geneEndPix = xLeftOffset + plotWidth; # clip the last in-range gene
+ geneEndPix = xLeftOffset + plotWidth # clip the last in-range gene
if (geneStartPix > xLeftOffset + plotWidth):
- return; # we are outside the valid on-screen range, so stop drawing genes
+ return # we are outside the valid on-screen range, so stop drawing genes
elif (geneStartPix < xLeftOffset):
- geneStartPix = xLeftOffset; # clip the first in-range gene
+ geneStartPix = xLeftOffset # clip the first in-range gene
# color the gene based on SNP density
# found earlier, needs to be recomputed as snps are added
@@ -1397,13 +1397,13 @@ class DisplayMappingResults:
(float(txEnd) - startMb) # at least one pixel
if (geneEndPix < xLeftOffset):
- return; # this gene is not on the screen
+ return # this gene is not on the screen
elif (geneEndPix > xLeftOffset + plotWidth):
- geneEndPix = xLeftOffset + plotWidth; # clip the last in-range gene
+ geneEndPix = xLeftOffset + plotWidth # clip the last in-range gene
if (geneStartPix > xLeftOffset + plotWidth):
- return; # we are outside the valid on-screen range, so stop drawing genes
+ return # we are outside the valid on-screen range, so stop drawing genes
elif (geneStartPix < xLeftOffset):
- geneStartPix = xLeftOffset; # clip the first in-range gene
+ geneStartPix = xLeftOffset # clip the first in-range gene
outlineColor = DARKBLUE
fillColor = DARKBLUE
@@ -1603,9 +1603,9 @@ class DisplayMappingResults:
drawit = 1
if (geneStartPix < xLeftOffset):
- drawit = 0;
+ drawit = 0
if (geneStartPix > xLeftOffset + plotWidth):
- drawit = 0;
+ drawit = 0
if drawit == 1:
if _chr[i].name != " - ":
@@ -1755,7 +1755,7 @@ class DisplayMappingResults:
geneYLocation + 17 + 2*maxind*self.EACH_GENE_HEIGHT*zoom),
fill=BLACK, angle=-90)
- oldgeneEndPix = geneEndPix;
+ oldgeneEndPix = geneEndPix
oldgeno = _chr[j].genotype
firstGene = 0
else:
@@ -3208,5 +3208,6 @@ class DisplayMappingResults:
if lCorr:
lCorr = lCorr[0]
break
- except: raise # lCorr = None
+ except:
+ raise # lCorr = None
return lCorr
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index c2b165a4..741d6c23 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -19,24 +19,24 @@ logger = utility.logger.getLogger(__name__)
def get_trait_data_type(trait_db_string):
- logger.info("get_trait_data_type");
+ logger.info("get_trait_data_type")
the_query = "SELECT value FROM TraitMetadata WHERE type='trait_data_type'"
- logger.info("the_query done");
+ logger.info("the_query done")
results_json = g.db.execute(the_query).fetchone()
- logger.info("the_query executed");
+ logger.info("the_query executed")
results_ob = json.loads(results_json[0])
- logger.info("json results loaded");
+ logger.info("json results loaded")
if trait_db_string in results_ob:
- logger.info("found");
+ logger.info("found")
return results_ob[trait_db_string]
else:
- logger.info("not found");
+ logger.info("not found")
return "numeric"
# Run qtl mapping using R/qtl
def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permCheck, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, pair_scan, cofactors):
- logger.info("Start run_rqtl_geno");
+ logger.info("Start run_rqtl_geno")
# Get pointers to some common R functions
r_library = ro.r["library"] # Map the library function
r_c = ro.r["c"] # Map the c function
@@ -46,7 +46,7 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
print((r_library("qtl"))) # Load R/qtl
- logger.info("QTL library loaded");
+ logger.info("QTL library loaded")
# Get pointers to some R/qtl functions
scanone = ro.r["scanone"] # Map the scanone function
@@ -75,29 +75,29 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
genofilelocation = locate(dataset.group.genofile, "genotype")
else:
genofilelocation = locate(dataset.group.name + ".geno", "genotype")
- logger.info("Going to create a cross from geno");
+ logger.info("Going to create a cross from geno")
# TODO: Add the SEX if that is available
cross_object = GENOtoCSVR(genofilelocation, crossfilelocation)
- logger.info("before calc_genoprob");
+ logger.info("before calc_genoprob")
if manhattan_plot:
cross_object = calc_genoprob(cross_object)
else:
cross_object = calc_genoprob(cross_object, step=5, stepwidth="max")
- logger.info("after calc_genoprob");
+ logger.info("after calc_genoprob")
pheno_string = sanitize_rqtl_phenotype(vals)
- logger.info("phenostring done");
+ logger.info("phenostring done")
names_string = sanitize_rqtl_names(samples)
- logger.info("sanitized pheno and names");
+ logger.info("sanitized pheno and names")
# Add the phenotype
cross_object = add_phenotype(cross_object, pheno_string, "the_pheno")
# Add the phenotype
cross_object = add_names(cross_object, names_string, "the_names")
- logger.info("Added pheno and names");
+ logger.info("Added pheno and names")
# Create the additive covariate markers
marker_covars = create_marker_covariates(control_marker, cross_object)
- logger.info("Marker covars done");
+ logger.info("Marker covars done")
if cofactors != "":
