merge changes

1 files changed, 0 insertions, 182 deletions

diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
deleted file mode 100644
index c7a1ea59..00000000
--- a/wqflask/utility/gen_geno_ob.py
+++ /dev/null
@@ -1,182 +0,0 @@
-class genotype:
-    """
-    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_rdata_output(self, qtl_results):
-        # ZS: This is necessary because R/qtl requires centimorgan marker positions, which it normally gets from the .geno file, but that doesn't exist for HET3-ITP (which only has RData), so it needs to read in the marker cM positions from the results
-        # ZS: Overwriting since the .geno file's contents are just placeholders
-        self.chromosomes = []
-
-        this_chr = ""  # ZS: This is so it can track when the chromosome changes as it iterates through markers
-        chr_ob = None
-        for marker in qtl_results:
-            locus = Locus(self)
-            # ZS: This is really awkward but works as a temporary fix
-            if (str(marker['chr']) != this_chr) and this_chr != "X":
-                if this_chr != "":
-                    self.chromosomes.append(chr_ob)
-                this_chr = str(marker['chr'])
-                if this_chr == "20":
-                    this_chr = "X"
-                chr_ob = Chr(this_chr, self)
-            if 'chr' in marker:
-                locus.chr = str(marker['chr'])
-            if 'name' in marker:
-                locus.name = marker['name']
-            if 'Mb' in marker:
-                locus.Mb = marker['Mb']
-            if 'cM' in marker:
-                locus.cM = marker['cM']
-            chr_ob.loci.append(locus)
-
-        self.chromosomes.append(chr_ob)
-
-        return self
-
-    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].strip()
-                    elif label == "filler":
-                        if line.split(":")[1].strip() == "yes":
-                            self.filler = True
-                    elif label == "type":
-                        self.type = line.split(":")[1].strip()
-                    elif label == "mat":
-                        self.mat = line.split(":")[1].strip()
-                    elif label == "pat":
-                        self.pat = line.split(":")[1].strip()
-                    elif label == "het":
-                        self.het = line.split(":")[1].strip()
-                    elif label == "unk":
-                        self.unk = line.split(":")[1].strip()
-                    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:
-    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(self.geno_ob, marker_row))
-
-
-class Locus:
-    def __init__(self, geno_ob, marker_row=None):
-        self.chr = None
-        self.name = None
-        self.cM = None
-        self.Mb = None
-        self.genotype = []
-        if marker_row:
-            self.chr = marker_row[0]
-            self.name = marker_row[1]
-            try:
-                self.cM = float(marker_row[geno_ob.cm_column])
-            except:
-                self.cM = float(
-                    marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else 0
-            try:
-                self.Mb = float(
-                    marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None
-            except:
-                self.Mb = self.cM
-
-            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 list(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")