merge changes

1 files changed, 0 insertions, 196 deletions

diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
deleted file mode 100644
index 32e0e34b..00000000
--- a/wqflask/maintenance/geno_to_json.py
+++ /dev/null
@@ -1,196 +0,0 @@
-#!/usr/bin/python
-
-"""
-Convert .geno files to json
-
-This file goes through all of the genofiles in the genofile directory (.geno)
-and converts them to json files that are used when running the marker regression
-code
-
-"""
-
-import sys
-sys.path.append("..")
-import os
-import glob
-import traceback
-import gzip
-
-#import numpy as np
-#from pyLMM import lmm
-
-import simplejson as json
-
-from pprint import pformat as pf
-
-#from utility.tools import flat_files
-
-
-class EmptyConfigurations(Exception):
-    pass
-
-
-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, output_file):
-
-        self.input_file = input_file
-        self.output_file = output_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
-
-    def convert(self):
-
-        self.haplotype_notation = {
-            '@mat': "1",
-            '@pat': "0",
-            '@het': "0.5",
-            '@unk': "NA"
-        }
-
-        self.configurations = {}
-        #self.skipped_cols = 3
-
-        # if self.input_file.endswith(".geno.gz"):
-        #    print("self.input_file: ", self.input_file)
-        #    self.input_fh = gzip.open(self.input_file)
-        # else:
-        self.input_fh = open(self.input_file)
-
-        with open(self.output_file, "w") as self.output_fh:
-            # if self.file_type == "geno":
-            self.process_csv()
-            # elif self.file_type == "snps":
-            #    self.process_snps_file()
-
-    def process_csv(self):
-        for row_count, row in enumerate(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() in self.configurations:
-                    this_marker.genotypes.append(
-                        self.configurations[genotype.upper()])
-                else:
-                    this_marker.genotypes.append("NA")
-
-            #print("this_marker is:", pf(this_marker.__dict__))
-            # if this_marker.chr == "14":
-            self.markers.append(this_marker.__dict__)
-
-        with open(self.output_file, 'w') as fh:
-            json.dump(self.markers, fh, indent="   ", sort_keys=True)
-
-            # print('configurations:', str(configurations))
-            #self.latest_col_pos = item_count + self.skipped_cols
-            #self.latest_col_value = item
-
-            # if item_count != 0:
-            #    self.output_fh.write(" ")
-            # self.output_fh.write(self.configurations[item.upper()])
-
-            # self.output_fh.write("\n")
-
-    def process_rows(self):
-        for self.latest_row_pos, row in enumerate(self.input_fh):
-            # if self.input_file.endswith(".geno.gz"):
-            #    print("row: ", row)
-            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
-                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
-
-    @classmethod
-    def process_all(cls, old_directory, new_directory):
-        os.chdir(old_directory)
-        for input_file in glob.glob("*"):
-            if not input_file.endswith(('geno', '.geno.gz')):
-                continue
-            group_name = ".".join(input_file.split('.')[:-1])
-            output_file = os.path.join(new_directory, group_name + ".json")
-            print("%s -> %s" % (
-                os.path.join(old_directory, input_file), output_file))
-            convertob = ConvertGenoFile(input_file, output_file)
-            try:
-                convertob.convert()
-            except EmptyConfigurations as why:
-                print("  No config info? Continuing...")
-                #excepted = True
-                continue
-            except Exception as why:
-
-                print("  Exception:", why)
-                print(traceback.print_exc())
-                print("    Found in row %s at tabular column %s" % (convertob.latest_row_pos,
-                                                                    convertob.latest_col_pos))
-                print("    Column is:", convertob.latest_col_value)
-                print("    Row is:", convertob.latest_row_value)
-                break
-
-    # def process_snps_file(cls, snps_file, new_directory):
-    #    output_file = os.path.join(new_directory, "mouse_families.json")
-    #    print("%s -> %s" % (snps_file, output_file))
-    #    convertob = ConvertGenoFile(input_file, output_file)
-
-
-if __name__ == "__main__":
-    Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype"""
-    New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/json"""
-    #Input_File = """/home/zas1024/gene/genotype_files/genotypes/BXD.geno"""
-    #Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps"""
-    #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json")
-    # convertob.convert()
-    ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
-    # ConvertGenoFiles(Geno_Directory)
-
-    #process_csv(Input_File, Output_File)