#! /usr/bin/env python

'''

Created on Aug 8, 2013

@author: smirarab

'''

import sys

from pasta.alignment import CompactAlignment

import argparse

from copy import copy

if __name__ == '__main__':

parser = argparse.ArgumentParser(description='Manipulate Alignments')

parser.add_argument('-infile', nargs='?', type=argparse.FileType('r'), default=sys.stdin,

help='name of the input file (default: standard input)')

parser.add_argument('-outfile', nargs='?', type=argparse.FileType('w'), default=sys.stdout,

help='name of the output file (default: standard output)')

parser.add_argument('-informat', nargs='?', default="FASTA", choices = ["COMPACT3", "FASTA"],

help='format of the input file (default: FASTA)')

parser.add_argument('-outformat', nargs='?', default="FASTA", choices = ["COMPACT3", "FASTA", "PHYLIP"],

help='format of the output file (default: FASTA)')

parser.add_argument('-masksites', metavar='N', type=int,

help='sites with less than N non-gap characters will be masked out')

parser.add_argument('-filterfragments', metavar='N', type=int,

help='sequences with less than N non-gap sequences will be removed')

parser.add_argument('-rename', metavar='MappingFile', type=argparse.FileType('r'),

help='Rename sequences, according to the mapping file generated by PASTA')

# parser.add_argument('actions', nargs='*',

# help='a list of actions (separated by space). Supported actions are: mask (see maskmin), rename (see namemap)')

args = parser.parse_args()

alg = CompactAlignment()

alg.read_file_object(args.infile,args.informat)

# if args.actions:

# print >>sys.stderr, "will perform the following actions: %s" %",".join(args.actions)

# else:

# print >>sys.stderr, "No actions will be taken. Input in %s will be written to output in %s." %(args.informat,args.outformat)

if args.masksites:

alg.mask_gapy_sites(args.masksites)

if args.filterfragments:

rem = []

for k, v in alg.items():

if len(v.seq) < args.filterfragments:

rem.append(k)

for k in rem:

alg.pop(k, None)

if args.rename:

lines=[x for x in args.rename.readlines() if x!="\n"]

namemap=dict(list(zip((x.strip() for i,x in enumerate(lines) if i%2 == 0),

(x.strip() for i,x in enumerate(lines) if i%2 == 1))))

names = copy(list(alg.keys()))

for k in names:

alg[namemap[k]] = alg.pop(k)

alg.write(args.outfile, args.outformat)