Merge branch 'testing' into 360_update_htmlgen

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: