Script for conversion of datafiles from Genepop to metapop

g2m.py

#! /usr/bin/env python
__author__="Andres Perez-Figueroa"
__date__ ="$14-jan-2016$"
__version_="2.0"

### Conversor from genepop to metapop
### Requires Biopython

### run: python g2m.py
### The program will ask for your datafile in genepop format
### Then will create a metapop file with the extension .mtp

### IF you want to include sex information in the genepop coded as /m or /f at the end of the individual labels

from sys import exit
from Bio.PopGen import GenePop

if __name__ == "__main__":
    print "G2M 2.0 - File conversor from Genepop to Metapop"
    genepopfile=raw_input('Name of the source file (genepop format): ')

    try:
        handle = open(genepopfile)
        rec = GenePop.read(handle)
        handle.close()
    except IOError:
        print "Can not open file " + genepopfile + " to read. Exiting"
        exit(2)

    loci=len(rec.loci_list)
    pops=len(rec.populations)

    print""
    metapopfile=genepopfile+".mtp"
    try:
        f = open(metapopfile, "w")
    except IOError:
        print "Can not open file " + metapopfile + " to write. Exiting"
        exit(2)

    f.write("n\t%d\n" % (pops))
    f.write("nloci\t%d\n" % (loci))
    counter = 1
    for p in range(pops):
        
        thisPop=rec.populations[p]
        popName=thisPop[0][0].lstrip().split('/')[0]
        f.write("%s\n" %(popName))
        inds=len(thisPop)
        f.write("N\t%d\n"%(inds))
        f.write("Ne\t%d\n"%(inds))
        f.write("newN\t%d\t%d\n"%(inds/2, inds/2))
        for i in range(inds):
            name = thisPop[i][0].lstrip()
            sex = 0
            if name.endswith("/1") or name.endswith("/m"):
                sex = 1
            name = popName + '_'+ str(i)
            f.write("%d\t%s\t%d\t" % (counter, name, sex))
            for l in range(loci):
                al1=str(thisPop[i][1][l][0]).replace('None','0')
                al2=str(thisPop[i][1][l][1]).replace('None','0')
                f.write("%s  %s\t" % (al1, al2))
            f.write("\n")
            counter +=1
    f.close()
    print "Finished!"