merge changes

1 files changed, 0 insertions, 100 deletions

diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
deleted file mode 100644
index 86d9823e..00000000
--- a/wqflask/utility/genofile_parser.py
+++ /dev/null
@@ -1,100 +0,0 @@
-# CTL analysis for GN2
-# Author / Maintainer: Danny Arends <Danny.Arends@gmail.com>
-
-import sys
-import os
-import glob
-import traceback
-import gzip
-
-
-import simplejson as json
-
-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 = []
-
-
-class ConvertGenoFile:
-
-    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_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_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__)