--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CreateGermlines.py	Mon Jul 17 07:44:27 2017 -0400
@@ -0,0 +1,707 @@
+#!/usr/bin/env python3
+"""
+Reconstructs germline sequences from alignment data
+"""
+# 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
+
+# Presto and change imports
+from presto.Defaults import default_out_args
+from presto.IO import getOutputHandle, printLog, printProgress
+from changeo.Commandline import CommonHelpFormatter, checkArgs, getCommonArgParser, parseCommonArgs
+from changeo.IO import getDbWriter, readDbFile, countDbFile, readRepo
+from changeo.Receptor import allele_regex, parseAllele
+
+# Defaults
+default_germ_types = 'dmask'
+default_v_field = 'V_CALL'
+default_seq_field = 'SEQUENCE_IMGT'
+
+    
+def joinGermline(align, repo_dict, germ_types, v_field, seq_field):
+    """
+    Join gapped germline sequences aligned with sample sequences
+    
+    Arguments:
+    align = iterable yielding dictionaries of sample sequence data
+    repo_dict = dictionary of IMGT gapped germline sequences
+    germ_types = types of germline sequences to be output
+                     (full germline, D-region masked, only V-region germline)
+    v_field = field in which to look for V call
+    seq_field = field in which to look for sequence
+    
+    Returns:
+    dictionary of germline_type: germline_sequence
+    """
+    j_field = 'J_CALL'
+    germlines = {'full': '', 'dmask': '', 'vonly': '', 'regions': ''}
+    result_log = OrderedDict()
+    result_log['ID'] = align['SEQUENCE_ID']
+
+    # Find germline V-region gene
+    if v_field == 'V_CALL_GENOTYPED':
+        vgene = parseAllele(align[v_field], allele_regex, 'list')
+        vkey = vgene
+    else:
+        vgene = parseAllele(align[v_field], allele_regex, 'first')
+        vkey = (vgene, )
+
+    try:
+        int(align['P3V_LENGTH'])
+        int(align['N1_LENGTH'])
+        int(align['P5D_LENGTH'])
+        int(align['P3D_LENGTH'])
+        int(align['N2_LENGTH'])
+        int(align['P5J_LENGTH'])
+    except:
+        regions_style = 'IgBLAST'
+    else:
+        regions_style = 'IMGT'
+
+    # Build V-region germline
+    if vgene is not None:
+        result_log['V_CALL'] = ','.join(vkey)
+        if vkey in repo_dict:
+            vseq = repo_dict[vkey]
+            # Germline start
+            try: vstart = int(align['V_GERM_START_IMGT']) - 1
+            except (TypeError, ValueError): vstart = 0
+            # Germline length
+            try: vlen = int(align['V_GERM_LENGTH_IMGT'])
+            except (TypeError, ValueError): vlen = 0
+            # TODO:  not sure what this line is doing here. it no make no sense.
