ddrad_scripts/popmap2exDFOIL.py at master · btmartin721/ddrad_scripts · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
#!/usr/bin/env python3

### This script was written by Bradley T. Martin, PhD candidate,
### University of Arkansas, Dept. of Biological Sciences
### Please submit any issues or bug reports to: btm002@email.uark.edu

import argparse
import sys

import numpy as np
import pandas as pd

from functools import reduce

def main():

    args = Get_Arguments()

    pop = args.popmap
    batch = args.batch
    species = args.species
    subspecies = args.subspecies

    validate_file_exists(pop)
    poplist = read_popmap(pop)
    popdf = pd.DataFrame.from_records(poplist, columns = ["Individual", "popID"])

    batchdf = pd.DataFrame()
    spdf = pd.DataFrame()
    subspdf = pd.DataFrame()

    if batch is not None:
        validate_file_exists(batch)
        batchlist = read_popmap(batch)
        batchdf = pd.DataFrame.from_records(batchlist, columns = ["Individual", "batch"])

    if species is not None:
        validate_file_exists(species)
        splist = read_popmap(species)
        spdf = pd.DataFrame.from_records(splist, columns = ["Individual", "speciesID"])

    if subspecies is not None:
        validate_file_exists(subspecies)
        subsplist = read_popmap(subspecies)
        subspdf = pd.DataFrame.from_records(subsplist, columns = ["Individual", "subspeciesID"])

    tmpdfs = [batchdf, popdf, spdf, subspdf]

    dfs = list()
    for df in tmpdfs:
        if not df.empty:
            dfs.append(df)

    if not dfs:
        print("Error: Was not able to join files. Make sure each individualID is present in all files.")

    df_final = merge_dataframes(dfs)
    df_final.to_csv(args.outfile, sep = " ", header = True, index = False)

    return 0

def merge_dataframes(dfs):

    df_final = reduce(lambda left, right: pd.merge(left, right, on="Individual"), dfs)
    return df_final

def read_popmap(file):
    """
    Function to read a population map file in the format: indID\tpopID
    Input:
        filename (string)
        Returns:
        list of tuples containing (indID, popID) (list)
        """
    list_of_tuples = list()
    with open(file, "r") as fin:
        for line in fin:
            line = line.strip()
            if not line:
                continue
            cols = line.split()
            my_tuple = (cols[0], cols[1])
            list_of_tuples.append(my_tuple)
    return list_of_tuples


def validate_file_exists(filename):
    """
    Function to validate that an input file exists.
    Input:
        filename (string)
    Returns:
        None
    """
    try:
        file = open(filename, "r")
        file.close()
    except IOError:
        print("\nError: The file " + filename + " does not exist or could not be read.\n")
        sys.exit(1)

def Get_Arguments():
    """
    Parse command-line arguments. Imported with argparse.
    Returns: object of command-line arguments.
    """
    parser = argparse.ArgumentParser(description="Adds batch, species, subspecies "
                                    "columns to popmap file for summarizing ExDFOIL output",
                                    add_help=False)

    required_args = parser.add_argument_group("Required Arguments")
    optional_args = parser.add_argument_group("Optional Arguments")

    ## Required Arguments
    required_args.add_argument("-p", "--popmap",
                                type=str,
                                required=True,
                                help="String; Tab-separated popmap file: indID\tpopID")

    ## Optional Arguments
    optional_args.add_argument("-b", "--batch",
                                type=str,
                                required=False,
                                default=None,
                                nargs="?",
                                help="Filename containing batchIDs")
    optional_args.add_argument("-S", "--species",
                                type=str,
                                required=False,
                                default=None,
                                nargs="?",
                                help="Filename containing speciesIDs")
    optional_args.add_argument("-s", "--subspecies",
                                type=str,
                                required=False,
                                default=None,
                                nargs="?",
                                help="Filename containing subspeciesIDs")
    optional_args.add_argument("-o", "--outfile",
                                type=str,
                                required=False,
                                default="mysampleinfo.txt",
                                nargs="?",
                                help="Specify output filename; default=mysampleinfo.txt")
    optional_args.add_argument("-h", "--help",
                                action="help",
                                help="Displays this help menu")


    args = parser.parse_args()

    return args


if __name__ == "__main__":

    rtrn_code = main()
    print("\nProgram finished with exit status " + str(rtrn_code) + "\n")
    sys.exit(rtrn_code)