aboutsummaryrefslogtreecommitdiff
path: root/wqflask/utility
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask/utility')
-rw-r--r--wqflask/utility/gen_geno_ob.py270
-rw-r--r--wqflask/utility/tools.py9
-rw-r--r--wqflask/utility/type_checking.py2
3 files changed, 145 insertions, 136 deletions
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
index 5824b0b3..5172369f 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/wqflask/utility/gen_geno_ob.py
@@ -1,135 +1,137 @@
-from __future__ import absolute_import, division, print_function
-
-class genotype(object):
- """
- Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure
- """
-
- def __init__(self, filename):
- self.group = None
- self.type = "riset"
- self.prgy = []
- self.nprgy = 0
- self.mat = -1
- self.pat = 1
- self.het = 0
- self.unk = "U"
- self.filler = False
- self.mb_exists = False
-
- #ZS: This is because I'm not sure if some files switch the column that contains Mb/cM positions; might be unnecessary
- self.cm_column = 2
- self.mb_column = 3
-
- self.chromosomes = []
-
- self.read_file(filename)
-
- def __iter__(self):
- return iter(self.chromosomes)
-
- def __getitem__(self, index):
- return self.chromosomes[index]
-
- def __len__(self):
- return len(self.chromosomes)
-
- def read_file(self, filename):
-
- with open(filename, 'r') as geno_file:
- lines = geno_file.readlines()
-
- this_chr = "" #ZS: This is so it can track when the chromosome changes as it iterates through markers
- chr_ob = None
- for line in lines:
- if line[0] == "#":
- continue
- elif line[0] == "@":
- label = line.split(":")[0][1:]
- if label == "name":
- self.group = line.split(":")[1]
- elif label == "filler":
- if line.split(":")[1] == "yes":
- self.filler = True
- elif label == "type":
- self.type = line.split(":")[1]
- elif label == "mat":
- self.mat = line.split(":")[1]
- elif label == "pat":
- self.pat = line.split(":")[1]
- elif label == "het":
- self.het = line.split(":")[1]
- elif label == "unk":
- self.unk = line.split(":")[1]
- else:
- continue
- elif line[:3] == "Chr":
- header_row = line.split("\t")
- if header_row[2] == "Mb":
- self.mb_exists = True
- self.mb_column = 2
- self.cm_column = 3
- elif header_row[3] == "Mb":
- self.mb_exists = True
- self.mb_column = 3
- elif header_row[2] == "cM":
- self.cm_column = 2
-
- if self.mb_exists:
- self.prgy = header_row[4:]
- else:
- self.prgy = header_row[3:]
- self.nprgy = len(self.prgy)
- else:
- if line.split("\t")[0] != this_chr:
- if this_chr != "":
- self.chromosomes.append(chr_ob)
- this_chr = line.split("\t")[0]
- chr_ob = Chr(line.split("\t")[0], self)
- chr_ob.add_marker(line.split("\t"))
-
-class Chr(object):
- def __init__(self, name, geno_ob):
- self.name = name
- self.loci = []
- self.mb_exists = geno_ob.mb_exists
- self.cm_column = geno_ob.cm_column
- self.mb_column = geno_ob.mb_column
- self.geno_ob = geno_ob
-
- def __iter__(self):
- return iter(self.loci)
-
- def __getitem__(self, index):
- return self.loci[index]
-
- def __len__(self):
- return len(self.loci)
-
- def add_marker(self, marker_row):
- self.loci.append(Locus(marker_row, self.geno_ob))
-
-class Locus(object):
- def __init__(self, marker_row, geno_ob):
- self.chr = marker_row[0]
- self.name = marker_row[1]
- self.cM = float(marker_row[geno_ob.cm_column])
- self.Mb = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None
-
- geno_table = {
- geno_ob.mat: -1,
- geno_ob.pat: 1,
- geno_ob.het: 0,
- geno_ob.unk: "U"
- }
-
- self.genotype = []
- if geno_ob.mb_exists:
- start_pos = 4
- else:
- start_pos = 3
- for allele in marker_row[start_pos:]:
- if allele in geno_table.keys():
- self.genotype.append(geno_table[allele])
- else: #ZS: Some genotype appears that isn't specified in the metadata, make it unknown
+from __future__ import absolute_import, division, print_function
+
+class genotype(object):
+ """
+ Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure
+ """
+
+ def __init__(self, filename):
+ self.group = None
+ self.type = "riset"
+ self.prgy = []
+ self.nprgy = 0
+ self.mat = -1
+ self.pat = 1
+ self.het = 0
+ self.unk = "U"
+ self.filler = False
+ self.mb_exists = False
+
+ #ZS: This is because I'm not sure if some files switch the column that contains Mb/cM positions; might be unnecessary
+ self.cm_column = 2
+ self.mb_column = 3
+
+ self.chromosomes = []
+
+ self.read_file(filename)
+
+ def __iter__(self):
+ return iter(self.chromosomes)
+
+ def __getitem__(self, index):
+ return self.chromosomes[index]
+
+ def __len__(self):