+            vpad = vlen - len(vseq[vstart:])
+            if vpad < 0: vpad = 0
+            germ_vseq = vseq[vstart:(vstart + vlen)] + ('N' * vpad)
+        else:
+            result_log['ERROR'] = 'Germline %s not in repertoire' % ','.join(vkey)
+            return result_log, germlines
+    else:
+        result_log['V_CALL'] = None
+        try: vlen = int(align['V_GERM_LENGTH_IMGT'])
+        except (TypeError, ValueError): vlen = 0
+        germ_vseq = 'N' * vlen
+
+    # Find germline D-region gene
+    dgene = parseAllele(align['D_CALL'], allele_regex, 'first')
+
+    # Build D-region germline
+    if dgene is not None:
+        result_log['D_CALL'] = dgene
+        dkey = (dgene, )
+        if dkey in repo_dict:
+            dseq = repo_dict[dkey]
+            # Germline start
+            try: dstart = int(align['D_GERM_START']) - 1
+            except (TypeError, ValueError): dstart = 0
+            # Germline length
+            try: dlen = int(align['D_GERM_LENGTH'])
+            except (TypeError, ValueError): dlen = 0
+            germ_dseq = repo_dict[dkey][dstart:(dstart + dlen)]
+        else:
+            result_log['ERROR'] = 'Germline %s not in repertoire' % dgene
+            return result_log, germlines
+    else:
+        result_log['D_CALL'] = None
+        germ_dseq = ''
+
+    # Find germline J-region gene
+    jgene = parseAllele(align[j_field], allele_regex, 'first')
+
+    # Build D-region germline
+    if jgene is not None:
+        result_log['J_CALL'] = jgene
+        jkey = (jgene, )
+        if jkey in repo_dict:
+            jseq = repo_dict[jkey]
+            # Germline start
+            try: jstart = int(align['J_GERM_START']) - 1
+            except (TypeError, ValueError): jstart = 0
+            # Germline length
+            try: jlen = int(align['J_GERM_LENGTH'])
+            except (TypeError, ValueError): jlen = 0
+            # TODO:  not sure what this line is doing either
+            jpad = jlen - len(jseq[jstart:])
+            if jpad < 0: jpad = 0
+            germ_jseq = jseq[jstart:(jstart + jlen)] + ('N' * jpad)
+        else:
+            result_log['ERROR'] = 'Germline %s not in repertoire' % jgene
+            return result_log, germlines
+    else:
+        result_log['J_CALL'] = None
+        try: jlen = int(align['J_GERM_LENGTH'])
+        except (TypeError, ValueError): jlen = 0
+        germ_jseq = 'N' * jlen
+
+    # Assemble pieces starting with V-region
+    germ_seq = germ_vseq
+    regions = 'V' * len(germ_vseq)
+
+    try:
+        np1_len = int(align['NP1_LENGTH'])
+    except (TypeError, ValueError):
+        np1_len = 0
+
+    # NP nucleotide additions after V
+    if regions_style == 'IMGT':
+        # P nucleotide additions
+        try:
+            p3v_len = int(align['P3V_LENGTH'])
+        except (TypeError, ValueError):
+            p3v_len = 0
+        if p3v_len < 0:
+            result_log['ERROR'] = 'P3V_LENGTH is negative'
+            return result_log, germlines
+
+        regions += 'P' * p3v_len
+
+        # N1 nucleotide additions
+        try:
+            n1_len = int(align['N1_LENGTH'])
+        except (TypeError, ValueError):
+            n1_len = 0
+        if n1_len < 0:
+            result_log['ERROR'] = 'N1_LENGTH is negative'
+            return result_log, germlines
+
+        regions += 'N' * n1_len
+
+        # P nucleotide additions before D
+        try: p5d_len = int(align['P5D_LENGTH'])
+        except (TypeError, ValueError): p5d_len = 0
+        if p5d_len < 0:
+            result_log['ERROR'] = 'P5D_LENGTH is negative'
+            return result_log, germlines
+
+        regions += 'P' * p5d_len
+    else:
+        # IgBLAST style
+        # PNP nucleotide additions after V
+        if np1_len < 0:
+            result_log['ERROR'] = 'NP1_LENGTH is negative'
+            return result_log, germlines
+
+        regions += 'N' * np1_len
+
