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comparison 0.4.2/bin/prepare_nanopore_fastq_dir.py @ 0:082e0091e813 draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:27:47 +0000
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-1:000000000000 0:082e0091e813
1 #!/usr/bin/env python3
2
3 import os
4 import re
5 import glob
6 import argparse
7 import logging
8
9 def main():
10 # READ IN ARGUMENTS
11 desc = """
12 Takes in a file with flowcell ID, one per line and creates soft links
13 to 'fastq_pass' directory at target location.
14
15 Ex:
16
17 prepare_nanopore_fastq_dir.py \
18 -o /hpc/scratch/Kranti.Konganti/np_test \
19 -f flowcells.txt
20
21 where flowcells.txt contains the following lines:
22
23 FAL11127
24 FAL11151
25
26 """
27 parser = argparse.ArgumentParser(prog='prepare_nanopore_fastq_dir.py',
28 formatter_class=argparse.ArgumentDefaultsHelpFormatter,
29 description=desc)
30 required = parser.add_argument_group('required arguments')
31
32 required.add_argument("-f", dest='flowcells', required=True,
33 help="Path to a text file containing Nanopore flowcell IDs, one per line")
34 required.add_argument("-i", dest='inputdir',
35 required=False, action='append', nargs='*',
36 help="Path to search directory. This directory location is where" +
37 " the presence of 'fastq_pass' will be searched for each flowcell.")
38 required.add_argument("-o", dest='outputdir',
39 required=True,
40 help="Path to output directory. This directory is created by the script" +
41 " and new soft links (symlinks) are created in this directory.")
42
43 args = parser.parse_args()
44 flowcells = args.flowcells
45 output = args.outputdir
46 inputs = args.inputdir
47
48 logging.basicConfig(format='%(asctime)s - %(levelname)s => %(message)s', level=logging.DEBUG)
49
50 if not inputs:
51 inputs = ['/projects/nanopore/raw']
52 nanopore_machines = ['RazorCrest', 'Revolution', 'ObiWan', 'MinIT',
53 'Mayhem', 'CaptainMarvel', 'MinION', 'MinION_Padmini', 'RogueOne']
54 logging.info(f"Searching default path(s). Use -i option if custom path should be searched.")
55 else:
56 nanopore_machines = ['custom']
57
58 fastq_pass_found = {}
59 was_fastq_pass_found = []
60
61 for each_input in inputs:
62 for machine in nanopore_machines:
63 if ''.join(nanopore_machines) != 'custom':
64 input = os.path.join(each_input, machine)
65 else:
66 input = ''.join(each_input)
67
68 logging.info(f"Searching path: {input}")
69
70 if (os.path.exists(flowcells) and os.path.getsize(flowcells) > 0):
71 with open(flowcells, 'r') as fcells:
72 for flowcell in fcells:
73 if re.match('^\s*$', flowcell):
74 continue
75 flowcell = flowcell.strip()
76 fastq_pass_path = glob.glob(os.path.join(input, flowcell, f"**", f"*[!fast5]*", 'fastq_pass'))
77 # Try one more time since the flowcell user is trying to query may be the parent directory
78 # of fastq_pass
79 fastq_pass = fastq_pass_path if fastq_pass_path else glob.glob(os.path.join(input, f"**", f"*[!fast5]*", flowcell, 'fastq_pass'))
80 if not fastq_pass:
81 # logging.warning(f"Flowcell " +
82 # os.path.join(input, flowcell).strip() +
83 # f" does not seem to have a fastq_pass directory! Skipped!!")
84 if not flowcell in fastq_pass_found.keys():
85 fastq_pass_found[flowcell] = 0
86 else:
87 fastq_pass_found[flowcell] = 1
88 sym_link_dir = os.path.join(output, flowcell)
89 sym_link_dir_dest = os.path.join(sym_link_dir, 'fastq_pass')
90 if not os.path.exists(sym_link_dir):
91 os.makedirs(sym_link_dir)
92 os.symlink(
93 ''.join(fastq_pass),
94 sym_link_dir_dest, target_is_directory=True
95 )
96 logging.info(f"New soft link created: {sym_link_dir_dest}")
97 else:
98 logging.info(f"Soft link {sym_link_dir_dest} already exists! Skipped!!")
99 fcells.close()
100 else:
101 logging.error(f"File {flowcells} is empty or does not exist!\n")
102
103 for k,v in fastq_pass_found.items():
104 if not v:
105 was_fastq_pass_found.append(k)
106
107 if was_fastq_pass_found:
108 logging.warning("Did not find fastq_pass folder for the supplied flowcells: " +
109 ', '.join(was_fastq_pass_found))
110
111 if was_fastq_pass_found and len(was_fastq_pass_found) == len(fastq_pass_found):
112 logging.error(f"None of the supplied flowcells were found! The output directory, {output} may not have been created!")
113 else:
114 logging.info(f"NOTE: Now you can use {output} directory as --input to cpipes.\n")
115
116 if __name__ == "__main__":
117 main()