Mercurial > repos > nml > assemblystats

annotate assembly_stats_txt.py @ 1:7556309ffbaf draft default tip

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"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit fb4c29f720748f46ff501140f2cd306bab6614f9"
author nml
date Fri, 29 May 2020 13:51:50 -0400
parents ad2b274663f8
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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1 #!/usr/bin/env python
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2 # -*- coding: utf-8 -*-
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4 # Version 1.01 - bugs kindly corrected by Jan van Haarst
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5 # Modified by Matthew Gopez October 13th, 2017
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6 # Rewritten by Matthew Gopez May 25th, 2020
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7
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8 import argparse
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9 import os
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10 import shutil
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11 import subprocess
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12 from pathlib import Path
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14
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15 PERL_OUT_FILES = ['stats.txt', 'sorted_contigs.fa', 'histogram_bins.dat.png',
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16 'summed_contig_lengths.dat.png', 'histogram_bins.dat',
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17 'summed_contig_lengths.dat']
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20 def init_parser():
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21 """Create argument parser and return parser obj."""
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22 parser = argparse.ArgumentParser(description="usage: %prog [options]")
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24 parser.add_argument(
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25 "-d",
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26 "--working-dir",
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27 dest="working_dir",
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28 required=True)
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29
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30 parser.add_argument(
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31 "-t",
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32 "--type",
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33 dest="file_type",
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34 required=True)
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35
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36 parser.add_argument(
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37 "-b",
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38 "--bucket",
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39 dest="bucket",
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40 action='store_true')
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41
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42 parser.add_argument(
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43 "-i",
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44 "--input",
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45 dest="input",
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46 required=True)
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47
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48 parser.add_argument(
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49 "-s",
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50 "--stats",
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51 dest="stats",
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52 required=True)
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54 parser.add_argument(
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55 "-sc",
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56 "--sorted-contigs",
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57 dest="sorted_contigs",
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58 required=True)
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59
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60 parser.add_argument(
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61 "-hpng",
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62 "--histogram-png",
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63 dest="histogram_png",
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64 required=True)
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65
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66 parser.add_argument(
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67 "-spng",
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68 "--summed-contigs-png",
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69 dest="summed_contigs_png",
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70 required=True)
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72 parser.add_argument(
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73 "-hd",
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74 "--histogram-data",
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75 dest="histogram_data",
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76 required=True)
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78 parser.add_argument(
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79 "-scd",
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80 "--summed-config-data",
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81 dest="summed_contig_data",
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82 required=True)
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84 return parser
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87 def exec_fasta_summary(input_data, file_type, bucket, working_dir):
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88 """Execute fasta_summary.pl script with user arguments."""
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89 script_dir = Path(__file__).parent.absolute()
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90
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91 if bucket:
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92 bucket_arg = '-b'
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93 else:
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94 bucket_arg = ''
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95
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96 cli_command = \
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97 '{}/fasta_summary.pl -i {} -t {} {} -o {} > /dev/null'.format(
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98 script_dir, input_data, file_type, bucket_arg, working_dir)
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99
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100 try:
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101 subprocess.check_output(
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102 cli_command,
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103 stderr=subprocess.STDOUT,
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104 shell=True,
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105 universal_newlines=True)
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106 except subprocess.CalledProcessError as exc:
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107 raise RuntimeError('Error running assembly_stats.py!\n'
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108 'Return Code: {}\nOutput: {}'.format(
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109 exc.returncode, exc.output))
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110
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111
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112 def main():
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113 """This is where the magic happens. (not really)
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114
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115 1. Gets command line arguments.
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116 2. Grabs the user's desired parameters for running the perl script.
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117 3. Ensures the directories are in place.
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118 4. Executes fasta_summary.pl
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119 5. Move the out files from the perl script to the desired
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120 location the user specified.
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121
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122 """
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123 parser = init_parser()
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124 args = parser.parse_args()
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125
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126 working_dir = args.working_dir
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127
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128 out_file_names = [args.stats, args.sorted_contigs, args.histogram_png,
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129 args.summed_contigs_png, args.histogram_data,
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130 args.summed_contig_data]
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131
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132 # Ensure working directory is created.
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133 Path(working_dir).mkdir(parents=True, exist_ok=True)
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134
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135 # Execute Perl Script
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136 exec_fasta_summary(args.input, args.file_type, args.bucket, working_dir)
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137
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138 # Rename out files to desired file names
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139 for perl_out_file, dest_file in zip(PERL_OUT_FILES, out_file_names):
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140 shutil.move(os.path.join(working_dir, perl_out_file),
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141 dest_file)
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142
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143
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144 if __name__ == "__main__":
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145 main()