+    germ_seq += 'N' * np1_len
+
+    # Add D-region
+    germ_seq += germ_dseq
+    regions += 'D' * len(germ_dseq)
+
+    #print 'VD>', germ_seq, '\nVD>', regions
+
+    try:
+        np2_len = int(align['NP2_LENGTH'])
+    except (TypeError, ValueError):
+        np2_len = 0
+
+    # NP nucleotide additions before J
+    if regions_style == 'IMGT':
+        # P nucleotide additions
+        try:
+            p3d_len = int(align['P3D_LENGTH'])
+        except (TypeError, ValueError):
+            p3d_len = 0
+        if p3d_len < 0:
+            result_log['ERROR'] = 'P3D_LENGTH is negative'
+            return result_log, germlines
+
+        regions += 'P' * p3d_len
+
+        # N2 nucleotide additions
+        try:
+            n2_len = int(align['N2_LENGTH'])
+        except (TypeError, ValueError):
+            n2_len = 0
+        if n2_len < 0:
+            result_log['ERROR'] = 'N2_LENGTH is negative'
+            return result_log, germlines
+
+        regions += 'N' * n2_len
+
+        # P nucleotide additions
+        try:
+            p5j_len = int(align['P5J_LENGTH'])
+        except (TypeError, ValueError):
+            p5j_len = 0
+        if p5j_len < 0:
+            result_log['ERROR'] = 'P5J_LENGTH is negative'
+            return result_log, germlines
+
+        regions += 'P' * p5j_len
+    else:
+        # IgBLAST style
+        # NP nucleotide additions
+        if np2_len < 0:
+            result_log['ERROR'] = 'NP2_LENGTH is negative'
+            return result_log, germlines
+
+        regions += 'N' * np2_len
+
+    germ_seq += 'N' * np2_len
+
+    # Add J-region
+    germ_seq += germ_jseq
+    regions += 'J' * len(germ_jseq)
+
+    #print('\nREGIONS>',regions,'\n')
+
+    # Define return germlines
+    germlines['full'] = germ_seq
+    germlines['regions'] = regions
+
+    if 'dmask' in germ_types:
+        germlines['dmask'] = germ_seq[:len(germ_vseq)] + \
+                             'N' * (len(germ_seq) - len(germ_vseq) - len(germ_jseq)) + \
+                             germ_seq[-len(germ_jseq):]
+    if 'vonly' in germ_types:
+        germlines['vonly'] = germ_vseq
+
+    # Check that input and germline sequence match
+    if len(align[seq_field]) == 0:
+        result_log['ERROR'] = 'Sequence is missing from %s column' % seq_field
+    elif len(germlines['full']) != len(align[seq_field]):
+        result_log['ERROR'] = 'Germline sequence is %d nucleotides longer than input sequence' % \
+                              (len(germlines['full']) - len(align[seq_field]))
+
+    # Convert to uppercase
+    for k, v in germlines.items():  germlines[k] = v.upper()
+
+    return result_log, germlines
+
+
+def assembleEachGermline(db_file, repo, germ_types, v_field, seq_field, out_args=default_out_args):
+    """
+    Write germline sequences to tab-delimited database file
+
+    Arguments:
+    db_file = input tab-delimited database file
+    repo = folder with germline repertoire files
+    germ_types = types of germline sequences to be output
+                     (full germline, D-region masked, only V-region germline)
+    v_field = field in which to look for V call
+    seq_field = field in which to look for sequence
+    out_args = arguments for output preferences
+
+    Returns:
+    None
+    """
+    # Print parameter info
+    log = OrderedDict()
+    log['START'] = 'CreateGermlines'
+    log['DB_FILE'] = os.path.basename(db_file)
+    log['GERM_TYPES'] = germ_types if isinstance(germ_types, str) else ','.join(germ_types)
+    log['CLONED'] = 'False'
+    log['V_FIELD'] = v_field
+    log['SEQ_FIELD'] = seq_field
+    printLog(log)
+
+    # Get repertoire and open Db reader
+    repo_dict = readRepo(repo)
+    reader = readDbFile(db_file, ig=False)
+
+    # Exit if V call field does not exist in reader
+    if v_field not in reader.fieldnames:
+        sys.exit('Error: V field does not exist in input database file.')
