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-rw-r--r--wqflask/maintenance/geno_to_json.py12
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py26
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py64
-rw-r--r--wqflask/utility/Plot.py98
-rw-r--r--wqflask/utility/__init__.py2
-rw-r--r--wqflask/utility/genofile_parser.py150
-rw-r--r--wqflask/utility/tools.py2
-rw-r--r--wqflask/wqflask/collect.py12
-rw-r--r--wqflask/wqflask/correlation_matrix/show_corr_matrix.py4
-rw-r--r--wqflask/wqflask/ctl/ctl_analysis.py88
-rw-r--r--wqflask/wqflask/group_manager.py238
-rw-r--r--wqflask/wqflask/gsearch.py14
-rw-r--r--wqflask/wqflask/interval_analyst/GeneUtil.py130
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py44
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py14
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py352
-rw-r--r--wqflask/wqflask/model.py2
-rw-r--r--wqflask/wqflask/search_results.py2
-rw-r--r--wqflask/wqflask/user_login.py70
19 files changed, 662 insertions, 662 deletions
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index 27eb6553..c74489a8 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -113,13 +113,13 @@ class ConvertGenoFile:
with open(self.output_file, 'w') as fh:
json.dump(self.markers, fh, indent=" ", sort_keys=True)
- # print('configurations:', str(configurations))
- #self.latest_col_pos = item_count + self.skipped_cols
- #self.latest_col_value = item
+ # print('configurations:', str(configurations))
+ #self.latest_col_pos = item_count + self.skipped_cols
+ #self.latest_col_value = item
- # if item_count != 0:
- # self.output_fh.write(" ")
- # self.output_fh.write(self.configurations[item.upper()])
+ # if item_count != 0:
+ # self.output_fh.write(" ")
+ # self.output_fh.write(self.configurations[item.upper()])
# self.output_fh.write("\n")
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
index 1198740d..47377873 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
@@ -7,17 +7,17 @@ from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file
class TestQtlReaperMapping(unittest.TestCase):
- @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data")
- def test_gen_pheno_txt_file(self):
- vals = ["V1", "x", "V4", "V3","x"]
- samples = ["S1", "S2", "S3", "S4","S5"]
- trait_filename = "trait_file"
- with mock.patch("builtins.open", mock.mock_open())as mock_open:
- gen_pheno_txt_file(samples=samples, vals=vals,
- trait_filename=trait_filename)
- mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt", "w")
- filehandler = mock_open()
- write_calls = [mock.call('Trait\t'), mock.call(
- 'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')]
+ @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data")
+ def test_gen_pheno_txt_file(self):
+ vals = ["V1", "x", "V4", "V3","x"]
+ samples = ["S1", "S2", "S3", "S4","S5"]
+ trait_filename = "trait_file"
+ with mock.patch("builtins.open", mock.mock_open())as mock_open:
+ gen_pheno_txt_file(samples=samples, vals=vals,
+ trait_filename=trait_filename)
+ mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt", "w")
+ filehandler = mock_open()
+ write_calls = [mock.call('Trait\t'), mock.call(
+ 'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')]
- filehandler.write.assert_has_calls(write_calls)
+ filehandler.write.assert_has_calls(write_calls)
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
index d69a20d3..e518ec22 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -8,35 +8,35 @@ from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names
class TestRqtlMapping(unittest.TestCase):
- def setUp(self):
- self.app_context = app.app_context()
- self.app_context.push()
-
- def tearDown(self):
- self.app_context.pop()
-
- @mock.patch("wqflask.marker_regression.rqtl_mapping.g")
- @mock.patch("wqflask.marker_regression.rqtl_mapping.logger")
- def test_get_trait_data(self, mock_logger, mock_db):
- """test for getting trait data_type return True"""
- query_value = """SELECT value FROM TraitMetadata WHERE type='trait_data_type'"""
- mock_db.db.execute.return_value.fetchone.return_value = [
- """{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""]
- results = get_trait_data_type("traid_id")
- mock_db.db.execute.assert_called_with(query_value)
- self.assertEqual(results, "fer434f")
-
- def test_sanitize_rqtl_phenotype(self):
- """test for sanitizing rqtl phenotype"""
- vals = ['f', "x", "r", "x","x"]
- results = sanitize_rqtl_phenotype(vals)
- expected_phenotype_string = 'c(f,NA,r,NA,NA)'
-
- self.assertEqual(results, expected_phenotype_string)
-
- def test_sanitize_rqtl_names(self):
- """test for sanitzing rqtl names"""
- vals = ['f', "x", "r", "x","x"]
- expected_sanitized_name = "c('f',NA,'r',NA,NA)"
- results = sanitize_rqtl_names(vals)
- self.assertEqual(expected_sanitized_name, results)
+ def setUp(self):
+ self.app_context = app.app_context()
+ self.app_context.push()
+
+ def tearDown(self):
+ self.app_context.pop()
+
+ @mock.patch("wqflask.marker_regression.rqtl_mapping.g")
+ @mock.patch("wqflask.marker_regression.rqtl_mapping.logger")
+ def test_get_trait_data(self, mock_logger, mock_db):
+ """test for getting trait data_type return True"""
+ query_value = """SELECT value FROM TraitMetadata WHERE type='trait_data_type'"""
+ mock_db.db.execute.return_value.fetchone.return_value = [
+ """{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""]
+ results = get_trait_data_type("traid_id")
+ mock_db.db.execute.assert_called_with(query_value)
+ self.assertEqual(results, "fer434f")
+
+ def test_sanitize_rqtl_phenotype(self):
+ """test for sanitizing rqtl phenotype"""
+ vals = ['f', "x", "r", "x","x"]
+ results = sanitize_rqtl_phenotype(vals)
+ expected_phenotype_string = 'c(f,NA,r,NA,NA)'
+
+ self.assertEqual(results, expected_phenotype_string)
+
+ def test_sanitize_rqtl_names(self):
+ """test for sanitzing rqtl names"""
+ vals = ['f', "x", "r", "x","x"]
+ expected_sanitized_name = "c('f',NA,'r',NA,NA)"
+ results = sanitize_rqtl_names(vals)
+ self.assertEqual(expected_sanitized_name, results)
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 00658d10..f61e3b88 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -79,7 +79,7 @@ def frange(start, end=None, inc=1.0):
start += 0.0 # force it to be a float
count = int((end - start) / inc)
if start + count * inc != end:
- # Need to adjust the count. AFAICT, it always comes up one short.
+ # Need to adjust the count. AFAICT, it always comes up one short.
