From e304c2cfdf1b38da483efa607a2acd72b66ad0de Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 24 May 2019 11:35:12 -0500
Subject: Replaced qtlreaper Dataset object with python object

---
 wqflask/utility/gen_geno_ob.py | 135 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 135 insertions(+)
 create mode 100644 wqflask/utility/gen_geno_ob.py

(limited to 'wqflask/utility')

diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
new file mode 100644
index 00000000..5824b0b3
--- /dev/null
+++ b/wqflask/utility/gen_geno_ob.py
@@ -0,0 +1,135 @@
+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
+                self.genotype.append("U")
\ No newline at end of file
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