--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MakeDb.py	Mon Jul 17 07:44:27 2017 -0400
@@ -0,0 +1,556 @@
+#!/usr/bin/env python3
+"""
+Create tab-delimited database file to store sequence alignment information
+"""
+# Info
+__author__ = 'Namita Gupta, Jason Anthony Vander Heiden'
+from changeo import __version__, __date__
+
+# Imports
+import os
+import sys
+from argparse import ArgumentParser
+from collections import OrderedDict
+from textwrap import dedent
+from time import time
+from Bio import SeqIO
+
+# Presto and changeo imports
+from presto.Defaults import default_out_args
+from presto.Annotation import parseAnnotation
+from presto.IO import countSeqFile, printLog, printMessage, printProgress, readSeqFile
+from changeo.Commandline import CommonHelpFormatter, checkArgs, getCommonArgParser, parseCommonArgs
+from changeo.IO import countDbFile, extractIMGT, getDbWriter, readRepo
+from changeo.Parsers import IgBLASTReader, IMGTReader, IHMMuneReader, getIDforIMGT
+
+
+def getFilePrefix(aligner_output, out_args):
+    """
+    Get file name prefix and create output directory
+
+    Arguments:
+      aligner_output : aligner output file or directory.
+      out_args : dictionary of output arguments.
+
+    Returns:
+        str : file name prefix.
+    """
+    # Determine output directory
+    if not out_args['out_dir']:
+        out_dir = os.path.dirname(os.path.abspath(aligner_output))
+    else:
+        out_dir = os.path.abspath(out_args['out_dir'])
+        if not os.path.exists(out_dir):
+            os.mkdir(out_dir)
+
+    # Determine file prefix
+    if out_args['out_name']:
+        file_prefix = out_args['out_name']
+    else:
+        file_prefix = os.path.splitext(os.path.split(os.path.abspath(aligner_output))[1])[0]
+
+    return os.path.join(out_dir, file_prefix)
+
+
+def getSeqDict(seq_file):
+    """
+    Create a dictionary from a sequence file.
+
+    Arguments:
+      seq_file : sequence file.
+
+    Returns:
+        dict : sequence description as keys with Bio.SeqRecords as values.
+    """
+    seq_dict = SeqIO.to_dict(readSeqFile(seq_file),
+                             key_function=lambda x: x.description)
+
+    return seq_dict
+
+
+def writeDb(db, fields, file_prefix, total_count, id_dict=None, no_parse=True, partial=False,
+            out_args=default_out_args):
+    """
+    Writes tab-delimited database file in output directory.
+    
+    Arguments:
+      db : a iterator of IgRecord objects containing alignment data.
+      fields : a list of ordered field names to write.
+      file_prefix : directory and prefix for CLIP tab-delim file.
+      total_count : number of records (for progress bar).
+      id_dict : a dictionary of the truncated sequence ID mapped to the full sequence ID.
+      no_parse : if ID is to be parsed for pRESTO output with default delimiters.
+      partial : if True put incomplete alignments in the pass file.
+      out_args : common output argument dictionary from parseCommonArgs.
+
+    Returns:
+      None
+    """
+    # Function to check for valid records strictly
+    def _pass_strict(rec):
+        valid = [rec.v_call and rec.v_call != 'None',
+                 rec.j_call and rec.j_call != 'None',
+                 rec.functional is not None,
+                 rec.seq_vdj,
+                 rec.junction]
+        return all(valid)
+
+    # Function to check for valid records loosely
+    def _pass_gentle(rec):
+        valid = [rec.v_call and rec.v_call != 'None',
+                 rec.d_call and rec.d_call != 'None',
+                 rec.j_call and rec.j_call != 'None']
+        return any(valid)
+
+    # Set pass criteria
+    _pass = _pass_gentle if partial else _pass_strict
+
+    # Define output file names
+    pass_file = '%s_db-pass.tab' % file_prefix
+    fail_file = '%s_db-fail.tab' % file_prefix
+
+    # Initiate handles, writers and counters
+    pass_handle = None
+    fail_handle = None
+    pass_writer = None
+    fail_writer = None
+    start_time = time()
+    rec_count = pass_count = fail_count = 0
+
+    # Validate and write output
+    printProgress(0, total_count, 0.05, start_time)
+    for i, record in enumerate(db, start=1):
+
+        # Replace sequence description with full string, if required
+        if id_dict is not None and record.id in id_dict:
+            record.id = id_dict[record.id]
+
+        # Parse sequence description into new columns
+        if not no_parse:
+            try:
+                record.annotations = parseAnnotation(record.id, delimiter=out_args['delimiter'])
+                record.id = record.annotations['ID']
+                del record.annotations['ID']
+
+                # TODO:  This is not the best approach. should pass in output fields.