count += 1
L = [start] * count
for i in range(1, count):
@@ -131,16 +131,16 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
if plotHeight <= 0 or plotWidth <= 0:
- return
+ return
if len(data) < 2:
- return
+ return
max_D = max(data)
min_D = min(data)
# add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong
if max_D == float('inf') or max_D > webqtlConfig.MAXLRS:
- max_D = webqtlConfig.MAXLRS # maximum LRS value
+ max_D = webqtlConfig.MAXLRS # maximum LRS value
xLow, xTop, stepX = detScale(min_D, max_D)
@@ -151,15 +151,15 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
dataXY = []
Count = []
while j <= xTop:
- dataXY.append(j)
- Count.append(0)
- j += step
+ dataXY.append(j)
+ Count.append(0)
+ j += step
for i, item in enumerate(data):
- if item == float('inf') or item > webqtlConfig.MAXLRS:
- item = webqtlConfig.MAXLRS # maximum LRS value
- j = int((item - xLow) / step)
- Count[j] += 1
+ if item == float('inf') or item > webqtlConfig.MAXLRS:
+ item = webqtlConfig.MAXLRS # maximum LRS value
+ j = int((item - xLow) / step)
+ Count[j] += 1
yLow, yTop, stepY = detScale(0, max(Count))
@@ -169,12 +169,12 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
barWidth = xScale * step
for i, count in enumerate(Count):
- if count:
- xc = (dataXY[i] - xLow) * xScale + xLeftOffset
- yc = -(count - yLow) * yScale + yTopOffset + plotHeight
- im_drawer.rectangle(
- xy=((xc + 2, yc), (xc + barWidth - 2, yTopOffset + plotHeight)),
- outline=barColor, fill=barColor)
+ if count:
+ xc = (dataXY[i] - xLow) * xScale + xLeftOffset
+ yc = -(count - yLow) * yScale + yTopOffset + plotHeight
+ im_drawer.rectangle(
+ xy=((xc + 2, yc), (xc + barWidth - 2, yTopOffset + plotHeight)),
+ outline=barColor, fill=barColor)
# draw drawing region
im_drawer.rectangle(
@@ -186,39 +186,39 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
scaleFont = ImageFont.truetype(font=COUR_FILE, size=11)
x = xLow
for i in range(int(stepX) + 1):
- xc = xLeftOffset + (x - xLow) * xScale
- im_drawer.line(
- xy=((xc, yTopOffset + plotHeight), (xc, yTopOffset + plotHeight + 5)),
- fill=axesColor)
- strX = cformat(d=x, rank=0)
- im_drawer.text(
- text=strX,
- xy=(xc - im_drawer.textsize(strX, font=scaleFont)[0] / 2,
- yTopOffset + plotHeight + 14), font=scaleFont)
- x += (xTop - xLow) / stepX
+ xc = xLeftOffset + (x - xLow) * xScale
+ im_drawer.line(
+ xy=((xc, yTopOffset + plotHeight), (xc, yTopOffset + plotHeight + 5)),
+ fill=axesColor)
+ strX = cformat(d=x, rank=0)
+ im_drawer.text(
+ text=strX,
+ xy=(xc - im_drawer.textsize(strX, font=scaleFont)[0] / 2,
+ yTopOffset + plotHeight + 14), font=scaleFont)
+ x += (xTop - xLow) / stepX
y = yLow
for i in range(int(stepY) + 1):
- yc = yTopOffset + plotHeight - (y - yLow) * yScale
- im_drawer.line(
- xy=((xLeftOffset, yc), (xLeftOffset - 5, yc)), fill=axesColor)
- strY = "%d" % y
- im_drawer.text(
- text=strY,
- xy=(xLeftOffset - im_drawer.textsize(strY,
- font=scaleFont)[0] - 6, yc + 5),
- font=scaleFont)
- y += (yTop - yLow) / stepY
+ yc = yTopOffset + plotHeight - (y - yLow) * yScale
+ im_drawer.line(
+ xy=((xLeftOffset, yc), (xLeftOffset - 5, yc)), fill=axesColor)
+ strY = "%d" % y
+ im_drawer.text(
+ text=strY,
+ xy=(xLeftOffset - im_drawer.textsize(strY,
+ font=scaleFont)[0] - 6, yc + 5),
+ font=scaleFont)
+ y += (yTop - yLow) / stepY
# draw label
labelFont = ImageFont.truetype(font=TAHOMA_FILE, size=17)
if XLabel:
- im_drawer.text(
- text=XLabel,
- xy=(xLeftOffset + (
- plotWidth - im_drawer.textsize(XLabel, font=labelFont)[0]) / 2.0,
- yTopOffset + plotHeight + yBottomOffset-10),
- font=labelFont, fill=labelColor)
+ im_drawer.text(
+ text=XLabel,
+ xy=(xLeftOffset + (
+ plotWidth - im_drawer.textsize(XLabel, font=labelFont)[0]) / 2.0,
+ yTopOffset + plotHeight + yBottomOffset-10),
+ font=labelFont, fill=labelColor)
if YLabel:
draw_rotated_text(canvas, text=YLabel,
@@ -230,12 +230,12 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
labelFont = ImageFont.truetype(font=VERDANA_FILE, size=16)
if title:
- im_drawer.text(
- text=title,
- xy=(xLeftOffset + (plotWidth - im_drawer.textsize(
- title, font=labelFont)[0]) / 2.0,
- 20),
- font=labelFont, fill=labelColor)
+ im_drawer.text(
+ text=title,
+ xy=(xLeftOffset + (plotWidth - im_drawer.textsize(
+ title, font=labelFont)[0]) / 2.0,
+ 20),
+ font=labelFont, fill=labelColor)
# This function determines the scale of the plot
diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py
index 816bc4df..6c8cd546 100644
--- a/wqflask/utility/__init__.py
+++ b/wqflask/utility/__init__.py
@@ -7,7 +7,7 @@ class Bunch:
"""Like a dictionary but using object notation"""
def __init__(self, **kw):
- self.__dict__ = kw
+ self.__dict__ = kw
def __repr__(self):
return pf(self.__dict__)
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
index c0629b5d..eb545478 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/wqflask/utility/genofile_parser.py
@@ -14,87 +14,87 @@ from pprint import pformat as pf
class Marker:
- def __init__(self):
- self.name = None
- self.chr = None
- self.cM = None
- self.Mb = None
- self.genotypes = []
+ def __init__(self):
+ self.name = None
+ self.chr = None
+ self.cM = None
+ self.Mb = None
+ self.genotypes = []
class ConvertGenoFile:
- def __init__(self, input_file):
- self.mb_exists = False
- self.cm_exists = False
- self.markers = []
+ def __init__(self, input_file):
+ self.mb_exists = False
+ self.cm_exists = False
+ self.markers = []
- self.latest_row_pos = None
- self.latest_col_pos = None
+ self.latest_row_pos = None
+ self.latest_col_pos = None
- self.latest_row_value = None
- self.latest_col_value = None
- self.input_fh = open(input_file)
- print("!!!!!!!!!!!!!!!!PARSER!!!!!!!!!!!!!!!!!!")
- self.haplotype_notation = {
- '@mat': "1",
- '@pat': "2",
- '@het': "-999",
- '@unk': "-999"
- }
- self.configurations = {}
+ self.latest_row_value = None
+ self.latest_col_value = None
+ self.input_fh = open(input_file)
+ print("!!!!!!!!!!!!!!!!PARSER!!!!!!!!!!!!!!!!!!")
