--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/utils/strip_alignment.py	Wed Jan 22 08:41:44 2020 -0500
@@ -0,0 +1,167 @@
+#!/usr/bin/env python
+
+# -*- coding: utf-8 -*-
+
+"""
+strip_alignment.py - Strip alignment positions containing gaps,
+missing data and invariable positions
+<https://github.com/B-UMMI/ReMatCh/>
+
+Copyright (C) 2017 Miguel Machado <mpmachado@medicina.ulisboa.pt>
+
+Last modified: March 20, 2017
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+from Bio import SeqIO
+import os
+import argparse
+import sys
+
+
+version = '0.1'
+
+
+def get_sequences(infile):
+    print 'Getting sequences'
+    sequences_SeqIO = list(SeqIO.parse(infile, 'fasta'))
+
+    sequence_length = None
+    sequences_dict = {}
+    all_executed_printed = False
+    for x, sequence in enumerate(sequences_SeqIO):
+        if sequence_length is None:
+            sequence_length = len(sequence.seq)
+        if sequence_length != len(sequence.seq):
+            sys.exit('Sequences with different length!')
+        sequences_dict[sequence.id] = list(sequence.seq)
+
+        if (x + 1) % 10 == 0:
+            print '\n' + str(round((float(x + 1) / len(sequences_SeqIO)) * 100, 2)) + '% of sequences already processed (getting sequences)'
+            if x + 1 == len(sequences_SeqIO):
+                all_executed_printed = True
+    if not all_executed_printed:
+        print '\n' + str(round((float(x + 1) / len(sequences_SeqIO)) * 100, 2)) + '% of sequences already processed (getting sequences)'
+
+    return sequences_dict, sequence_length
+
+
+def positions_type(sequences_dict, sequence_length, notGAPs, notMissing, notInvariable):
+    print 'Determining positions type'
+    positions_2_keep = []
+    invariable = []
+    missing = []
+    gaps = []
+    gaps_missing = 0
+    all_executed_printed = False
+    for i in range(0, sequence_length):
+        data = []
+        for sample in sequences_dict:
+            data.append(sequences_dict[sample][i])
+        possibilities = set(data)
+        if len(possibilities) == 1:
+            invariable.append(i)
+        if len(possibilities.intersection(set(['N']))) > 0:
+            missing.append(i)
+        if len(possibilities.intersection(set(['-']))) > 0:
+            gaps.append(i)
+        if len(possibilities.intersection(set(['N', '-']))) > 0:
+            gaps_missing += 1
+        if len(possibilities) > 1 and len(possibilities.intersection(set(['N', '-']))) == 0:
+            positions_2_keep.append(i)
+
+        if (i + 1) % 10000 == 0:
+            print '\n' + str(round((float(i + 1) / sequence_length) * 100, 2)) + '% of positions already processed (determining positions type)'
+            if i + 1 == len(sequences_dict):
+                all_executed_printed = True
+        if not all_executed_printed:
+            print '\n' + str(round((float(i + 1) / sequence_length) * 100, 2)) + '% of positions already processed (determining positions type)'
+
+    print 'Positions to keep (no matter): ' + str(len(positions_2_keep))
+    print 'Invariable sites: ' + str(len(invariable))
+    print 'Positions with missing data ("N"): ' + str(len(missing))
+    print 'Positions with GAPs ("-"): ' + str(len(gaps))
+    print 'Positions with GAPs or missing data: ' + str(gaps_missing)
+
+    if notGAPs:
+        positions_2_keep.extend(gaps)
+    if notMissing:
+        positions_2_keep.extend(missing)
+    if notInvariable:
+        positions_2_keep.extend(invariable)
+
+    positions_2_keep = sorted(set(positions_2_keep))
+
+    print 'Positions to keep (final): ' + str(len(positions_2_keep))
+
+    return positions_2_keep
+
+
+def chunkstring(string, length):
+    return (string[0 + i:length + i] for i in range(0, len(string), length))
+
+
+def write_fasta(sequences_dict, positions_2_keep, outfile):
+    print 'Writing stripped sequences'
+    all_executed_printed = False
+    with open(outfile, 'wt') as writer:
+        for x, sample in enumerate(sequences_dict):
+            writer.write('>' + sample + '\n')
+            fasta_sequence_lines = chunkstring(''.join([sequences_dict[sample][i] for i in positions_2_keep]), 80)
+            for line in fasta_sequence_lines:
+                writer.write(line + '\n')
+
+            if (x + 1) % 100 == 0:
+                print '\n' + str(round((float(x + 1) / len(sequences_dict)) * 100, 2)) + '% of sequences already processed (writing stripped sequences)'
+                if x + 1 == len(sequences_dict):
+                    all_executed_printed = True
+        if not all_executed_printed:
+            print '\n' + str(round((float(x + 1) / len(sequences_dict)) * 100, 2)) + '% of sequences already processed (writing stripped sequences)'
+
+
+def strip_alignment(args):
+    outdir = os.path.dirname(os.path.abspath(args.outfile))
+    if not os.path.isdir(outdir):
+        os.makedirs(outdir)
+
+    outfile = os.path.abspath(args.outfile)
+
+    infile = os.path.abspath(args.infile.name)
+
+    sequences_dict, sequence_length = get_sequences(infile)
+    positions_2_keep = positions_type(sequences_dict, sequence_length, args.notGAPs, args.notMissing, args.notInvariable)
+    write_fasta(sequences_dict, positions_2_keep, outfile)
+
+
+def main():
+    parser = argparse.ArgumentParser(prog='strip_alignment.py', description='Strip alignment positions containing gaps, missing data and invariable positions', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument('--version', help='Version information', action='version', version=str('%(prog)s v' + version))
+
+    parser_required = parser.add_argument_group('Required options')
+    parser_required.add_argument('-i', '--infile', type=argparse.FileType('r'), metavar='/path/to/aligned/input/file.fasta', help='Path to the aligned fasta file', required=True)
+    parser_required.add_argument('-o', '--outfile', type=str, metavar='/path/to/stripped/output/file.fasta', help='Stripped output fasta file', required=True, default='alignment_stripped.fasta')
+
+    parser_optional_general = parser.add_argument_group('General facultative options')
+    parser_optional_general.add_argument('--notGAPs', action='store_true', help='Not strip positions with GAPs')
+    parser_optional_general.add_argument('--notMissing', action='store_true', help='Not strip positions with missing data')
+    parser_optional_general.add_argument('--notInvariable', action='store_true', help='Not strip invariable sites')
+
+    args = parser.parse_args()
+
+    strip_alignment(args)
+
+
+if __name__ == "__main__":
+    main()