+
+    # Define log handle
+    if out_args['log_file'] is None:
+        log_handle = None
+    else:
+        log_handle = open(out_args['log_file'], 'w')
+
+    add_fields = []
+    seq_type = seq_field.split('_')[-1]
+    if 'full' in germ_types: add_fields +=  ['GERMLINE_' + seq_type]
+    if 'dmask' in germ_types: add_fields += ['GERMLINE_' + seq_type + '_D_MASK']
+    if 'vonly' in germ_types: add_fields += ['GERMLINE_' + seq_type + '_V_REGION']
+    if 'regions' in germ_types: add_fields += ['GERMLINE_REGIONS']
+
+    # Create output file handle and Db writer
+    pass_handle = getOutputHandle(db_file, 'germ-pass',
+                                  out_dir=out_args['out_dir'],
+                                  out_name=out_args['out_name'],
+                                  out_type=out_args['out_type'])
+    pass_writer = getDbWriter(pass_handle, db_file, add_fields=add_fields)
+
+    if out_args['failed']:
+        fail_handle = getOutputHandle(db_file, 'germ-fail',
+                                      out_dir=out_args['out_dir'],
+                                      out_name=out_args['out_name'],
+                                      out_type=out_args['out_type'])
+        fail_writer = getDbWriter(fail_handle, db_file, add_fields=add_fields)
+    else:
+        fail_handle = None
+        fail_writer = None
+
+    # Initialize time and total count for progress bar
+    start_time = time()
+    rec_count = countDbFile(db_file)
+    pass_count = fail_count = 0
+    # Iterate over rows
+    for i, row in enumerate(reader):
+        # Print progress
+        printProgress(i, rec_count, 0.05, start_time)
+
+        result_log, germlines = joinGermline(row, repo_dict, germ_types, v_field, seq_field)
+
+        # Add germline field(s) to dictionary
+        if 'full' in germ_types: row['GERMLINE_' + seq_type] = germlines['full']
+        if 'dmask' in germ_types: row['GERMLINE_' + seq_type + '_D_MASK'] = germlines['dmask']
+        if 'vonly' in germ_types: row['GERMLINE_' + seq_type + '_V_REGION'] = germlines['vonly']
+        if 'regions' in germ_types: row['GERMLINE_REGIONS'] = germlines['regions']
+
+        # Write row to pass or fail file
+        if 'ERROR' in result_log:
+            fail_count += 1
+            if fail_writer is not None: fail_writer.writerow(row)
+        else:
+            result_log['SEQUENCE'] = row[seq_field]
+            result_log['GERMLINE'] = germlines['full']
+            result_log['REGIONS'] = germlines['regions']
+
+            pass_count += 1
+            pass_writer.writerow(row)
+        printLog(result_log, handle=log_handle)
+
+    # Print log
+    printProgress(i + 1, rec_count, 0.05, start_time)
+    log = OrderedDict()
+    log['OUTPUT'] = os.path.basename(pass_handle.name)
+    log['RECORDS'] = rec_count
+    log['PASS'] = pass_count
+    log['FAIL'] = fail_count
+    log['END'] = 'CreateGermlines'
+    printLog(log)
+
+    # Close file handles
+    pass_handle.close()
+    if fail_handle is not None: fail_handle.close()
+    if log_handle is not None:  log_handle.close()
+
+
+def makeCloneGermline(clone, clone_dict, repo_dict, germ_types, v_field,
+                      seq_field, counts, writers, out_args):
+    """
+    Determine consensus clone sequence and create germline for clone
+
+    Arguments:
+    clone = clone ID
+    clone_dict = iterable yielding dictionaries of sequence data from clone
+    repo_dict = dictionary of IMGT gapped germline sequences
+    germ_types = types of germline sequences to be output
+                     (full germline, D-region masked, only V-region germline)
+    v_field = field in which to look for V call
+    seq_field = field in which to look for sequence
+    counts = dictionary of pass counter and fail counter
+    writers = dictionary with pass and fail DB writers
+    out_args = arguments for output preferences
+
+    Returns:
+    None
+    """
+    seq_type = seq_field.split('_')[-1]
+    j_field = 'J_CALL'
+
+    # Create dictionaries to count observed V/J calls
+    v_dict = OrderedDict()
+    j_dict = OrderedDict()
+
+    # Find longest sequence in clone
+    max_length = 0
+    for val in clone_dict.values():
+        v = val[v_field]
+        v_dict[v] = v_dict.get(v, 0) + 1
+        j = val[j_field]
+        j_dict[j] = j_dict.get(j, 0) + 1
+        if len(val[seq_field]) > max_length:
+            max_length = len(val[seq_field])
+
+    # Consensus V and J having most observations
+    v_cons = [k for k in list(v_dict.keys()) if v_dict[k] == max(v_dict.values())]