+ self.haplotype_notation = {
+ '@mat': "1",
+ '@pat': "2",
+ '@het': "-999",
+ '@unk': "-999"
+ }
+ self.configurations = {}
- def process_rows(self):
- for self.latest_row_pos, row in enumerate(self.input_fh):
- self.latest_row_value = row
- # Take care of headers
- if not row.strip():
- continue
- if row.startswith('#'):
- continue
- if row.startswith('Chr'):
- if 'Mb' in row.split():
- self.mb_exists = True
- if 'cM' in row.split():
- self.cm_exists = True
- skip = 2 + self.cm_exists + self.mb_exists
- self.individuals = row.split()[skip:]
- continue
- if row.startswith('@'):
- key, _separater, value = row.partition(':')
- key = key.strip()
- value = value.strip()
- if key in self.haplotype_notation:
- self.configurations[value] = self.haplotype_notation[key]
- continue
- if not len(self.configurations):
- raise EmptyConfigurations
- yield row
+ def process_rows(self):
+ for self.latest_row_pos, row in enumerate(self.input_fh):
+ self.latest_row_value = row
+ # Take care of headers
+ if not row.strip():
+ continue
+ if row.startswith('#'):
+ continue
+ if row.startswith('Chr'):
+ if 'Mb' in row.split():
+ self.mb_exists = True
+ if 'cM' in row.split():
+ self.cm_exists = True
+ skip = 2 + self.cm_exists + self.mb_exists
+ self.individuals = row.split()[skip:]
+ continue
+ if row.startswith('@'):
+ key, _separater, value = row.partition(':')
+ key = key.strip()
+ value = value.strip()
+ if key in self.haplotype_notation:
+ self.configurations[value] = self.haplotype_notation[key]
+ continue
+ if not len(self.configurations):
+ raise EmptyConfigurations
+ yield row
- def process_csv(self):
- for row in self.process_rows():
- row_items = row.split("\t")
+ def process_csv(self):
+ for row in self.process_rows():
+ row_items = row.split("\t")
- this_marker = Marker()
- this_marker.name = row_items[1]
- this_marker.chr = row_items[0]
- if self.cm_exists and self.mb_exists:
- this_marker.cM = row_items[2]
- this_marker.Mb = row_items[3]
- genotypes = row_items[4:]
- elif self.cm_exists:
- this_marker.cM = row_items[2]
- genotypes = row_items[3:]
- elif self.mb_exists:
- this_marker.Mb = row_items[2]
- genotypes = row_items[3:]
- else:
- genotypes = row_items[2:]
- for item_count, genotype in enumerate(genotypes):
- if genotype.upper().strip() in self.configurations:
- this_marker.genotypes.append(
- self.configurations[genotype.upper().strip()])
- else:
- print("WARNING:", genotype.upper())
- this_marker.genotypes.append("NA")
- self.markers.append(this_marker.__dict__)
+ this_marker = Marker()
+ this_marker.name = row_items[1]
+ this_marker.chr = row_items[0]
+ if self.cm_exists and self.mb_exists:
+ this_marker.cM = row_items[2]
+ this_marker.Mb = row_items[3]
+ genotypes = row_items[4:]
+ elif self.cm_exists:
+ this_marker.cM = row_items[2]
+ genotypes = row_items[3:]
+ elif self.mb_exists:
+ this_marker.Mb = row_items[2]
+ genotypes = row_items[3:]
+ else:
+ genotypes = row_items[2:]
+ for item_count, genotype in enumerate(genotypes):
+ if genotype.upper().strip() in self.configurations:
+ this_marker.genotypes.append(
+ self.configurations[genotype.upper().strip()])
+ else:
+ print("WARNING:", genotype.upper())
+ this_marker.genotypes.append("NA")
+ self.markers.append(this_marker.__dict__)
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index d82e478d..4f09176a 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -73,7 +73,7 @@ def get_setting(command_id, guess=None):
def get_setting_bool(id):
v = get_setting(id)
if v not in [0, False, 'False', 'FALSE', None]:
- return True
+ return True
return False
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 9fd89524..b06d84ff 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -35,7 +35,7 @@ def process_traits(unprocessed_traits):
data, _separator, the_hmac = trait.rpartition(':')
data = data.strip()
if g.user_session.logged_in:
- assert the_hmac == hmac.hmac_creation(data), "Data tampering?"
+ assert the_hmac == hmac.hmac_creation(data), "Data tampering?"
traits.add(str(data))
return traits
@@ -52,14 +52,14 @@ def report_change(len_before, len_now):
@app.route("/collections/store_trait_list", methods=('POST',))
def store_traits_list():
- params = request.form
+ params = request.form
- traits = params['traits']
- hash = params['hash']
+ traits = params['traits']
+ hash = params['hash']
- Redis.set(hash, traits)
+ Redis.set(hash, traits)
- return hash
+ return hash
@app.route("/collections/add")
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 59469428..c04b17be 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -238,9 +238,9 @@ class CorrelationMatrix:
for i in range(len(self.trait_list)):
loadings_row = []
if len(self.trait_list) > 2:
- the_range = 3
+ the_range = 3
else:
- the_range = 2
+ the_range = 2
for j in range(the_range):
position = i + len(self.trait_list) * j
loadings_row.append(self.loadings[0][position])
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index f4eafbe7..820e81bc 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -115,8 +115,8 @@ class CTL:
markers = []
markernames = []
for marker in parser.markers:
- markernames.append(marker["name"])
- markers.append(marker["genotypes"])
+ markernames.append(marker["name"])
+ markers.append(marker["genotypes"])
genotypes = list(itertools.chain(*markers))
logger.debug(len(genotypes) / len(individuals),
@@ -128,16 +128,16 @@ class CTL:
# Create a phenotype matrix
traits = []
for trait in self.trait_db_list:
- logger.debug("retrieving data for", trait)
- if trait != "":
- ts = trait.split(':')
- gt = create_trait(name=ts[0], dataset_name=ts[1])
- gt = retrieve_sample_data(gt, dataset, individuals)
- for ind in individuals:
- if ind in list(gt.data.keys()):
- traits.append(gt.data[ind].value)
- else:
- traits.append("-999")
+ logger.debug("retrieving data for", trait)
+ if trait != "":
+ ts = trait.split(':')
+ gt = create_trait(name=ts[0], dataset_name=ts[1])
+ gt = retrieve_sample_data(gt, dataset, individuals)
+ for ind in individuals:
+ if ind in list(gt.data.keys()):
+ traits.append(gt.data[ind].value)
+ else:
+ traits.append("-999")
rPheno = r_t(ro.r.matrix(r_as_numeric(r_unlist(traits)), nrow=len(self.trait_db_list), ncol=len(
individuals), dimnames=r_list(self.trait_db_list, individuals), byrow=True))
@@ -177,42 +177,42 @@ class CTL:
# We start from 2, since R starts from 1 :)
n = 2
for trait in self.trait_db_list:
- # Create the QTL like CTL plots
- self.results['imgurl' + \
- str(n)] = webqtlUtil.genRandStr("CTL_") + ".png"
- self.results['imgloc' + str(n)] = GENERATED_IMAGE_DIR + \
- self.results['imgurl' + str(n)]
- r_png(self.results['imgloc' + str(n)],
- width=1000, height=600, type='cairo-png')
- self.r_plotCTLobject(
- res, (n - 1), significance=significance, main='Phenotype ' + trait)
- r_dev_off()
- n = n + 1
+ # Create the QTL like CTL plots
+ self.results['imgurl' + \
+ str(n)] = webqtlUtil.genRandStr("CTL_") + ".png"
+ self.results['imgloc' + str(n)] = GENERATED_IMAGE_DIR + \
+ self.results['imgurl' + str(n)]
+ r_png(self.results['imgloc' + str(n)],
+ width=1000, height=600, type='cairo-png')
+ self.r_plotCTLobject(
+ res, (n - 1), significance=significance, main='Phenotype ' + trait)
+ r_dev_off()
+ n = n + 1
# Flush any output from R
sys.stdout.flush()
# Create the interactive graph for cytoscape visualization (Nodes and Edges)
if not isinstance(significant, ri.RNULLType):
- for x in range(len(significant[0])):
- logger.debug(significant[0][x], significant[1]
- [x], significant[2][x]) # Debug to console
- # Source
- tsS = significant[0][x].split(':')
- # Target
- tsT = significant[2][x].split(':')