+                # If first record, use parsed description to define extra columns
+                if i == 1:  fields.extend(list(record.annotations.keys()))
+            except IndexError:
+                # Could not parse pRESTO-style annotations so fall back to no parse
+                no_parse = True
+                sys.stderr.write('\nWARNING: Sequence annotation format not recognized. Sequence headers will not be parsed.\n')
+
+        # Count pass or fail and write to appropriate file
+        if _pass(record):
+            # Open pass file
+            if pass_writer is None:
+                pass_handle = open(pass_file, 'wt')
+                pass_writer = getDbWriter(pass_handle, add_fields=fields)
+
+            # Write row to pass file
+            pass_count += 1
+            pass_writer.writerow(record.toDict())
+        else:
+            # Open failed file
+            if out_args['failed'] and fail_writer is None:
+                fail_handle = open(fail_file, 'wt')
+                fail_writer = getDbWriter(fail_handle, add_fields=fields)
+
+            # Write row to fail file if specified
+            fail_count += 1
+            if fail_writer is not None:
+                fail_writer.writerow(record.toDict())
+
+        # Print progress
+        printProgress(i, total_count, 0.05, start_time)
+
+    # Print consol log
+    log = OrderedDict()
+    log['OUTPUT'] = pass_file
+    log['PASS'] = pass_count
+    log['FAIL'] = fail_count
+    log['END'] = 'MakeDb'
+    printLog(log)
+    
+    if pass_handle is not None: pass_handle.close()
+    if fail_handle is not None: fail_handle.close()
+
+
+# TODO:  may be able to merge with other mains
+def parseIMGT(aligner_output, seq_file=None, no_parse=True, partial=False,
+              parse_scores=False, parse_regions=False, parse_junction=False,
+              out_args=default_out_args):
+    """
+    Main for IMGT aligned sample sequences.
+
+    Arguments:
+      aligner_output : zipped file or unzipped folder output by IMGT.
+      seq_file : FASTA file input to IMGT (from which to get seqID).
+      no_parse : if ID is to be parsed for pRESTO output with default delimiters.
+      partial : If True put incomplete alignments in the pass file.
+      parse_scores : if True add alignment score fields to output file.
+      parse_regions : if True add FWR and CDR region fields to output file.
+      out_args : common output argument dictionary from parseCommonArgs.
+
+    Returns:
+      None
+    """
+    # Print parameter info
+    log = OrderedDict()
+    log['START'] = 'MakeDb'
+    log['ALIGNER'] = 'IMGT'
+    log['ALIGNER_OUTPUT'] = aligner_output
+    log['SEQ_FILE'] = os.path.basename(seq_file) if seq_file else ''
+    log['NO_PARSE'] = no_parse
+    log['PARTIAL'] = partial
+    log['SCORES'] = parse_scores
+    log['REGIONS'] = parse_regions
+    log['JUNCTION'] = parse_junction
+    printLog(log)
+
+    start_time = time()
+    printMessage('Loading sequence files', start_time=start_time, width=25)
+    # Extract IMGT files
+    temp_dir, imgt_files = extractIMGT(aligner_output)
+    # Count records in IMGT files
+    total_count = countDbFile(imgt_files['summary'])
+    # Get (parsed) IDs from fasta file submitted to IMGT
+    id_dict = getIDforIMGT(seq_file) if seq_file else {}
+    printMessage('Done', start_time=start_time, end=True, width=25)
+
+    # Parse IMGT output and write db
+    with open(imgt_files['summary'], 'r') as summary_handle, \
+            open(imgt_files['gapped'], 'r') as gapped_handle, \
+            open(imgt_files['ntseq'], 'r') as ntseq_handle, \
+            open(imgt_files['junction'], 'r') as junction_handle:
+        parse_iter = IMGTReader(summary_handle, gapped_handle, ntseq_handle, junction_handle,
+                                parse_scores=parse_scores, parse_regions=parse_regions,
+                                parse_junction=parse_junction)
+        file_prefix = getFilePrefix(aligner_output, out_args)
+        writeDb(parse_iter, parse_iter.fields, file_prefix, total_count, id_dict=id_dict,
+                no_parse=no_parse, partial=partial, out_args=out_args)
+
+    # Cleanup temp directory
+    temp_dir.cleanup()
+
+    return None
+
+
+# TODO:  may be able to merge with other mains
+def parseIgBLAST(aligner_output, seq_file, repo, no_parse=True, partial=False,
+                 parse_regions=False, parse_scores=False, parse_igblast_cdr3=False,
+                 out_args=default_out_args):
+    """
+    Main for IgBLAST aligned sample sequences.