+    j_cons = [k for k in list(j_dict.keys()) if j_dict[k] == max(j_dict.values())]
+
+    # Consensus sequence(s) with consensus V/J calls and longest sequence
+    cons = [val for val in list(clone_dict.values()) \
+            if val.get(v_field, '') in v_cons and \
+            val.get(j_field, '') in j_cons and \
+            len(val[seq_field]) == max_length]
+
+    # Sequence(s) with consensus V/J are not longest
+    if not cons:
+        # Sequence(s) with consensus V/J (not longest)
+        cons = [val for val in list(clone_dict.values()) \
+                if val.get(v_field, '') in v_cons and val.get(j_field, '') in j_cons]
+
+        # No sequence has both consensus V and J call
+        if not cons:
+            result_log = OrderedDict()
+            result_log['ID'] = clone
+            result_log['V_CALL'] = ','.join(v_cons)
+            result_log['J_CALL'] = ','.join(j_cons)
+            result_log['ERROR'] = 'No consensus sequence for clone found'
+        else:
+            # Pad end of consensus sequence with gaps to make it the max length
+            cons = cons[0]
+            cons['J_GERM_LENGTH'] = str(int(cons['J_GERM_LENGTH'] or 0) + max_length - len(cons[seq_field]))
+            cons[seq_field] += '.' * (max_length - len(cons[seq_field]))
+            result_log, germlines = joinGermline(cons, repo_dict, germ_types, v_field, seq_field)
+            result_log['ID'] = clone
+            result_log['CONSENSUS'] = cons['SEQUENCE_ID']
+    else:
+        cons = cons[0]
+        result_log, germlines = joinGermline(cons, repo_dict, germ_types, v_field, seq_field)
+        result_log['ID'] = clone
+        result_log['CONSENSUS'] = cons['SEQUENCE_ID']
+
+    # Write sequences of clone
+    for val in clone_dict.values():
+        if 'ERROR' not in result_log:
+            # Update lengths padded to longest sequence in clone
+            val['J_GERM_LENGTH'] = str(int(val['J_GERM_LENGTH'] or 0) + max_length - len(val[seq_field]))
+            val[seq_field] += '.' * (max_length - len(val[seq_field]))
+
+            # Add column(s) to tab-delimited database file
+            if 'full' in germ_types: val['GERMLINE_' + seq_type] = germlines['full']
+            if 'dmask' in germ_types: val['GERMLINE_' + seq_type + '_D_MASK'] = germlines['dmask']
+            if 'vonly' in germ_types: val['GERMLINE_' + seq_type + '_V_REGION'] = germlines['vonly']
+            if 'regions' in germ_types: val['GERMLINE_REGIONS'] = germlines['regions']
+
+            # Add field
+            val['GERMLINE_V_CALL'] = result_log['V_CALL']
+            val['GERMLINE_D_CALL'] = result_log['D_CALL']
+            val['GERMLINE_J_CALL'] = result_log['J_CALL']
+            
+            result_log['SEQUENCE'] = cons[seq_field]
+            result_log['GERMLINE'] = germlines['full']
+            result_log['REGIONS'] = germlines['regions']
+
+            # Write to pass file
+            counts['pass'] += 1
+            writers['pass'].writerow(val)
+        else:
+            # Write to fail file
+            counts['fail'] += 1
+            if writers['fail'] is not None:
+                writers['fail'].writerow(val)
+    # Return log
+    return result_log
+
+
+def assembleCloneGermline(db_file, repo, germ_types, v_field, seq_field, out_args=default_out_args):
+    """
+    Assemble one germline sequence for each clone in a tab-delimited database file
+
+    Arguments:
+    db_file = input tab-delimited database file
+    repo = folder with germline repertoire files
+    germ_types = types of germline sequences to be output
+                 (full germline, D-region masked, only V-region germline)
+    v_field = field in which to look for V call
+    seq_field = field in which to look for sequence
+    out_args = arguments for output preferences
+
+    Returns:
+    None
+    """
+    # Print parameter info
+    log = OrderedDict()
+    log['START'] = 'CreateGermlines'
+    log['DB_FILE'] = os.path.basename(db_file)
+    log['GERM_TYPES'] = germ_types if isinstance(germ_types, str) else ','.join(germ_types)
+    log['CLONED'] = 'True'
+    log['V_FIELD'] = v_field
+    log['SEQ_FIELD'] = seq_field
+    printLog(log)
+
+    # Get repertoire and open Db reader
+    repo_dict = readRepo(repo)
+    reader = readDbFile(db_file, ig=False)
+
+    # Exit if V call field does not exist in reader
+    if v_field not in reader.fieldnames:
+        sys.exit('Error: V field does not exist in input database file.')