- # Retrieve Source info from the DB
- gtS = create_trait(name=tsS[0], dataset_name=tsS[1])
- # Retrieve Target info from the DB
- gtT = create_trait(name=tsT[0], dataset_name=tsT[1])
- self.addNode(gtS)
- self.addNode(gtT)
- self.addEdge(gtS, gtT, significant, x)
-
- # Update the trait name for the displayed table
- significant[0][x] = "{} ({})".format(gtS.symbol, gtS.name)
- # Update the trait name for the displayed table
- significant[2][x] = "{} ({})".format(gtT.symbol, gtT.name)
+ for x in range(len(significant[0])):
+ logger.debug(significant[0][x], significant[1]
+ [x], significant[2][x]) # Debug to console
+ # Source
+ tsS = significant[0][x].split(':')
+ # Target
+ tsT = significant[2][x].split(':')
+ # Retrieve Source info from the DB
+ gtS = create_trait(name=tsS[0], dataset_name=tsS[1])
+ # Retrieve Target info from the DB
+ gtT = create_trait(name=tsT[0], dataset_name=tsT[1])
+ self.addNode(gtS)
+ self.addNode(gtT)
+ self.addEdge(gtS, gtT, significant, x)
+
+ # Update the trait name for the displayed table
+ significant[0][x] = "{} ({})".format(gtS.symbol, gtS.name)
+ # Update the trait name for the displayed table
+ significant[2][x] = "{} ({})".format(gtT.symbol, gtT.name)
self.elements = json.dumps(self.nodes_list + self.edges_list)
@@ -227,8 +227,8 @@ class CTL:
self.loadImage("imgloc1", "imgdata1")
n = 2
for trait in self.trait_db_list:
- self.loadImage("imgloc" + str(n), "imgdata" + str(n))
- n = n + 1
+ self.loadImage("imgloc" + str(n), "imgdata" + str(n))
+ n = n + 1
def process_results(self, results):
logger.info("Processing CTL output")
diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py
index 55a7da0e..995915a9 100644
--- a/wqflask/wqflask/group_manager.py
+++ b/wqflask/wqflask/group_manager.py
@@ -16,158 +16,158 @@ logger = getLogger(__name__)
@app.route("/groups/manage", methods=('GET', 'POST'))
def manage_groups():
- params = request.form if request.form else request.args
- if "add_new_group" in params:
- return redirect(url_for('add_group'))
- else:
- admin_groups, member_groups = get_user_groups(g.user_session.user_id)
- return render_template("admin/group_manager.html", admin_groups=admin_groups, member_groups=member_groups)
+ params = request.form if request.form else request.args
+ if "add_new_group" in params:
+ return redirect(url_for('add_group'))
+ else:
+ admin_groups, member_groups = get_user_groups(g.user_session.user_id)
+ return render_template("admin/group_manager.html", admin_groups=admin_groups, member_groups=member_groups)
@app.route("/groups/view", methods=('GET', 'POST'))
def view_group():
- params = request.form if request.form else request.args
- group_id = params['id']
- group_info = get_group_info(group_id)
- admins_info = []
- user_is_admin = False
- if g.user_session.user_id in group_info['admins']:
- user_is_admin = True
- for user_id in group_info['admins']:
- if user_id:
- user_info = get_user_by_unique_column("user_id", user_id)
- admins_info.append(user_info)
- members_info = []
- for user_id in group_info['members']:
- if user_id:
- user_info = get_user_by_unique_column("user_id", user_id)
- members_info.append(user_info)
-
- # ZS: This whole part might not scale well with many resources
- resources_info = []
- all_resources = get_resources()
- for resource_id in all_resources:
- resource_info = get_resource_info(resource_id)
- group_masks = resource_info['group_masks']
- if group_id in group_masks:
- this_resource = {}
- privileges = group_masks[group_id]
- this_resource['id'] = resource_id
- this_resource['name'] = resource_info['name']
- this_resource['data'] = privileges['data']
- this_resource['metadata'] = privileges['metadata']
- this_resource['admin'] = privileges['admin']
- resources_info.append(this_resource)
-
- return render_template("admin/view_group.html", group_info=group_info, admins=admins_info, members=members_info, user_is_admin=user_is_admin, resources=resources_info)
+ params = request.form if request.form else request.args
+ group_id = params['id']
+ group_info = get_group_info(group_id)
+ admins_info = []
+ user_is_admin = False
+ if g.user_session.user_id in group_info['admins']:
+ user_is_admin = True
+ for user_id in group_info['admins']:
+ if user_id:
+ user_info = get_user_by_unique_column("user_id", user_id)
+ admins_info.append(user_info)
+ members_info = []
+ for user_id in group_info['members']:
+ if user_id:
+ user_info = get_user_by_unique_column("user_id", user_id)
+ members_info.append(user_info)
+
+ # ZS: This whole part might not scale well with many resources
+ resources_info = []
+ all_resources = get_resources()
+ for resource_id in all_resources:
+ resource_info = get_resource_info(resource_id)
+ group_masks = resource_info['group_masks']
+ if group_id in group_masks:
+ this_resource = {}
+ privileges = group_masks[group_id]
+ this_resource['id'] = resource_id
+ this_resource['name'] = resource_info['name']
+ this_resource['data'] = privileges['data']
+ this_resource['metadata'] = privileges['metadata']
+ this_resource['admin'] = privileges['admin']
+ resources_info.append(this_resource)
+
+ return render_template("admin/view_group.html", group_info=group_info, admins=admins_info, members=members_info, user_is_admin=user_is_admin, resources=resources_info)
@app.route("/groups/remove", methods=('POST',))
def remove_groups():
- group_ids_to_remove = request.form['selected_group_ids']
- for group_id in group_ids_to_remove.split(":"):
- delete_group(g.user_session.user_id, group_id)
+ group_ids_to_remove = request.form['selected_group_ids']
+ for group_id in group_ids_to_remove.split(":"):
+ delete_group(g.user_session.user_id, group_id)
- return redirect(url_for('manage_groups'))
+ return redirect(url_for('manage_groups'))
@app.route("/groups/remove_users", methods=('POST',))
def remove_users():
- group_id = request.form['group_id']
- admin_ids_to_remove = request.form['selected_admin_ids']
- member_ids_to_remove = request.form['selected_member_ids']
+ group_id = request.form['group_id']
+ admin_ids_to_remove = request.form['selected_admin_ids']
+ member_ids_to_remove = request.form['selected_member_ids']
- remove_users_from_group(g.user_session.user_id, admin_ids_to_remove.split(
- ":"), group_id, user_type="admins")
- remove_users_from_group(g.user_session.user_id, member_ids_to_remove.split(
- ":"), group_id, user_type="members")
+ remove_users_from_group(g.user_session.user_id, admin_ids_to_remove.split(
+ ":"), group_id, user_type="admins")
+ remove_users_from_group(g.user_session.user_id, member_ids_to_remove.split(
+ ":"), group_id, user_type="members")
- return redirect(url_for('view_group', id=group_id))
+ return redirect(url_for('view_group', id=group_id))
@app.route("/groups/add_<path:user_type>", methods=('POST',))
def add_users(user_type='members'):
- group_id = request.form['group_id']
- if user_type == "admins":
- user_emails = request.form['admin_emails_to_add'].split(",")
- add_users_to_group(g.user_session.user_id, group_id,
- user_emails, admins=True)
- elif user_type == "members":
- user_emails = request.form['member_emails_to_add'].split(",")
- add_users_to_group(g.user_session.user_id, group_id,
- user_emails, admins=False)
+ group_id = request.form['group_id']
+ if user_type == "admins":
+ user_emails = request.form['admin_emails_to_add'].split(",")
+ add_users_to_group(g.user_session.user_id, group_id,
+ user_emails, admins=True)
+ elif user_type == "members":
+ user_emails = request.form['member_emails_to_add'].split(",")
+ add_users_to_group(g.user_session.user_id, group_id,
+ user_emails, admins=False)
- return redirect(url_for('view_group', id=group_id))