+
+    Arguments:
+      aligner_output : IgBLAST output file to process.
+      seq_file : fasta file input to IgBlast (from which to get sequence).
+      repo : folder with germline repertoire files.
+      no_parse : if ID is to be parsed for pRESTO output with default delimiters.
+      partial : If True put incomplete alignments in the pass file.
+      parse_regions : if True add FWR and CDR fields to output file.
+      parse_scores : if True add alignment score fields to output file.
+      parse_igblast_cdr3 : if True parse CDR3 sequences generated by IgBLAST
+      out_args : common output argument dictionary from parseCommonArgs.
+
+    Returns:
+      None
+    """
+    # Print parameter info
+    log = OrderedDict()
+    log['START'] = 'MakeDB'
+    log['ALIGNER'] = 'IgBlast'
+    log['ALIGNER_OUTPUT'] = os.path.basename(aligner_output)
+    log['SEQ_FILE'] = os.path.basename(seq_file)
+    log['NO_PARSE'] = no_parse
+    log['PARTIAL'] = partial
+    log['SCORES'] = parse_scores
+    log['REGIONS'] = parse_regions
+    printLog(log)
+
+    start_time = time()
+    printMessage('Loading sequence files', start_time=start_time, width=25)
+    # Count records in sequence file
+    total_count = countSeqFile(seq_file)
+    # Get input sequence dictionary
+    seq_dict = getSeqDict(seq_file)
+    # Create germline repo dictionary
+    repo_dict = readRepo(repo)
+    printMessage('Done', start_time=start_time, end=True, width=25)
+
+    # Parse and write output
+    with open(aligner_output, 'r') as f:
+        parse_iter = IgBLASTReader(f, seq_dict, repo_dict,
+                                   parse_scores=parse_scores, parse_regions=parse_regions,
+                                   parse_igblast_cdr3=parse_igblast_cdr3)
+        file_prefix = getFilePrefix(aligner_output, out_args)
+        writeDb(parse_iter, parse_iter.fields, file_prefix, total_count,
+                no_parse=no_parse, partial=partial, out_args=out_args)
+
+    return None
+
+
+# TODO:  may be able to merge with other mains
+def parseIHMM(aligner_output, seq_file, repo, no_parse=True, partial=False,
+              parse_scores=False, parse_regions=False, out_args=default_out_args):
+    """
+    Main for iHMMuneAlign aligned sample sequences.
+
+    Arguments:
+      aligner_output : iHMMune-Align output file to process.
+      seq_file : fasta file input to iHMMuneAlign (from which to get sequence).
+      repo : folder with germline repertoire files.
+      no_parse : if ID is to be parsed for pRESTO output with default delimiters.
+      partial : If True put incomplete alignments in the pass file.
+      parse_scores : if True parse alignment scores.
+      parse_regions : if True add FWR and CDR region fields.
+      out_args : common output argument dictionary from parseCommonArgs.
