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1 #!/usr/bin/env python3
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2
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3 import os
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4 import re
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5 import glob
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6 import argparse
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7 import logging
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8
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9 def main():
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10 # READ IN ARGUMENTS
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11 desc = """
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12 Takes in a file with flowcell ID, one per line and creates soft links
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13 to 'fastq_pass' directory at target location.
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14
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15 Ex:
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16
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17 prepare_nanopore_fastq_dir.py \
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18 -o /hpc/scratch/Kranti.Konganti/np_test \
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19 -f flowcells.txt
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20
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21 where flowcells.txt contains the following lines:
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22
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23 FAL11127
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24 FAL11151
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25
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26 """
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27 parser = argparse.ArgumentParser(prog='prepare_nanopore_fastq_dir.py',
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28 formatter_class=argparse.ArgumentDefaultsHelpFormatter,
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29 description=desc)
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30 required = parser.add_argument_group('required arguments')
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31
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32 required.add_argument("-f", dest='flowcells', required=True,
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33 help="Path to a text file containing Nanopore flowcell IDs, one per line")
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34 required.add_argument("-i", dest='inputdir',
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35 required=False, action='append', nargs='*',
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36 help="Path to search directory. This directory location is where" +
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37 " the presence of 'fastq_pass' will be searched for each flowcell.")
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38 required.add_argument("-o", dest='outputdir',
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39 required=True,
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40 help="Path to output directory. This directory is created by the script" +
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41 " and new soft links (symlinks) are created in this directory.")
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42
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43 args = parser.parse_args()
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44 flowcells = args.flowcells
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45 output = args.outputdir
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46 inputs = args.inputdir
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47
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48 logging.basicConfig(format='%(asctime)s - %(levelname)s => %(message)s', level=logging.DEBUG)
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49
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50 if not inputs:
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51 inputs = ['/projects/nanopore/raw']
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52 nanopore_machines = ['RazorCrest', 'Revolution', 'ObiWan', 'MinIT',
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53 'Mayhem', 'CaptainMarvel', 'MinION', 'MinION_Padmini', 'RogueOne']
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54 logging.info(f"Searching default path(s). Use -i option if custom path should be searched.")
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55 else:
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56 nanopore_machines = ['custom']
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57
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58 fastq_pass_found = {}
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59 was_fastq_pass_found = []
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60
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61 for each_input in inputs:
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62 for machine in nanopore_machines:
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63 if ''.join(nanopore_machines) != 'custom':
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64 input = os.path.join(each_input, machine)
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65 else:
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66 input = ''.join(each_input)
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67
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68 logging.info(f"Searching path: {input}")
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69
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70 if (os.path.exists(flowcells) and os.path.getsize(flowcells) > 0):
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71 with open(flowcells, 'r') as fcells:
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72 for flowcell in fcells:
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73 if re.match('^\s*$', flowcell):
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74 continue
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75 flowcell = flowcell.strip()
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76 fastq_pass_path = glob.glob(os.path.join(input, flowcell, f"**", f"*[!fast5]*", 'fastq_pass'))
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77 # Try one more time since the flowcell user is trying to query may be the parent directory
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78 # of fastq_pass
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79 fastq_pass = fastq_pass_path if fastq_pass_path else glob.glob(os.path.join(input, f"**", f"*[!fast5]*", flowcell, 'fastq_pass'))
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80 if not fastq_pass:
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81 # logging.warning(f"Flowcell " +
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82 # os.path.join(input, flowcell).strip() +
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83 # f" does not seem to have a fastq_pass directory! Skipped!!")
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84 if not flowcell in fastq_pass_found.keys():
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85 fastq_pass_found[flowcell] = 0
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86 else:
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87 fastq_pass_found[flowcell] = 1
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88 sym_link_dir = os.path.join(output, flowcell)
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89 sym_link_dir_dest = os.path.join(sym_link_dir, 'fastq_pass')
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90 if not os.path.exists(sym_link_dir):
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91 os.makedirs(sym_link_dir)
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92 os.symlink(
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93 ''.join(fastq_pass),
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94 sym_link_dir_dest, target_is_directory=True
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95 )
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96 logging.info(f"New soft link created: {sym_link_dir_dest}")
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97 else:
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98 logging.info(f"Soft link {sym_link_dir_dest} already exists! Skipped!!")
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99 fcells.close()
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100 else:
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101 logging.error(f"File {flowcells} is empty or does not exist!\n")
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102
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103 for k,v in fastq_pass_found.items():
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104 if not v:
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105 was_fastq_pass_found.append(k)
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106
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107 if was_fastq_pass_found:
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108 logging.warning("Did not find fastq_pass folder for the supplied flowcells: " +
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109 ', '.join(was_fastq_pass_found))
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110
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111 if was_fastq_pass_found and len(was_fastq_pass_found) == len(fastq_pass_found):
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112 logging.error(f"None of the supplied flowcells were found! The output directory, {output} may not have been created!")
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113 else:
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114 logging.info(f"NOTE: Now you can use {output} directory as --input to cpipes.\n")
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115
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116 if __name__ == "__main__":
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117 main() |