- logger.info("Cofactors: " + cofactors);
+ logger.info("Cofactors: " + cofactors)
# Create the covariates from selected traits
cross_object, trait_covars = add_cofactors(
cross_object, dataset, cofactors, samples)
@@ -108,10 +108,12 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
# DEBUG to save the session object to file
if pair_scan:
if do_control == "true":
- logger.info("Using covariate"); result_data_frame = scantwo(
+ logger.info("Using covariate")
+ result_data_frame = scantwo(
cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method, n_cluster = 16)
else:
- logger.info("No covariates"); result_data_frame = scantwo(
+ logger.info("No covariates")
+ result_data_frame = scantwo(
cross_object, pheno="the_pheno", model=model, method=method, n_cluster=16)
pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png"
@@ -122,11 +124,13 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
return process_pair_scan_results(result_data_frame)
else:
if do_control == "true" or cofactors != "":
- logger.info("Using covariate"); result_data_frame = scanone(
+ logger.info("Using covariate")
+ result_data_frame = scanone(
cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method)
ro.r('save.image(file = "/home/zas1024/gn2-zach/itp_cofactor_test.RData")')
else:
- logger.info("No covariates"); result_data_frame = scanone(
+ logger.info("No covariates")
+ result_data_frame = scanone(
cross_object, pheno="the_pheno", model=model, method=method)
# Do permutation (if requested by user)
@@ -275,18 +279,18 @@ def add_phenotype(cross, pheno_as_string, col_name):
def add_categorical_covar(cross, covar_as_string, i):
ro.globalenv["the_cross"] = cross
- logger.info("cross set");
+ logger.info("cross set")
ro.r('covar <- as.factor(' + covar_as_string + ')')
- logger.info("covar set");
+ logger.info("covar set")
ro.r('newcovar <- model.matrix(~covar-1)')
- logger.info("model.matrix finished");
+ logger.info("model.matrix finished")
ro.r('cat("new covar columns", ncol(newcovar), "\n")')
nCol = ro.r('ncol(newcovar)')
- logger.info("ncol covar done: " + str(nCol[0]));
+ logger.info("ncol covar done: " + str(nCol[0]))
ro.r('pheno <- data.frame(pull.pheno(the_cross))')
- logger.info("pheno pulled from cross");
+ logger.info("pheno pulled from cross")
nCol = int(nCol[0])
- logger.info("nCol python int:" + str(nCol));
+ logger.info("nCol python int:" + str(nCol))
col_names = []
# logger.info("loop")
for x in range(1, (nCol + 1)):
@@ -298,7 +302,7 @@ def add_categorical_covar(cross, covar_as_string, i):
col_names.append(col_name)
#logger.info("loop" + str(x) + "done");
- logger.info("returning from add_categorical_covar");
+ logger.info("returning from add_categorical_covar")
return ro.r["the_cross"], col_names
@@ -323,7 +327,7 @@ def add_cofactors(cross, this_dataset, covariates, samples):
covariate_list = covariates.split(",")
covar_name_string = "c("
for i, covariate in enumerate(covariate_list):
- logger.info("Covariate: " + covariate);
+ logger.info("Covariate: " + covariate)
this_covar_data = []
covar_as_string = "c("
trait_name = covariate.split(":")[0]
@@ -352,12 +356,12 @@ def add_cofactors(cross, this_dataset, covariates, samples):
covar_as_string += ")"
datatype = get_trait_data_type(covariate)
- logger.info("Covariate: " + covariate + " is of type: " + datatype);
+ logger.info("Covariate: " + covariate + " is of type: " + datatype)
if(datatype == "categorical"): # Cat variable
- logger.info("call of add_categorical_covar");
+ logger.info("call of add_categorical_covar")
cross, col_names = add_categorical_covar(
cross, covar_as_string, i) # Expand and add it to the cross
- logger.info("add_categorical_covar returned");
+ logger.info("add_categorical_covar returned")
# Go through the additional covar names
for z, col_name in enumerate(col_names):
if i < (len(covariate_list) - 1):
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 7fcbe984..e98cfb71 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -673,13 +673,13 @@ def get_browser_sample_lists(species_id=1):
strain_lists = {}
mouse_strain_list = []
query = "SHOW COLUMNS FROM SnpPattern;"
- results = g.db.execute(query).fetchall();
+ results = g.db.execute(query).fetchall()
for result in results[1:]:
mouse_strain_list.append(result[0])
rat_strain_list = []
query = "SHOW COLUMNS FROM RatSnpPattern;"
- results = g.db.execute(query).fetchall();
+ results = g.db.execute(query).fetchall()
for result in results[2:]:
rat_strain_list.append(result[0])
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 5610833b..9ebec405 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -765,10 +765,10 @@ class LoginUser:
user = None
valid = None
if user_details:
- user = model.User();
+ user = model.User()
for key in user_details:
user.__dict__[key] = user_details[key]
- valid = False;
+ valid = False
submitted_password = params['password']
pwfields = Struct(json.loads(user.password))
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 01:05:45 +0000