+ return len(self.chromosomes)
+
+ def read_file(self, filename):
+
+ with open(filename, 'r') as geno_file:
+ lines = geno_file.readlines()
+
+ this_chr = "" #ZS: This is so it can track when the chromosome changes as it iterates through markers
+ chr_ob = None
+ for line in lines:
+ if line[0] == "#":
+ continue
+ elif line[0] == "@":
+ label = line.split(":")[0][1:]
+ if label == "name":
+ self.group = line.split(":")[1]
+ elif label == "filler":
+ if line.split(":")[1] == "yes":
+ self.filler = True
+ elif label == "type":
+ self.type = line.split(":")[1]
+ elif label == "mat":
+ self.mat = line.split(":")[1]
+ elif label == "pat":
+ self.pat = line.split(":")[1]
+ elif label == "het":
+ self.het = line.split(":")[1]
+ elif label == "unk":
+ self.unk = line.split(":")[1]
+ else:
+ continue
+ elif line[:3] == "Chr":
+ header_row = line.split("\t")
+ if header_row[2] == "Mb":
+ self.mb_exists = True
+ self.mb_column = 2
+ self.cm_column = 3
+ elif header_row[3] == "Mb":
+ self.mb_exists = True
+ self.mb_column = 3
+ elif header_row[2] == "cM":
+ self.cm_column = 2
+
+ if self.mb_exists:
+ self.prgy = header_row[4:]
+ else:
+ self.prgy = header_row[3:]
+ self.nprgy = len(self.prgy)
+ else:
+ if line.split("\t")[0] != this_chr:
+ if this_chr != "":
+ self.chromosomes.append(chr_ob)
+ this_chr = line.split("\t")[0]
+ chr_ob = Chr(line.split("\t")[0], self)
+ chr_ob.add_marker(line.split("\t"))
+
+ self.chromosomes.append(chr_ob)
+
+class Chr(object):
+ def __init__(self, name, geno_ob):
+ self.name = name
+ self.loci = []
+ self.mb_exists = geno_ob.mb_exists
+ self.cm_column = geno_ob.cm_column
+ self.mb_column = geno_ob.mb_column
+ self.geno_ob = geno_ob
+
+ def __iter__(self):
+ return iter(self.loci)
+
+ def __getitem__(self, index):
+ return self.loci[index]
+
+ def __len__(self):
+ return len(self.loci)
+
+ def add_marker(self, marker_row):
+ self.loci.append(Locus(marker_row, self.geno_ob))
+
+class Locus(object):
+ def __init__(self, marker_row, geno_ob):
+ self.chr = marker_row[0]
+ self.name = marker_row[1]
+ self.cM = float(marker_row[geno_ob.cm_column])
+ self.Mb = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None
+
+ geno_table = {
+ geno_ob.mat: -1,
+ geno_ob.pat: 1,
+ geno_ob.het: 0,
+ geno_ob.unk: "U"
+ }
+
+ self.genotype = []
+ if geno_ob.mb_exists:
+ start_pos = 4
+ else:
+ start_pos = 3
+ for allele in marker_row[start_pos:]:
+ if allele in geno_table.keys():
+ self.genotype.append(geno_table[allele])
+ else: #ZS: Some genotype appears that isn't specified in the metadata, make it unknown
self.genotype.append("U") \ No newline at end of file
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 8b2260f5..ec9f01bd 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -107,6 +107,9 @@ def js_path(module=None):
return try_guix
raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)"
+def reaper_command(guess=None):
+ return get_setting("REAPER_COMMAND",guess)
+
def gemma_command(guess=None):
return assert_bin(get_setting("GEMMA_COMMAND",guess))
@@ -274,6 +277,7 @@ SMTP_CONNECT = get_setting('SMTP_CONNECT')
SMTP_USERNAME = get_setting('SMTP_USERNAME')
SMTP_PASSWORD = get_setting('SMTP_PASSWORD')
+REAPER_COMMAND = app_set("REAPER_COMMAND",reaper_command())
GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command())
assert(GEMMA_COMMAND is not None)
PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command())
@@ -285,11 +289,14 @@ assert_dir(TEMPDIR)
JS_GUIX_PATH = get_setting("JS_GUIX_PATH")
assert_dir(JS_GUIX_PATH)
assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom')
+
CSS_PATH = "UNKNOWN"
# assert_dir(JS_PATH)
-JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("Twitter-Post-Fetcher"))
+
+JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("javascript-twitter-post-fetcher"))
assert_dir(JS_TWITTER_POST_FETCHER_PATH)
assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js")
+
JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH",js_path("cytoscape"))
assert_dir(JS_CYTOSCAPE_PATH)
assert_file(JS_CYTOSCAPE_PATH+'/cytoscape.min.js')
diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py
index 220e5f62..f15b17e2 100644
--- a/wqflask/utility/type_checking.py
+++ b/wqflask/utility/type_checking.py
@@ -27,7 +27,7 @@ def get_float(vars,name,default=None):
if name in vars:
if is_float(vars[name]):
return float(vars[name])
- return None
+ return default
def get_int(vars,name,default=None):
if name in vars:
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-25 15:15:55 +0000