+
+    Returns:
+      None
+    """
+    # Print parameter info
+    log = OrderedDict()
+    log['START'] = 'MakeDB'
+    log['ALIGNER'] = 'iHMMune-Align'
+    log['ALIGNER_OUTPUT'] = os.path.basename(aligner_output)
+    log['SEQ_FILE'] = os.path.basename(seq_file)
+    log['NO_PARSE'] = no_parse
+    log['PARTIAL'] = partial
+    log['SCORES'] = parse_scores
+    log['REGIONS'] = parse_regions
+    printLog(log)
+
+    start_time = time()
+    printMessage('Loading sequence files', start_time=start_time, width=25)
+    # Count records in sequence file
+    total_count = countSeqFile(seq_file)
+    # Get input sequence dictionary
+    seq_dict = getSeqDict(seq_file)
+    # Create germline repo dictionary
+    repo_dict = readRepo(repo)
+    printMessage('Done', start_time=start_time, end=True, width=25)
+
+    # Parse and write output
+    with open(aligner_output, 'r') as f:
+        parse_iter = IHMMuneReader(f, seq_dict, repo_dict,
+                                   parse_scores=parse_scores, parse_regions=parse_regions)
+        file_prefix = getFilePrefix(aligner_output, out_args)
+        writeDb(parse_iter, parse_iter.fields, file_prefix, total_count,
+                no_parse=no_parse, partial=partial, out_args=out_args)
+
+    return None
+
+
+def getArgParser():
+    """
+    Defines the ArgumentParser.
+
+    Returns: 
+      argparse.ArgumentParser
+    """
+    fields = dedent(
+             '''
+              output files:
+                  db-pass
+                      database of alignment records with functionality information,
+                      V and J calls, and a junction region.
+                  db-fail
+                      database with records that fail due to no functionality information
+                      (did not pass IMGT), no V call, no J call, or no junction region.
+
+              universal output fields:
+                  SEQUENCE_ID, SEQUENCE_INPUT, SEQUENCE_VDJ, SEQUENCE_IMGT,
+                  FUNCTIONAL, IN_FRAME, STOP, MUTATED_INVARIANT, INDELS,
+                  V_CALL, D_CALL, J_CALL,
+                  V_SEQ_START, V_SEQ_LENGTH,
+                  D_SEQ_START, D_SEQ_LENGTH, D_GERM_START, D_GERM_LENGTH,
+                  J_SEQ_START, J_SEQ_LENGTH, J_GERM_START, J_GERM_LENGTH,
+                  JUNCTION_LENGTH, JUNCTION, NP1_LENGTH, NP2_LENGTH,
+                  FWR1_IMGT, FWR2_IMGT, FWR3_IMGT, FWR4_IMGT,
+                  CDR1_IMGT, CDR2_IMGT, CDR3_IMGT
+
+              imgt specific output fields:
+                  V_GERM_START_IMGT, V_GERM_LENGTH_IMGT,
+                  N1_LENGTH, N2_LENGTH, P3V_LENGTH, P5D_LENGTH, P3D_LENGTH, P5J_LENGTH,
+                  D_FRAME, V_SCORE, V_IDENTITY, J_SCORE, J_IDENTITY,
+
+              igblast specific output fields:
+                  V_GERM_START_VDJ, V_GERM_LENGTH_VDJ,
+                  V_EVALUE, V_SCORE, V_IDENTITY, V_BTOP,
+                  J_EVALUE, J_SCORE, J_IDENTITY, J_BTOP.
+                  CDR3_IGBLAST_NT, CDR3_IGBLAST_AA
+
+              ihmm specific output fields:
+                  V_GERM_START_VDJ, V_GERM_LENGTH_VDJ,
+                  HMM_SCORE
+              ''')
+                
+    # Define ArgumentParser
+    parser = ArgumentParser(description=__doc__, epilog=fields,
+                            formatter_class=CommonHelpFormatter)
+    parser.add_argument('--version', action='version',
+                        version='%(prog)s:' + ' %s-%s' %(__version__, __date__))
+    subparsers = parser.add_subparsers(title='subcommands', dest='command',
+                                       help='Aligner used', metavar='')
+    # TODO:  This is a temporary fix for Python issue 9253
+    subparsers.required = True
+
+    # Parent parser    
+    parser_parent = getCommonArgParser(seq_in=False, seq_out=False, log=False)
+
+    # IgBlast Aligner
+    parser_igblast = subparsers.add_parser('igblast', parents=[parser_parent],
+                                           formatter_class=CommonHelpFormatter,
+                                           help='Process IgBLAST output.',
+                                           description='Process IgBLAST output.')
+    parser_igblast.add_argument('-i', nargs='+', action='store', dest='aligner_outputs',
+                                required=True,
+                                help='''IgBLAST output files in format 7 with query sequence
+                                     (IgBLAST argument \'-outfmt "7 std qseq sseq btop"\').''')
