aboutsummaryrefslogtreecommitdiff
path: root/wqflask/maintenance/convert_geno_to_bimbam.py
diff options
context:
space:
mode:
authoracenteno2020-04-21 17:35:34 -0500
committerGitHub2020-04-21 17:35:34 -0500
commit660589b9c2a507529e8e51ca6ce66ca97ad982c5 (patch)
tree27f63957278581bc2fce2b88744bfe20c8a81558 /wqflask/maintenance/convert_geno_to_bimbam.py
parentd97fdc18359233f07c1a1c7b83fe7e88eb225043 (diff)
parentf2a3ae13231a7d270a5bb6911c248aa713f1ef91 (diff)
downloadgenenetwork2-660589b9c2a507529e8e51ca6ce66ca97ad982c5.tar.gz
Merge pull request #1 from genenetwork/testing
Updating my testing branch
Diffstat (limited to 'wqflask/maintenance/convert_geno_to_bimbam.py')
-rw-r--r--wqflask/maintenance/convert_geno_to_bimbam.py190
1 files changed, 190 insertions, 0 deletions
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
new file mode 100644
index 00000000..528b98cf
--- /dev/null
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -0,0 +1,190 @@
+#!/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
+
+"""
+
+from __future__ import print_function, division, absolute_import
+import sys
+sys.path.append("..")
+import os
+import glob
+import traceback
+import gzip
+
+import simplejson as json
+
+from pprint import pformat as pf
+
+class EmptyConfigurations(Exception): pass
+
+class Marker(object):
+ def __init__(self):
+ self.name = None
+ self.chr = None
+ self.cM = None
+ self.Mb = None
+ self.genotypes = []
+
+class ConvertGenoFile(object):
+
+ def __init__(self, input_file, output_files):
+ self.input_file = input_file
+ self.output_files = output_files
+
+ 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.input_fh = open(self.input_file)
+
+ self.process_csv()
+
+ 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:
+ this_marker.genotypes.append("NA")
+
+ self.markers.append(this_marker.__dict__)
+
+ self.write_to_bimbam()
+
+ def write_to_bimbam(self):
+ with open(self.output_files[0], "w") as geno_fh:
+ for marker in self.markers:
+ geno_fh.write(marker['name'])
+ geno_fh.write(", X, Y")
+ geno_fh.write(", " + ", ".join(marker['genotypes']))
+ geno_fh.write("\n")
+
+ with open(self.output_files[1], "w") as pheno_fh:
+ for sample in self.sample_list:
+ pheno_fh.write("1\n")
+
+ with open(self.output_files[2], "w") as snp_fh:
+ for marker in self.markers:
+ if self.mb_exists:
+ snp_fh.write(marker['name'] +", " + str(int(float(marker['Mb'])*1000000)) + ", " + marker['chr'] + "\n")
+ else:
+ snp_fh.write(marker['name'] +", " + str(int(float(marker['cM'])*1000000)) + ", " + marker['chr'] + "\n")
+
+ def get_sample_list(self, row_contents):
+ self.sample_list = []
+ if self.mb_exists:
+ if self.cm_exists:
+ self.sample_list = row_contents[4:]
+ else:
+ self.sample_list = row_contents[3:]
+ else:
+ if self.cm_exists:
+ self.sample_list = row_contents[3:]
+ else:
+ self.sample_list = row_contents[2:]
+
+ 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
+ self.get_sample_list(row.split())
+ continue
+ if row.startswith('@'):
+ key, _separater, value = row.partition(':')
+ key = key.strip()
+ value = value.strip()
+ if key == "@filler":
+ raise EmptyConfigurations
+ 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])
+ if group_name == "HSNIH-Palmer":
+ continue
+ geno_output_file = os.path.join(new_directory, group_name + "_geno.txt")
+ pheno_output_file = os.path.join(new_directory, group_name + "_pheno.txt")
+ snp_output_file = os.path.join(new_directory, group_name + "_snps.txt")
+ output_files = [geno_output_file, pheno_output_file, snp_output_file]
+ print("%s -> %s" % (
+ os.path.join(old_directory, input_file), geno_output_file))
+ convertob = ConvertGenoFile(input_file, output_files)
+ try:
+ convertob.convert()
+ except EmptyConfigurations as why:
+ print(" No config info? Continuing...")
+ 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
+
+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/bimbam"""
+ #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) \ No newline at end of file