+ return redirect(url_for('view_group', id=group_id))
@app.route("/groups/change_name", methods=('POST',))
def change_name():
- group_id = request.form['group_id']
- new_name = request.form['new_name']
- group_info = change_group_name(g.user_session.user_id, group_id, new_name)
+ group_id = request.form['group_id']
+ new_name = request.form['new_name']
+ group_info = change_group_name(g.user_session.user_id, group_id, new_name)
- return new_name
+ return new_name
@app.route("/groups/create", methods=('GET', 'POST'))
def add_or_edit_group():
- params = request.form if request.form else request.args
- if "group_name" in params:
- member_user_ids = set()
- admin_user_ids = set()
- # ZS: Always add the user creating the group as an admin
- admin_user_ids.add(g.user_session.user_id)
- if "admin_emails_to_add" in params:
- admin_emails = params['admin_emails_to_add'].split(",")
- for email in admin_emails:
- user_details = get_user_by_unique_column("email_address", email)
- if user_details:
- admin_user_ids.add(user_details['user_id'])
- #send_group_invites(params['group_id'], user_email_list = admin_emails, user_type="admins")
- if "member_emails_to_add" in params:
- member_emails = params['member_emails_to_add'].split(",")
- for email in member_emails:
- user_details = get_user_by_unique_column("email_address", email)
- if user_details:
- member_user_ids.add(user_details['user_id'])
- #send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members")
-
- create_group(list(admin_user_ids), list(
- member_user_ids), params['group_name'])
- return redirect(url_for('manage_groups'))
- else:
- return render_template("admin/create_group.html")
+ params = request.form if request.form else request.args
+ if "group_name" in params:
+ member_user_ids = set()
+ admin_user_ids = set()
+ # ZS: Always add the user creating the group as an admin
+ admin_user_ids.add(g.user_session.user_id)
+ if "admin_emails_to_add" in params:
+ admin_emails = params['admin_emails_to_add'].split(",")
+ for email in admin_emails:
+ user_details = get_user_by_unique_column("email_address", email)
+ if user_details:
+ admin_user_ids.add(user_details['user_id'])
+ #send_group_invites(params['group_id'], user_email_list = admin_emails, user_type="admins")
+ if "member_emails_to_add" in params:
+ member_emails = params['member_emails_to_add'].split(",")
+ for email in member_emails:
+ user_details = get_user_by_unique_column("email_address", email)
+ if user_details:
+ member_user_ids.add(user_details['user_id'])
+ #send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members")
+
+ create_group(list(admin_user_ids), list(
+ member_user_ids), params['group_name'])
+ return redirect(url_for('manage_groups'))
+ else:
+ return render_template("admin/create_group.html")
# ZS: Will integrate this later, for now just letting users be added directly
def send_group_invites(group_id, user_email_list=[], user_type="members"):
- for user_email in user_email_list:
- user_details = get_user_by_unique_column("email_address", user_email)
- if user_details:
- group_info = get_group_info(group_id)
- # ZS: Probably not necessary since the group should normally always exist if group_id is being passed here,
- # but it's technically possible to hit it if Redis is cleared out before submitting the new users or something
- if group_info:
- # ZS: Don't add user if they're already an admin or if they're being added a regular user and are already a regular user,
- # but do add them if they're a regular user and are added as an admin
- if (user_details['user_id'] in group_info['admins']) or \
- ((user_type == "members") and (user_details['user_id'] in group_info['members'])):
- continue
- else:
- send_verification_email(user_details, template_name="email/group_verification.txt",
- key_prefix="verification_code", subject = "You've been invited to join a GeneNetwork user group")
- else:
- temp_password = ''.join(random.choice(
- string.ascii_uppercase + string.digits) for _ in range(6))
- user_details = {
- 'user_id': str(uuid.uuid4()),
- 'email_address': user_email,
- 'registration_info': basic_info(),
- 'password': set_password(temp_password),
- 'confirmed': 0
- }
- save_user(user_details, user_details['user_id'])
- send_invitation_email(user_email, temp_password)
+ for user_email in user_email_list:
+ user_details = get_user_by_unique_column("email_address", user_email)
+ if user_details:
+ group_info = get_group_info(group_id)
+ # ZS: Probably not necessary since the group should normally always exist if group_id is being passed here,
+ # but it's technically possible to hit it if Redis is cleared out before submitting the new users or something
+ if group_info:
+ # ZS: Don't add user if they're already an admin or if they're being added a regular user and are already a regular user,
+ # but do add them if they're a regular user and are added as an admin
+ if (user_details['user_id'] in group_info['admins']) or \
+ ((user_type == "members") and (user_details['user_id'] in group_info['members'])):
+ continue
+ else:
+ send_verification_email(user_details, template_name="email/group_verification.txt",
+ key_prefix="verification_code", subject = "You've been invited to join a GeneNetwork user group")
+ else:
+ temp_password = ''.join(random.choice(
+ string.ascii_uppercase + string.digits) for _ in range(6))
+ user_details = {
+ 'user_id': str(uuid.uuid4()),
+ 'email_address': user_email,
+ 'registration_info': basic_info(),
+ 'password': set_password(temp_password),
+ 'confirmed': 0
+ }
+ save_user(user_details, user_details['user_id'])
+ send_invitation_email(user_email, temp_password)
# @app.route()
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 9548d130..f02da27c 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -247,13 +247,13 @@ class GSearch:
if not trait_ob:
continue
if this_trait['dataset'] == this_trait['group'] + "Publish":
- try:
- if trait_ob.locus_chr != "" and trait_ob.locus_mb != "":
- this_trait['max_lrs_text'] = "Chr" + \
- str(trait_ob.locus_chr) + \
- ": " + str(trait_ob.locus_mb)
- except:
- this_trait['max_lrs_text'] = "N/A"
+ try:
+ if trait_ob.locus_chr != "" and trait_ob.locus_mb != "":
+ this_trait['max_lrs_text'] = "Chr" + \
+ str(trait_ob.locus_chr) + \
+ ": " + str(trait_ob.locus_mb)
+ except:
+ this_trait['max_lrs_text'] = "N/A"
trait_list.append(this_trait)
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index e624a146..2f1c142c 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -7,79 +7,79 @@ from flask import Flask, g
def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
- fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd',
- 'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID',
- 'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd']
+ fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd',
+ 'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID',
+ 'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd']
- # List All Species in the Gene Table
- speciesDict = {}
- results = g.db.execute("""
+ # List All Species in the Gene Table
+ speciesDict = {}
+ results = g.db.execute("""
SELECT Species.Name, GeneList.SpeciesId
FROM Species, GeneList
WHERE GeneList.SpeciesId = Species.Id
GROUP BY GeneList.SpeciesId""").fetchall()
- for item in results:
- speciesDict[item[0]] = item[1]
+ for item in results:
+ speciesDict[item[0]] = item[1]
- # List current Species and other Species
- speciesId = speciesDict[species]
- otherSpecies = [[X, speciesDict[X]] for X in list(speciesDict.keys())]
- otherSpecies.remove([species, speciesId])
+ # List current Species and other Species