+    parser_igblast.add_argument('-r', nargs='+', action='store', dest='repo', required=True,
+                                help='''List of folders and/or fasta files containing
+                                     IMGT-gapped germline sequences corresponding to the
+                                     set of germlines used in the IgBLAST alignment.''')
+    parser_igblast.add_argument('-s', action='store', nargs='+', dest='seq_files',
+                                required=True,
+                                help='''List of input FASTA files (with .fasta, .fna or .fa
+                                     extension), containing sequences.''')
+    parser_igblast.add_argument('--noparse', action='store_true', dest='no_parse',
+                                help='''Specify to prevent input sequence headers from being parsed
+                                    to add new columns to database. Parsing of sequence headers requires
+                                    headers to be in the pRESTO annotation format, so this should be specified
+                                    when sequence headers are incompatible with the pRESTO annotation scheme.
+                                    Note, unrecognized header formats will default to this behavior.''')
+    parser_igblast.add_argument('--partial', action='store_true', dest='partial',
+                                help='''If specified, include incomplete V(D)J alignments in
+                                     the pass file instead of the fail file.''')
+    parser_igblast.add_argument('--scores', action='store_true', dest='parse_scores',
+                                help='''Specify if alignment score metrics should be
+                                     included in the output. Adds the V_SCORE, V_IDENTITY,
+                                     V_EVALUE, V_BTOP, J_SCORE, J_IDENTITY,
+                                     J_BTOP, and J_EVALUE columns.''')
+    parser_igblast.add_argument('--regions', action='store_true', dest='parse_regions',
+                                help='''Specify if IMGT FWR and CDRs should be
+                                     included in the output. Adds the FWR1_IMGT, FWR2_IMGT,
+                                     FWR3_IMGT, FWR4_IMGT, CDR1_IMGT, CDR2_IMGT, and
+                                     CDR3_IMGT columns.''')
+    parser_igblast.add_argument('--cdr3', action='store_true',
+                                dest='parse_igblast_cdr3', 
+                                help='''Specify if the CDR3 sequences generated by IgBLAST 
+                                     should be included in the output. Adds the columns
+                                     CDR3_IGBLAST_NT and CDR3_IGBLAST_AA. Requires IgBLAST
+                                     version 1.5 or greater.''')
+    parser_igblast.set_defaults(func=parseIgBLAST)
+
+    # IMGT aligner
+    parser_imgt = subparsers.add_parser('imgt', parents=[parser_parent],
+                                        formatter_class=CommonHelpFormatter,
+                                        help='''Process IMGT/HighV-Quest output
+                                             (does not work with V-QUEST).''',
+                                        description='''Process IMGT/HighV-Quest output
+                                             (does not work with V-QUEST).''')
+    parser_imgt.add_argument('-i', nargs='+', action='store', dest='aligner_outputs',
+                             help='''Either zipped IMGT output files (.zip or .txz) or a
+                                  folder containing unzipped IMGT output files (which must
+                                  include 1_Summary, 2_IMGT-gapped, 3_Nt-sequences,
+                                  and 6_Junction).''')
+    parser_imgt.add_argument('-s', nargs='*', action='store', dest='seq_files',
+                             required=False,
+                             help='''List of input FASTA files (with .fasta, .fna or .fa
+                                  extension) containing sequences.''')
+    parser_imgt.add_argument('--noparse', action='store_true', dest='no_parse', 
+                             help='''Specify to prevent input sequence headers from being parsed
+                                  to add new columns to database. Parsing of sequence headers requires
+                                  headers to be in the pRESTO annotation format, so this should be specified
+                                  when sequence headers are incompatible with the pRESTO annotation scheme.
+                                  Note, unrecognized header formats will default to this behavior.''')
+    parser_imgt.add_argument('--partial', action='store_true', dest='partial',
+                             help='''If specified, include incomplete V(D)J alignments in
+                                  the pass file instead of the fail file.''')
+    parser_imgt.add_argument('--scores', action='store_true', dest='parse_scores',
+                             help='''Specify if alignment score metrics should be
+                                  included in the output. Adds the V_SCORE, V_IDENTITY,
+                                  J_SCORE and J_IDENTITY.''')
+    parser_imgt.add_argument('--regions', action='store_true', dest='parse_regions',
+                             help='''Specify if IMGT FWRs and CDRs should be
+                                  included in the output. Adds the FWR1_IMGT, FWR2_IMGT,
+                                  FWR3_IMGT, FWR4_IMGT, CDR1_IMGT, CDR2_IMGT, and
+                                  CDR3_IMGT columns.''')
