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1 #!/usr/bin/env python
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2
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50
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3 import argparse
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4 import logging
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5 import re
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6 from sys import stdout
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7 from Bio.SeqIO.QualityIO import FastqGeneralIterator
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8 # avoid ugly python IOError when stdout output is piped into another program
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9 # and then truncated (such as piping to head)
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10 from signal import signal, SIGPIPE, SIG_DFL
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11 signal(SIGPIPE, SIG_DFL)
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12
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2
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13 tool_description = """
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14 Exract barcodes from a FASTQ file according to a user-specified pattern.
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15
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16 By default output is written to stdout.
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17
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18 Example usage:
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5
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19 - remove barcode nucleotides at positions 1-3 and 6-7 from FASTQ; write modified
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20 FASTQ entries to output.fastq and barcode nucleotides to barcodes.fa:
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21 fastq_extract_barcodes.py barcoded_input.fastq XXXNNXX --out output.fastq --bcs barcodes.fastq
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22 """
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23
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24 epilog = """
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25 Author: Daniel Maticzka
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26 Copyright: 2015
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27 License: Apache
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28 Email: maticzkd@informatik.uni-freiburg.de
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29 Status: Testing
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30 """
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31
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32 # parse command line arguments
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33 parser = argparse.ArgumentParser(description=tool_description,
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34 epilog=epilog,
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35 formatter_class=argparse.RawDescriptionHelpFormatter)
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36 # positional arguments
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37 parser.add_argument(
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38 "infile",
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39 help="Path to fastq file.")
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40 parser.add_argument(
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41 "pattern",
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42 help="Pattern of barcode nucleotides starting at 5'-end. X positions will be moved to the header, N positions will be kept.")
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43 # optional arguments
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44 parser.add_argument(
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45 "-o", "--outfile",
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46 help="Write results to this file.")
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47 parser.add_argument(
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48 "-b", "--bcs",
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49 dest="out_bc_fasta",
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50 help="Write barcodes to this file in FASTQ format.")
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51 parser.add_argument(
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52 "--fasta-barcodes",
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53 dest="save_bcs_as_fa",
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54 action="store_true",
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55 help="Save extracted barcodes in FASTA format.")
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2
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56 parser.add_argument(
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5
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57 "-a", "--add-bc-to-fastq",
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58 dest="add_to_head",
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59 help="Append extracted barcodes to the FASTQ headers.",
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60 action="store_true")
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5
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61 parser.add_argument(
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2
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62 "-v", "--verbose",
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63 help="Be verbose.",
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64 action="store_true")
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65 parser.add_argument(
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66 "-d", "--debug",
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67 help="Print lots of debugging information",
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68 action="store_true")
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69 parser.add_argument(
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70 '--version',
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71 action='version',
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7
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72 version='0.1.0')
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2
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73
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74 args = parser.parse_args()
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75 if args.debug:
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76 logging.basicConfig(level=logging.DEBUG, format="%(asctime)s - %(filename)s - %(levelname)s - %(message)s")
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77 elif args.verbose:
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78 logging.basicConfig(level=logging.INFO, format="%(filename)s - %(levelname)s - %(message)s")
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79 else:
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80 logging.basicConfig(format="%(filename)s - %(levelname)s - %(message)s")
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81 logging.info("Parsed arguments:")
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82 logging.info(" infile: '{}'".format(args.infile))
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83 logging.info(" pattern: '{}'".format(args.pattern))
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84 if args.outfile:
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85 logging.info(" outfile: enabled writing to file")
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86 logging.info(" outfile: '{}'".format(args.outfile))
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87 if args.out_bc_fasta:
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88 logging.info(" bcs: enabled writing barcodes to fastq file")
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89 logging.info(" bcs: {}".format(args.out_bc_fasta))
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90 if args.save_bcs_as_fa:
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91 logging.info(" fasta-barcodes: write barcodes in fasta format instead of fastq")
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92 logging.info("")
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93
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94 # check if supplied pattern is valid
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95 valid_pattern = re.compile("^[XN]+$")