+ speciesId = speciesDict[species]
+ otherSpecies = [[X, speciesDict[X]] for X in list(speciesDict.keys())]
+ otherSpecies.remove([species, speciesId])
- results = g.db.execute("""
+ results = g.db.execute("""
SELECT %s FROM GeneList
WHERE SpeciesId = %d AND
Chromosome = '%s' AND
((TxStart > %f and TxStart <= %f) OR (TxEnd > %f and TxEnd <= %f))
ORDER BY txStart
""" % (", ".join(fetchFields),
- speciesId, chrName,
- startMb, endMb,
- startMb, endMb)).fetchall()
-
- GeneList = []
-
- if results:
- for result in results:
- newdict = {}
- for j, item in enumerate(fetchFields):
- newdict[item] = result[j]
- # count SNPs if possible
- if diffCol and species == 'mouse':
- newdict["snpCount"] = g.db.execute("""
+ speciesId, chrName,
+ startMb, endMb,
+ startMb, endMb)).fetchall()
+
+ GeneList = []
+
+ if results:
+ for result in results:
+ newdict = {}
+ for j, item in enumerate(fetchFields):
+ newdict[item] = result[j]
+ # count SNPs if possible
+ if diffCol and species == 'mouse':
+ newdict["snpCount"] = g.db.execute("""
SELECT count(*)
FROM BXDSnpPosition
WHERE Chr = '%s' AND
Mb >= %2.6f AND Mb < %2.6f AND
StrainId1 = %d AND StrainId2 = %d
""" % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1])).fetchone()[0]
- newdict["snpDensity"] = newdict["snpCount"] / \
- (newdict["TxEnd"] - newdict["TxStart"]) / 1000.0
- else:
- newdict["snpDensity"] = newdict["snpCount"] = 0
-
- try:
- newdict['GeneLength'] = 1000.0 * (newdict['TxEnd'] - newdict['TxStart'])
- except:
- pass
-
- # load gene from other Species by the same name
- for item in otherSpecies:
- othSpec, othSpecId = item
- newdict2 = {}
-
- resultsOther = g.db.execute("SELECT %s FROM GeneList WHERE SpeciesId = %d AND geneSymbol= '%s' LIMIT 1" % (", ".join(fetchFields),
- othSpecId,
- newdict["GeneSymbol"])).fetchone()
-
- if resultsOther:
- for j, item in enumerate(fetchFields):
- newdict2[item] = resultsOther[j]
-
- # count SNPs if possible, could be a separate function
- if diffCol and othSpec == 'mouse':
- newdict2["snpCount"] = g.db.execute("""
+ newdict["snpDensity"] = newdict["snpCount"] / \
+ (newdict["TxEnd"] - newdict["TxStart"]) / 1000.0
+ else:
+ newdict["snpDensity"] = newdict["snpCount"] = 0
+
+ try:
+ newdict['GeneLength'] = 1000.0 * (newdict['TxEnd'] - newdict['TxStart'])
+ except:
+ pass
+
+ # load gene from other Species by the same name
+ for item in otherSpecies:
+ othSpec, othSpecId = item
+ newdict2 = {}
+
+ resultsOther = g.db.execute("SELECT %s FROM GeneList WHERE SpeciesId = %d AND geneSymbol= '%s' LIMIT 1" % (", ".join(fetchFields),
+ othSpecId,
+ newdict["GeneSymbol"])).fetchone()
+
+ if resultsOther:
+ for j, item in enumerate(fetchFields):
+ newdict2[item] = resultsOther[j]
+
+ # count SNPs if possible, could be a separate function
+ if diffCol and othSpec == 'mouse':
+ newdict2["snpCount"] = g.db.execute("""
SELECT count(*)
FROM BXDSnpPosition
WHERE Chr = '%s' AND
@@ -87,19 +87,19 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
StrainId1 = %d AND StrainId2 = %d
""" % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1])).fetchone()[0]
- newdict2["snpDensity"] = newdict2["snpCount"] / \
- (newdict2["TxEnd"] - newdict2["TxStart"]) / 1000.0
- else:
- newdict2["snpDensity"] = newdict2["snpCount"] = 0
+ newdict2["snpDensity"] = newdict2["snpCount"] / \
+ (newdict2["TxEnd"] - newdict2["TxStart"]) / 1000.0
+ else:
+ newdict2["snpDensity"] = newdict2["snpCount"] = 0
- try:
- newdict2['GeneLength'] = 1000.0 * \
- (newdict2['TxEnd'] - newdict2['TxStart'])
- except:
- pass
+ try:
+ newdict2['GeneLength'] = 1000.0 * \
+ (newdict2['TxEnd'] - newdict2['TxStart'])
+ except:
+ pass
- newdict['%sGene' % othSpec] = newdict2
+ newdict['%sGene' % othSpec] = newdict2
- GeneList.append(newdict)
+ GeneList.append(newdict)
- return GeneList
+ return GeneList
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 8d0134d8..c68e0fde 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -395,17 +395,17 @@ class DisplayMappingResults:
# Darwing Options
try:
- if self.selectedChr > -1:
- self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(
- self.GRAPH_MIN_WIDTH, int(start_vars['graphWidth'])))
- else:
- self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(
- self.MULT_GRAPH_MIN_WIDTH, int(start_vars['graphWidth'])))
+ if self.selectedChr > -1:
+ self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(
+ self.GRAPH_MIN_WIDTH, int(start_vars['graphWidth'])))
+ else:
+ self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(
+ self.MULT_GRAPH_MIN_WIDTH, int(start_vars['graphWidth'])))
except:
- if self.selectedChr > -1:
- self.graphWidth = self.GRAPH_DEFAULT_WIDTH
- else:
- self.graphWidth = self.MULT_GRAPH_DEFAULT_WIDTH
+ if self.selectedChr > -1:
+ self.graphWidth = self.GRAPH_DEFAULT_WIDTH
+ else:
+ self.graphWidth = self.MULT_GRAPH_DEFAULT_WIDTH
# BEGIN HaplotypeAnalyst
if 'haplotypeAnalystCheck' in list(start_vars.keys()):
@@ -574,15 +574,15 @@ class DisplayMappingResults:
chrName, self.diffCol, self.startMb, self.endMb, "rat")
if self.geneCol and self.intervalAnalystChecked:
- #######################################################################
- #Nick use GENEID as RefGene to get Literature Correlation Informations#
- #For Interval Mapping, Literature Correlation isn't useful, so skip it#
- #through set GENEID is None #
- #######################################################################
+ #######################################################################
+ #Nick use GENEID as RefGene to get Literature Correlation Informations#
+ #For Interval Mapping, Literature Correlation isn't useful, so skip it#
+ #through set GENEID is None #
+ #######################################################################
- GENEID = None
+ GENEID = None
- self.geneTable(self.geneCol, GENEID)
+ self.geneTable(self.geneCol, GENEID)
################################################################
# Plots goes here
@@ -2636,11 +2636,11 @@ class DisplayMappingResults:
LRSCoordXY.append((Xc, Yc))
if not self.multipleInterval and self.additiveChecked:
- if additiveMax == 0.0:
- additiveMax = 0.000001
- Yc = yZero - qtlresult['additive'] * \
- AdditiveHeightThresh / additiveMax
- AdditiveCoordXY.append((Xc, Yc))
+ if additiveMax == 0.0:
+ additiveMax = 0.000001
+ Yc = yZero - qtlresult['additive'] * \
+ AdditiveHeightThresh / additiveMax
+ AdditiveCoordXY.append((Xc, Yc))
m += 1
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index b3c9fddf..32dbad1f 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -294,13 +294,13 @@ def add_categorical_covar(cross, covar_as_string, i):
col_names = []
# logger.info("loop")
for x in range(1, (nCol + 1)):
- #logger.info("loop" + str(x));
- col_name = "covar_" + str(i) + "_" + str(x)
- #logger.info("col_name" + col_name);
- ro.r('the_cross$pheno <- cbind(pheno, ' + \
- col_name + ' = newcovar[,' + str(x) + '])')
- col_names.append(col_name)
- #logger.info("loop" + str(x) + "done");
+ #logger.info("loop" + str(x));
+ col_name = "covar_" + str(i) + "_" + str(x)
+ #logger.info("col_name" + col_name);
+ ro.r('the_cross$pheno <- cbind(pheno, ' + \
+ col_name + ' = newcovar[,' + str(x) + '])')
+ col_names.append(col_name)
+ #logger.info("loop" + str(x) + "done");
logger.info("returning from add_categorical_covar")
return ro.r["the_cross"], col_names
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index d9b28fba..041f4348 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -65,10 +65,10 @@ class RunMapping:
# ZS: Sometimes a group may have a genofile that only includes a subset of samples
genofile_samplelist = []
if 'genofile' in start_vars:
- if start_vars['genofile'] != "":
- self.genofile_string = start_vars['genofile']
- self.dataset.group.genofile = self.genofile_string.split(":")[0]
- genofile_samplelist = get_genofile_samplelist(self.dataset)
+ if start_vars['genofile'] != "":
+ self.genofile_string = start_vars['genofile']
+ self.dataset.group.genofile = self.genofile_string.split(":")[0]
+ genofile_samplelist = get_genofile_samplelist(self.dataset)
all_samples_ordered = self.dataset.group.all_samples_ordered()
@@ -324,182 +324,182 @@ class RunMapping:
self.no_results = False
if len(results) == 0:
- self.no_results = True
+ self.no_results = True
else:
- if self.pair_scan == True:
- self.qtl_results = []
- highest_chr = 1 # This is needed in order to convert the highest chr to X/Y
- for marker in results:
- if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
- if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
- highest_chr = marker['chr1']
- if 'lod_score' in list(marker.keys()):
- self.qtl_results.append(marker)
-
- self.trimmed_markers = results
-
- for qtl in enumerate(self.qtl_results):
- self.json_data['chr1'].append(str(qtl['chr1']))
- self.json_data['chr2'].append(str(qtl['chr2']))
- self.json_data['Mb'].append(qtl['Mb'])
- self.json_data['markernames'].append(qtl['name'])
-
- self.js_data = dict(
- json_data=self.json_data,
- this_trait=self.this_trait.name,
- data_set=self.dataset.name,
- maf=self.maf,
- manhattan_plot=self.manhattan_plot,
- mapping_scale=self.mapping_scale,
- qtl_results=self.qtl_results
- )
-
- else:
- self.qtl_results = []
- self.results_for_browser = []
- self.annotations_for_browser = []
- highest_chr = 1 # This is needed in order to convert the highest chr to X/Y
- for marker in results:
- if 'Mb' in marker:
- this_ps = marker['Mb'] * 1000000
- else:
- this_ps = marker['cM'] * 1000000
-
- browser_marker = dict(
- chr=str(marker['chr']),
- rs=marker['name'],
- ps=this_ps,
- url="/show_trait?trait_id=" + \
- marker['name'] + "&dataset=" + \
- self.dataset.group.name + "Geno"
- )
-
- if self.geno_db_exists == "True":
- annot_marker = dict(
- name=str(marker['name']),
- chr=str(marker['chr']),
- rs=marker['name'],
- pos=this_ps,
- url="/show_trait?trait_id=" + \
- marker['name'] + "&dataset=" + \
- self.dataset.group.name + "Geno"
- )
- else:
- annot_marker = dict(
- name=str(marker['name']),
- chr=str(marker['chr']),
- rs=marker['name'],
- pos=this_ps
- )
-
- if 'lrs_value' in marker and marker['lrs_value'] > 0:
- browser_marker['p_wald'] = 10**- \
- (marker['lrs_value'] / 4.61)
- elif 'lod_score' in marker and marker['lod_score'] > 0:
- browser_marker['p_wald'] = 10**-(marker['lod_score'])
- else:
- browser_marker['p_wald'] = 0
-
- self.results_for_browser.append(browser_marker)
- self.annotations_for_browser.append(annot_marker)
- if str(marker['chr']) > '0' or str(marker['chr']) == "X" or str(marker['chr']) == "X/Y":
- if str(marker['chr']) > str(highest_chr) or str(marker['chr']) == "X" or str(marker['chr']) == "X/Y":
- highest_chr = marker['chr']
- if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
- if 'Mb' in marker.keys():
- marker['display_pos'] = "Chr" + \
- str(marker['chr']) + ": " + \
- "{:.6f}".format(marker['Mb'])
- elif 'cM' in marker.keys():
- marker['display_pos'] = "Chr" + \
- str(marker['chr']) + ": " + \
- "{:.3f}".format(marker['cM'])
- else:
- marker['display_pos'] = "N/A"
- self.qtl_results.append(marker)
-
- total_markers = len(self.qtl_results)
-
- with Bench("Exporting Results"):
- export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path,
- self.mapping_scale, self.score_type, self.transform, self.covariates, self.n_samples)
-
- with Bench("Trimming Markers for Figure"):
- if len(self.qtl_results) > 30000:
- self.qtl_results = trim_markers_for_figure(
- self.qtl_results)
- self.results_for_browser = trim_markers_for_figure(
- self.results_for_browser)
- filtered_annotations = []
- for marker in self.results_for_browser:
- for annot_marker in self.annotations_for_browser:
- if annot_marker['rs'] == marker['rs']:
- filtered_annotations.append(annot_marker)
- break
- self.annotations_for_browser = filtered_annotations
- browser_files = write_input_for_browser(
- self.dataset, self.results_for_browser, self.annotations_for_browser)
- else:
- browser_files = write_input_for_browser(
- self.dataset, self.results_for_browser, self.annotations_for_browser)
-
- with Bench("Trimming Markers for Table"):
- self.trimmed_markers = trim_markers_for_table(results)
-
- chr_lengths = get_chr_lengths(
- self.mapping_scale, self.mapping_method, self.dataset, self.qtl_results)
-
- # ZS: For zooming into genome browser, need to pass chromosome name instead of number
- if self.dataset.group.species == "mouse":
- if self.selected_chr == 20:
- this_chr = "X"
- else:
- this_chr = str(self.selected_chr)
- elif self.dataset.group.species == "rat":
- if self.selected_chr == 21:
- this_chr = "X"
- else:
- this_chr = str(self.selected_chr)
- else:
- if self.selected_chr == 22:
- this_chr = "X"
- elif self.selected_chr == 23:
- this_chr = "Y"
- else:
- this_chr = str(self.selected_chr)
-
- if self.mapping_method != "gemma":
- if self.score_type == "LRS":
- significant_for_browser = self.significant / 4.61
- else:
- significant_for_browser = self.significant
-
- self.js_data = dict(
- #result_score_type = self.score_type,
- #this_trait = self.this_trait.name,
- #data_set = self.dataset.name,
- #maf = self.maf,
- #manhattan_plot = self.manhattan_plot,
- #mapping_scale = self.mapping_scale,
- #chromosomes = chromosome_mb_lengths,
- #qtl_results = self.qtl_results,
- categorical_vars=self.categorical_vars,
- chr_lengths=chr_lengths,
- num_perm=self.num_perm,
- perm_results=self.perm_output,
- significant=significant_for_browser,
- browser_files=browser_files,
- selected_chr=this_chr,
- total_markers=total_markers
- )
- else:
+ if self.pair_scan == True:
+ self.qtl_results = []
+ highest_chr = 1 # This is needed in order to convert the highest chr to X/Y
+ for marker in results:
+ if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
+ if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
+ highest_chr = marker['chr1']
+ if 'lod_score' in list(marker.keys()):
+ self.qtl_results.append(marker)
+
+ self.trimmed_markers = results
+
+ for qtl in enumerate(self.qtl_results):
+ self.json_data['chr1'].append(str(qtl['chr1']))
+ self.json_data['chr2'].append(str(qtl['chr2']))
+ self.json_data['Mb'].append(qtl['Mb'])
+ self.json_data['markernames'].append(qtl['name'])
+
self.js_data = dict(
- chr_lengths=chr_lengths,
- browser_files=browser_files,
- selected_chr=this_chr,
- total_markers=total_markers
+ json_data=self.json_data,
+ this_trait=self.this_trait.name,
+ data_set=self.dataset.name,
+ maf=self.maf,
+ manhattan_plot=self.manhattan_plot,
+ mapping_scale=self.mapping_scale,
+ qtl_results=self.qtl_results
)
+ else:
+ self.qtl_results = []
+ self.results_for_browser = []
+ self.annotations_for_browser = []
+ highest_chr = 1 # This is needed in order to convert the highest chr to X/Y
+ for marker in results:
+ if 'Mb' in marker:
+ this_ps = marker['Mb'] * 1000000
+ else:
+ this_ps = marker['cM'] * 1000000
+
+ browser_marker = dict(
+ chr=str(marker['chr']),
+ rs=marker['name'],
+ ps=this_ps,
+ url="/show_trait?trait_id=" + \
+ marker['name'] + "&dataset=" + \
+ self.dataset.group.name + "Geno"
+ )
+
+ if self.geno_db_exists == "True":
+ annot_marker = dict(
+ name=str(marker['name']),
+ chr=str(marker['chr']),
+ rs=marker['name'],
+ pos=this_ps,
+ url="/show_trait?trait_id=" + \
+ marker['name'] + "&dataset=" + \
+ self.dataset.group.name + "Geno"
+ )
+ else:
+ annot_marker = dict(
+ name=str(marker['name']),
+ chr=str(marker['chr']),
+ rs=marker['name'],
+ pos=this_ps
+ )
+
+ if 'lrs_value' in marker and marker['lrs_value'] > 0:
+ browser_marker['p_wald'] = 10**- \
+ (marker['lrs_value'] / 4.61)
+ elif 'lod_score' in marker and marker['lod_score'] > 0:
+ browser_marker['p_wald'] = 10**-(marker['lod_score'])
+ else:
+ browser_marker['p_wald'] = 0
+
+ self.results_for_browser.append(browser_marker)
+ self.annotations_for_browser.append(annot_marker)
+ if str(marker['chr']) > '0' or str(marker['chr']) == "X" or str(marker['chr']) == "X/Y":
+ if str(marker['chr']) > str(highest_chr) or str(marker['chr']) == "X" or str(marker['chr']) == "X/Y":
+ highest_chr = marker['chr']
+ if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
+ if 'Mb' in marker.keys():
+ marker['display_pos'] = "Chr" + \
+ str(marker['chr']) + ": " + \
+ "{:.6f}".format(marker['Mb'])
+ elif 'cM' in marker.keys():
+ marker['display_pos'] = "Chr" + \
+ str(marker['chr']) + ": " + \
+ "{:.3f}".format(marker['cM'])
+ else:
+ marker['display_pos'] = "N/A"
+ self.qtl_results.append(marker)
+
+ total_markers = len(self.qtl_results)
+
+ with Bench("Exporting Results"):
+ export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path,
+ self.mapping_scale, self.score_type, self.transform, self.covariates, self.n_samples)
+
+ with Bench("Trimming Markers for Figure"):
+ if len(self.qtl_results) > 30000:
+ self.qtl_results = trim_markers_for_figure(
+ self.qtl_results)
+ self.results_for_browser = trim_markers_for_figure(
+ self.results_for_browser)
+ filtered_annotations = []
+ for marker in self.results_for_browser:
+ for annot_marker in self.annotations_for_browser:
+ if annot_marker['rs'] == marker['rs']:
+ filtered_annotations.append(annot_marker)
+ break
+ self.annotations_for_browser = filtered_annotations
+ browser_files = write_input_for_browser(
+ self.dataset, self.results_for_browser, self.annotations_for_browser)
+ else:
+ browser_files = write_input_for_browser(
+ self.dataset, self.results_for_browser, self.annotations_for_browser)
+
+ with Bench("Trimming Markers for Table"):
+ self.trimmed_markers = trim_markers_for_table(results)
+
+ chr_lengths = get_chr_lengths(
+ self.mapping_scale, self.mapping_method, self.dataset, self.qtl_results)
+
+ # ZS: For zooming into genome browser, need to pass chromosome name instead of number
+ if self.dataset.group.species == "mouse":
+ if self.selected_chr == 20:
+ this_chr = "X"
+ else:
+ this_chr = str(self.selected_chr)
+ elif self.dataset.group.species == "rat":
+ if self.selected_chr == 21:
+ this_chr = "X"
+ else:
+ this_chr = str(self.selected_chr)
+ else:
+ if self.selected_chr == 22:
+ this_chr = "X"
+ elif self.selected_chr == 23:
+ this_chr = "Y"
+ else:
+ this_chr = str(self.selected_chr)
+
+ if self.mapping_method != "gemma":
+ if self.score_type == "LRS":
+ significant_for_browser = self.significant / 4.61
+ else:
+ significant_for_browser = self.significant
+
+ self.js_data = dict(
+ #result_score_type = self.score_type,
+ #this_trait = self.this_trait.name,
+ #data_set = self.dataset.name,
+ #maf = self.maf,
+ #manhattan_plot = self.manhattan_plot,
+ #mapping_scale = self.mapping_scale,
+ #chromosomes = chromosome_mb_lengths,
+ #qtl_results = self.qtl_results,
+ categorical_vars=self.categorical_vars,
+ chr_lengths=chr_lengths,
+ num_perm=self.num_perm,
+ perm_results=self.perm_output,
+ significant=significant_for_browser,
+ browser_files=browser_files,
+ selected_chr=this_chr,
+ total_markers=total_markers
+ )
+ else:
+ self.js_data = dict(
+ chr_lengths=chr_lengths,
+ browser_files=browser_files,
+ selected_chr=this_chr,
+ total_markers=total_markers
+ )
+
def run_rqtl_plink(self):
# os.chdir("") never do this inside a webserver!!
diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py
index 7b9ff8fe..55b0278a 100644
--- a/wqflask/wqflask/model.py
+++ b/wqflask/wqflask/model.py
@@ -36,7 +36,7 @@ class User(Base):
# json detailing when they became a superuser, otherwise empty
superuser = Column(Text)
- # if not superuser
+ # if not superuser
logins = relationship("Login",
order_by="desc(Login.timestamp)",
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 0d2fb2f8..2e1cb992 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -78,7 +78,7 @@ class SearchResultPage:
try:
self.search()
except:
- self.search_term_exists = False
+ self.search_term_exists = False
self.too_many_results = False
if self.search_term_exists:
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index bfaed9c2..725e7c9e 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -464,49 +464,49 @@ def password_reset_step2():
def register_user(params):
- thank_you_mode = False
- errors = []
- user_details = {}
-
- user_details['email_address'] = params.get(
- 'email_address', '').encode("utf-8").strip()
- if not (5 <= len(user_details['email_address']) <= 50):
- errors.append(
- 'Email Address needs to be between 5 and 50 characters.')
- else:
- email_exists = get_user_by_unique_column(
- "email_address", user_details['email_address'])
- if email_exists:
- errors.append('User already exists with that email')
+ thank_you_mode = False
+ errors = []
+ user_details = {}
- user_details['full_name'] = params.get(
- 'full_name', '').encode("utf-8").strip()
- if not (5 <= len(user_details['full_name']) <= 50):
- errors.append('Full Name needs to be between 5 and 50 characters.')
+ user_details['email_address'] = params.get(
+ 'email_address', '').encode("utf-8").strip()
+ if not (5 <= len(user_details['email_address']) <= 50):
+ errors.append(
+ 'Email Address needs to be between 5 and 50 characters.')
+ else:
+ email_exists = get_user_by_unique_column(
+ "email_address", user_details['email_address'])
+ if email_exists:
+ errors.append('User already exists with that email')
- user_details['organization'] = params.get(
- 'organization', '').encode("utf-8").strip()
- if user_details['organization'] and not (5 <= len(user_details['organization']) <= 50):
- errors.append(
- 'Organization needs to be empty or between 5 and 50 characters.')
+ user_details['full_name'] = params.get(
+ 'full_name', '').encode("utf-8").strip()
+ if not (5 <= len(user_details['full_name']) <= 50):
+ errors.append('Full Name needs to be between 5 and 50 characters.')
- password = str(params.get('password', ''))
- if not (6 <= len(password)):
- errors.append('Password needs to be at least 6 characters.')
+ user_details['organization'] = params.get(
+ 'organization', '').encode("utf-8").strip()
+ if user_details['organization'] and not (5 <= len(user_details['organization']) <= 50):
+ errors.append(
+ 'Organization needs to be empty or between 5 and 50 characters.')
- if params.get('password_confirm') != password:
- errors.append("Passwords don't match.")
+ password = str(params.get('password', ''))
+ if not (6 <= len(password)):
+ errors.append('Password needs to be at least 6 characters.')
- user_details['password'] = set_password(password)
- user_details['user_id'] = str(uuid.uuid4())
- user_details['confirmed'] = 1
+ if params.get('password_confirm') != password:
+ errors.append("Passwords don't match.")
- user_details['registration_info'] = basic_info()
+ user_details['password'] = set_password(password)
+ user_details['user_id'] = str(uuid.uuid4())
+ user_details['confirmed'] = 1
- if len(errors) == 0:
- save_user(user_details, user_details['user_id'])
+ user_details['registration_info'] = basic_info()
+
+ if len(errors) == 0:
+ save_user(user_details, user_details['user_id'])
- return errors
+ return errors
@app.route("/n/register", methods=('GET', 'POST'))