#!/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 simplejson as json

from pprint import pformat as pf


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_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)