script to produce msa and hmm in the format fDOG-Assembly requires from a fasta file

Author: HannahBioI

fdog/makeCoreGroupFromFasta.py

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+# -*- coding: utf-8 -*-
+
+#######################################################################
+# Copyright (C) 2021 Hannah Muelbaier
+#
+#  This script is used to prepare the core group used as input for fDOG-Assembly from a fasta file of an ortholog group.
+#
+#  This script 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 <http://www.gnu.org/licenses/> for
+#  more details
+#
+#  Contact: [email protected]
+#
+#######################################################################
+
+############################ imports ##################################
+import os
+import os.path
+import sys
+import argparse
+import fdog.libs.alignment as align_fn
+import fdog.libs.zzz as general_fn
+
+def check_fasta(file):
+    nHeader = general_fn.count_line(file, '>', True)
+    nSeq = general_fn.count_line(file, '>', False)
+    if not nHeader == nSeq:
+        return(1)
+    return(0)
+
+def make_single_line_fasta(input, gene, out_folder):
+    print(out_folder)
+    output = out_folder + gene + ".fa"
+    print(output)
+    with open(input, 'r') as f_input, open(output, 'w') as f_output:
+        block = []
+        for line in f_input:
+            if line.startswith('>'):
+                if block:
+                    f_output.write(''.join(block) + '\n')
+                    block = []
+                f_output.write(line)
+            else:
+                block.append(line.strip())
+
+        if block:
+            f_output.write(''.join(block) + '\n')
+    return (output)
+
+def makeMSA(out_folder, gene, fasta_file):
+    aln_file = out_folder + gene + '.aln'
+    if align_fn.get_muscle_version('muscle') == 'v3':
+        os.system('muscle -quiet -in %s -out %s' % (fasta_file, aln_file))
+        #print("muscle -quiet -in " + output_file + " -out " + aln_file)
+    else:
+        os.system('muscle -quiet -align %s -out %s' % (fasta_file, aln_file))
+    return aln_file
+
+def makeHMM(out_folder, gene, aln_file):
+    hmm_dir = out_folder + 'hmm_dir'
+    os.system('mkdir %s >/dev/null 2>&1' % (hmm_dir))
+    out_file = '%s/%s.hmm' % (hmm_dir, gene)
+    hmmbuild_cmd = 'hmmbuild --amino %s %s' % (out_file, aln_file)
+    os.system(hmmbuild_cmd)
+    return out_file
+
+
+def main():
+
+    #################### handle user input #####################################
+    version = '0.0.1'
+    ################### initialize parser ######################################
+    parser = argparse.ArgumentParser(description='You are running fdog.addCoreGroup version ' + str(version) + '.')
+    ################## required arguments ######################################
+    required = parser.add_argument_group('Required arguments')
+    required.add_argument('--fasta', help='Path to fasta file of ortholog group.', action='store', default='', required=True)
+    required.add_argument('--out', help='Path to output folder.', action='store', default='', required=True)
+    required.add_argument('--geneName', help='Path to output folder.', action='store', default='', required=True)
+    args = parser.parse_args()
+
+    fasta_file_input = args.fasta
+    out_folder = args.out
+    gene = args.geneName
+
+
+    out_folder = out_folder + '/' + gene + '/'
+    os.system('mkdir %s >/dev/null 2>&1' % (out_folder))
+
+    if check_fasta(fasta_file_input) == 1:
+        fasta_file = make_single_line_fasta(fasta_file_input, gene, out_folder)
+    else:
+        fasta_file = out_folder + gene + '.fa'
+        os.system('cp ' + fasta_file_input + ' ' + fasta_file)
+
+    aln_file = makeMSA(out_folder, gene, fasta_file)
+    hmm_file = makeHMM(out_folder, gene, aln_file)
+
+    print('Core group located at %s. Fasta file: %s; MSA: %s; HMM: %s' % (out_folder, fasta_file, aln_file, hmm_file))
+
+main()