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96 pattern_match = valid_pattern.match(args.pattern)
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97 if pattern_match is None:
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98 raise ValueError("Error: supplied pattern '{}' is not valid.".format(args.pattern))
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99
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100 # check if at least one barcode position is included in the pattern
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101 has_bcpos_pattern = re.compile("X")
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102 pattern_match = has_bcpos_pattern.search(args.pattern)
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103 if pattern_match is None:
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104 raise ValueError("Error: supplied pattern '{}' does not contain a barcode position 'X'.".format(args.pattern))
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105
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106 logging.info("Barcode pattern analysis:")
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107 # get X positions of pattern string
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108 barcode_nt_pattern = re.compile("X+")
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109 barcode_positions = []
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110 for m in re.finditer(barcode_nt_pattern, args.pattern):
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111 logging.info(' found barcode positions in pattern: %02d-%02d: %s' % (m.start(), m.end(), m.group(0)))
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112 barcode_positions.append((m.start(), m.end()))
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113 logging.info(" barcode positions: {}".format(barcode_positions))
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114 # get last position of a barcode nt in the pattern
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115 # reads must be long enough for all
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116 min_readlen = barcode_positions[-1][-1]
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117 logging.info(" last position of a barcode nt in pattern: {}".format(min_readlen))
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118 logging.info("")
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119
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120 # get coordinates of nucleotides to keep
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121 # the tail after the last barcode nt is handled separately
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122 seq_positions = []
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123 last_seq_start = 0
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124 for bcstart, bcstop in barcode_positions:
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125 seq_positions.append((last_seq_start, bcstart))
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126 last_seq_start = bcstop
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127 logging.info(" sequence positions: {}".format(seq_positions))
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128 logging.info(" start of sequence tail: {}".format(last_seq_start))
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129
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130 samout = (open(args.outfile, "w") if args.outfile is not None else stdout)
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131 if args.out_bc_fasta is not None:
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132 faout = open(args.out_bc_fasta, "w")
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133 for header, seq, qual in FastqGeneralIterator(open(args.infile)):
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134
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135 # skip reads that are too short to extract the full requested barcode
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136 if len(seq) < min_readlen:
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137 logging.warning("skipping read '{}', is too short to extract the full requested barcode".format(header))
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138 logging.debug("seq: {}".format(seq))
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139 logging.debug("len(seq): {}".format(len(seq)))
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140 continue
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141
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142 # extract barcode nucleotides
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143 barcode_list = []
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144 barcode_qual_list = []
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2
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145 for bcstart, bcstop in barcode_positions:
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146 barcode_list.append(seq[bcstart:bcstop])
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147 barcode_qual_list.append(qual[bcstart:bcstop])
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148 barcode = "".join(barcode_list)
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149 barcode_quals = "".join(barcode_qual_list)
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150 logging.debug("extracted barcode: {}".format(barcode))
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151
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152 # create new sequence and quality string without barcode nucleotides
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153 new_seq_list = []
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154 new_qual_list = []
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155 for seqstart, seqstop in seq_positions:
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156 new_seq_list.append(seq[seqstart:seqstop])
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157 new_qual_list.append(qual[seqstart:seqstop])
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158 new_seq_list.append(seq[last_seq_start:])
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159 new_qual_list.append(qual[last_seq_start:])
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160 new_seq = "".join(new_seq_list)
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161 new_qual = "".join(new_qual_list)
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162 # check if at least one nucleotide is left. having none would break fastq
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163 if len(new_seq) == 0:
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164 logging.warning("skipping read '{}', no sequence remains after barcode extraction".format(header))
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165 logging.debug("seq: {}".format(seq))
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166 logging.debug("len(seq): {}".format(len(seq)))
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167 continue
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168
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169 # write barcode nucleotides into header
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170 if args.add_to_head:
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171 annotated_header = " ".join([header, barcode])
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172 else:
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173 annotated_header = header
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174 samout.write("@%s\n%s\n+\n%s\n" % (annotated_header, new_seq, new_qual))
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175
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176 # write barcode to fasta if requested
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177 if args.out_bc_fasta is not None:
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178 if args.save_bcs_as_fa:
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179 faout.write(">{}\n{}\n".format(header, barcode))
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180 else:
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181 faout.write("@{}\n{}\n+\n{}\n".format(header, barcode, barcode_quals))
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182
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183 # close files
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184 samout.close()
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185 if args.out_bc_fasta is not None:
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186 faout.close()
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