diff options
Diffstat (limited to 'wqflask/maintenance/geno_to_json.py')
| -rw-r--r-- | wqflask/maintenance/geno_to_json.py | 82 |
1 files changed, 41 insertions, 41 deletions
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py index 7e7fd241..32e0e34b 100644 --- a/wqflask/maintenance/geno_to_json.py +++ b/wqflask/maintenance/geno_to_json.py @@ -25,11 +25,12 @@ from pprint import pformat as pf #from utility.tools import flat_files -class EmptyConfigurations(Exception): pass - +class EmptyConfigurations(Exception): + pass -class Marker(object): + +class Marker: def __init__(self): self.name = None self.chr = None @@ -37,23 +38,24 @@ class Marker(object): self.Mb = None self.genotypes = [] -class ConvertGenoFile(object): + +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 = { @@ -61,24 +63,23 @@ class ConvertGenoFile(object): '@pat': "0", '@het': "0.5", '@unk': "NA" - } - + } + self.configurations = {} #self.skipped_cols = 3 - - #if self.input_file.endswith(".geno.gz"): + + # if self.input_file.endswith(".geno.gz"): # print("self.input_file: ", self.input_file) # self.input_fh = gzip.open(self.input_file) - #else: + # else: self.input_fh = open(self.input_file) - + with open(self.output_file, "w") as self.output_fh: - #if self.file_type == "geno": + # if self.file_type == "geno": self.process_csv() - #elif self.file_type == "snps": + # 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") @@ -100,31 +101,31 @@ class ConvertGenoFile(object): 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()]) + 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": + + #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") + # 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"): + # if self.input_file.endswith(".geno.gz"): # print("row: ", row) self.latest_row_value = row # Take care of headers @@ -171,26 +172,25 @@ class ConvertGenoFile(object): print(" Exception:", why) print(traceback.print_exc()) print(" Found in row %s at tabular column %s" % (convertob.latest_row_pos, - convertob.latest_col_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): + + # 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__": +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() + # convertob.convert() ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory) - #ConvertGenoFiles(Geno_Directory) - + # ConvertGenoFiles(Geno_Directory) + #process_csv(Input_File, Output_File) |