+    parser_imgt.add_argument('--junction', action='store_true', dest='parse_junction',
+                             help='''Specify if detailed junction fields should be
+                                  included in the output. Adds the columns 
+                                  N1_LENGTH, N2_LENGTH, P3V_LENGTH, P5D_LENGTH, P3D_LENGTH,
+                                  P5J_LENGTH, D_FRAME.''')
+    parser_imgt.set_defaults(func=parseIMGT)
+
+    # iHMMuneAlign Aligner
+    parser_ihmm = subparsers.add_parser('ihmm', parents=[parser_parent],
+                                        formatter_class=CommonHelpFormatter,
+                                        help='Process iHMMune-Align output.',
+                                        description='Process iHMMune-Align output.')
+    parser_ihmm.add_argument('-i', nargs='+', action='store', dest='aligner_outputs',
+                             required=True,
+                             help='''iHMMune-Align output file.''')
+    parser_ihmm.add_argument('-r', nargs='+', action='store', dest='repo', required=True,
+                             help='''List of folders and/or FASTA files containing
+                                  IMGT-gapped germline sequences corresponding to the
+                                  set of germlines used in the IgBLAST alignment.''')
+    parser_ihmm.add_argument('-s', action='store', nargs='+', dest='seq_files',
+                             required=True,
+                             help='''List of input FASTA files (with .fasta, .fna or .fa
+                                  extension) containing sequences.''')
+    parser_ihmm.add_argument('--noparse', action='store_true', dest='no_parse',
+                             help='''Specify to prevent input sequence headers from being parsed
+                                  to add new columns to database. Parsing of sequence headers requires
+                                  headers to be in the pRESTO annotation format, so this should be specified
+                                  when sequence headers are incompatible with the pRESTO annotation scheme.
+                                  Note, unrecognized header formats will default to this behavior.''')
+    parser_ihmm.add_argument('--partial', action='store_true', dest='partial',
+                             help='''If specified, include incomplete V(D)J alignments in
+                                  the pass file instead of the fail file.''')
+    parser_ihmm.add_argument('--scores', action='store_true', dest='parse_scores',
+                             help='''Specify if alignment score metrics should be
+                                  included in the output. Adds the path score of the
+                                  iHMMune-Align hidden Markov model to HMM_SCORE.''')
+    parser_ihmm.add_argument('--regions', action='store_true', dest='parse_regions',
+                             help='''Specify if IMGT FWRs and CDRs should be
+                                  included in the output. Adds the FWR1_IMGT, FWR2_IMGT,
+                                  FWR3_IMGT, FWR4_IMGT, CDR1_IMGT, CDR2_IMGT, and
+                                  CDR3_IMGT columns.''')
+    parser_ihmm.set_defaults(func=parseIHMM)
+
+    return parser
+    
+    
+if __name__ == "__main__":
+    """
+    Parses command line arguments and calls main
+    """
+    parser = getArgParser()
+    checkArgs(parser)
+    args = parser.parse_args()
+    args_dict = parseCommonArgs(args, in_arg='aligner_outputs')
+
+    # Set no ID parsing if sequence files are not provided
+    if 'seq_files' in args_dict and not args_dict['seq_files']:
+        args_dict['no_parse'] = True
+
+    # Delete
+    if 'seq_files' in args_dict: del args_dict['seq_files']
+    if 'aligner_outputs' in args_dict: del args_dict['aligner_outputs']
+    if 'command' in args_dict: del args_dict['command']
+    if 'func' in args_dict: del args_dict['func']           
+    
+    if args.command == 'imgt':
+        for i in range(len(args.__dict__['aligner_outputs'])):
+            args_dict['aligner_output'] = args.__dict__['aligner_outputs'][i]
+            args_dict['seq_file'] = args.__dict__['seq_files'][i] \
+                                    if args.__dict__['seq_files'] else None
+            args.func(**args_dict)
+    elif args.command == 'igblast' or args.command == 'ihmm':
+        for i in range(len(args.__dict__['aligner_outputs'])):
+            args_dict['aligner_output'] =  args.__dict__['aligner_outputs'][i]
+            args_dict['seq_file'] = args.__dict__['seq_files'][i]
+            args.func(**args_dict)