+
+    # Define log handle
+    if out_args['log_file'] is None:
+        log_handle = None
+    else:
+        log_handle = open(out_args['log_file'], 'w')
+
+    add_fields = []
+    seq_type = seq_field.split('_')[-1]
+    if 'full' in germ_types: add_fields +=  ['GERMLINE_' + seq_type]
+    if 'dmask' in germ_types: add_fields += ['GERMLINE_' + seq_type + '_D_MASK']
+    if 'vonly' in germ_types: add_fields += ['GERMLINE_' + seq_type + '_V_REGION']
+    if 'regions' in germ_types: add_fields += ['GERMLINE_REGIONS']
+
+    add_fields += ['GERMLINE_V_CALL']
+    add_fields += ['GERMLINE_D_CALL']
+    add_fields += ['GERMLINE_J_CALL']
+    
+    # Create output file handle and Db writer
+    writers = {}
+    pass_handle = getOutputHandle(db_file, 'germ-pass', out_dir=out_args['out_dir'],
+                                  out_name=out_args['out_name'], out_type=out_args['out_type'])
+    writers['pass'] = getDbWriter(pass_handle, db_file, add_fields=add_fields)
+
+    if out_args['failed']:
+        fail_handle = getOutputHandle(db_file, 'germ-fail', out_dir=out_args['out_dir'],
+                                     out_name=out_args['out_name'], out_type=out_args['out_type'])
+        writers['fail'] = getDbWriter(fail_handle, db_file, add_fields=add_fields)
+    else:
+        fail_handle = None
+        writers['fail'] = None
+
+    # Initialize time and total count for progress bar
+    start_time = time()
+    rec_count = countDbFile(db_file)
+    counts = {}
+    clone_count = counts['pass'] = counts['fail'] = 0
+    # Iterate over rows
+    clone = 'initial'
+    clone_dict = OrderedDict()
+    for i, row in enumerate(reader):
+        # Print progress
+        printProgress(i, rec_count, 0.05, start_time)
+
+        # Clone isn't over yet
+        if row.get('CLONE', '') == clone:
+            clone_dict[i] = row
+        # Clone just finished
+        elif clone_dict:
+            clone_count += 1
+            result_log = makeCloneGermline(clone, clone_dict, repo_dict, germ_types,
+                                           v_field, seq_field, counts, writers, out_args)
+            printLog(result_log, handle=log_handle)
+            # Now deal with current row (first of next clone)
+            clone = row['CLONE']
+            clone_dict = OrderedDict([(i, row)])
+        # Last case is only for first row of file
+        else:
+            clone = row['CLONE']
+            clone_dict = OrderedDict([(i, row)])
+
+    clone_count += 1
+    result_log = makeCloneGermline(clone, clone_dict, repo_dict, germ_types, v_field,
+                                   seq_field, counts, writers, out_args)
+    printLog(result_log, handle=log_handle)
+
+    # Print log
+    printProgress(i + 1, rec_count, 0.05, start_time)
+    log = OrderedDict()
+    log['OUTPUT'] = os.path.basename(pass_handle.name)
+    log['CLONES'] = clone_count
+    log['RECORDS'] = rec_count
+    log['PASS'] = counts['pass']
+    log['FAIL'] = counts['fail']
+    log['END'] = 'CreateGermlines'
+    printLog(log)
+
+    # Close file handles
+    pass_handle.close()
+    if fail_handle is not None: fail_handle.close()
+    if log_handle is not None:  log_handle.close()
+
+
+def getArgParser():
+    """
+    Defines the ArgumentParser
+
+    Arguments:
+    None
+
+    Returns:
+    an ArgumentParser object
+    """
+    # Define input and output field help message
+    fields = dedent(
+             '''
+             output files:
+                 germ-pass
+                    database with assigned germline sequences.
