diff options
Diffstat (limited to 'wqflask/maintenance/geno_to_json.py')
| -rw-r--r-- | wqflask/maintenance/geno_to_json.py | 196 |
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) |