+                 germ-fail
+                    database with records failing germline assignment.
+
+             required fields:
+                 SEQUENCE_ID, SEQUENCE_VDJ or SEQUENCE_IMGT,
+                 V_CALL or V_CALL_GENOTYPED, D_CALL, J_CALL,
+                 V_SEQ_START, V_SEQ_LENGTH, V_GERM_START_IMGT, V_GERM_LENGTH_IMGT,
+                 D_SEQ_START, D_SEQ_LENGTH, D_GERM_START, D_GERM_LENGTH,
+                 J_SEQ_START, J_SEQ_LENGTH, J_GERM_START, J_GERM_LENGTH,
+                 NP1_LENGTH, NP2_LENGTH
+
+             optional fields:
+                 N1_LENGTH, N2_LENGTH, P3V_LENGTH, P5D_LENGTH, P3D_LENGTH, P5J_LENGTH,
+                 CLONE
+
+
+             output fields:
+                 GERMLINE_VDJ, GERMLINE_VDJ_D_MASK, GERMLINE_VDJ_V_REGION,
+                 GERMLINE_IMGT, GERMLINE_IMGT_D_MASK, GERMLINE_IMGT_V_REGION,
+                 GERMLINE_V_CALL, GERMLINE_D_CALL, GERMLINE_J_CALL,
+                 GERMLINE_REGIONS
+              ''')
+
+    # Parent parser
+    parser_parent = getCommonArgParser(seq_in=False, seq_out=False, db_in=True,
+                                       annotation=False)
+    # Define argument parser
+    parser = ArgumentParser(description=__doc__, epilog=fields,
+                            parents=[parser_parent],
+                            formatter_class=CommonHelpFormatter)
+    parser.add_argument('--version', action='version',
+                        version='%(prog)s:' + ' %s-%s' %(__version__, __date__))
+
+    parser.add_argument('-r', nargs='+', action='store', dest='repo', required=True,
+                        help='''List of folders and/or fasta files (with .fasta, .fna or .fa
+                         extension) with germline sequences.''')
+    parser.add_argument('-g', action='store', dest='germ_types', default=default_germ_types,
+                        nargs='+', choices=('full', 'dmask', 'vonly', 'regions'),
+                        help='''Specify type(s) of germlines to include full germline,
+                             germline with D-region masked, or germline for V region only.''')
+    parser.add_argument('--cloned', action='store_true', dest='cloned',
+                        help='''Specify to create only one germline per clone. Assumes input file is
+                             sorted by clone column, and will not yield correct results if the data
+                             is unsorted. Note, if allele calls are ambiguous within a clonal group,
+                             this will place the germline call used for the entire clone within the
+                             GERMLINE_V_CALL, GERMLINE_D_CALL and GERMLINE_J_CALL fields.''')
+    parser.add_argument('--vf', action='store', dest='v_field', default=default_v_field,
+                        help='Specify field to use for germline V call')
+    parser.add_argument('--sf', action='store', dest='seq_field', default=default_seq_field,
+                        help='Specify field to use for sequence')
+
+    return parser
+
+
+if __name__ == "__main__":
+    """
+    Parses command line arguments and calls main
+    """
+
+    # Parse command line arguments
+    parser = getArgParser()
+    checkArgs(parser)
+    args = parser.parse_args()
+    args_dict = parseCommonArgs(args)
+    del args_dict['db_files']
+    del args_dict['cloned']
+    args_dict['v_field'] = args_dict['v_field'].upper()
+    args_dict['seq_field'] = args_dict['seq_field'].upper()
+    
+    for f in args.__dict__['db_files']:
+        args_dict['db_file'] = f
+        if args.__dict__['cloned']:
+            assembleCloneGermline(**args_dict)
+        else:
+            assembleEachGermline(**args_dict)