Mercurial > repos > jdv > albacore

annotate albacore_1D.py @ 3:d561e3f9ccbb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
author jdv
date Tue, 03 Oct 2017 20:12:09 -0400
parents 0a4f83207e53
children 8a9f61d08201
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
1 #!/usr/bin/env python3
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
2
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
3 import sys, os
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
4 import glob
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
5 import tarfile
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
6 import subprocess
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
7 import shutil
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
8 import h5py
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
9 import numpy as np
1
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
10 from distutils.util import strtobool
0
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
11
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
12 def main():
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
13 tar_file = sys.argv[1]
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
14 out_file = sys.argv[2]
1
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
15 out_fmt = sys.argv[3]
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
16 demux = strtobool( sys.argv[4] )
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
17 threads = sys.argv[5]
0
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
18
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
19 (flowcell, kit) = parse_meta(tar_file)
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
20
1
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
21 subprocess.call(
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
22 ["read_fast5_basecaller.py",
0
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
23 "--input", "in_dir",
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
24 "--worker_threads", threads,
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
25 "--save_path", "out_dir",
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
26 "--flowcell", flowcell,
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
27 "--kit", kit,
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
28 "--recursive",
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
29 "--files_per_batch_folder", "0",
1
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
30 "--output_format", out_fmt,
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
31 "--reads_per_fastq_batch", "999999999" ] +
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
32 ["--barcoding"] * demux )
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
33
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
34 if demux:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
35 #check for demuxed albacore output and copy to Galaxy output
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
36 final_dir = "final"
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
37 if not os.path.exists(final_dir):
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
38 os.makedirs(final_dir)
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
39 dirs = glob.glob("out_dir/workspace/*")
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
40 for d in dirs:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
41
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
42 if out_fmt == 'fastq':
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
43 bc = os.path.basename( os.path.normpath( d ) ) + ".fastq"
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
44 print(d)
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
45 print(bc)
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
46 out = os.path.join( final_dir, bc )
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
47 files = glob.glob( os.path.join( d, "*.fastq") )
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
48 if len(files) != 1:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
49 raise ValueError('No or multiple FASTQ output files found')
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
50 found_file = files[0]
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
51 shutil.copy(found_file, out)
0
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
52
1
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
53 elif out_fmt == 'fast5':
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
54 bc = os.path.basename( os.path.normpath( d ) ) + ".fast5.tar.gz"
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
55 print(d)
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
56 print(bc)
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
57 out = os.path.join( final_dir, bc )
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
58 files = glob.glob( os.path.join( d, "**", "*.fast5"), recursive=True)
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
59 if len(files) < 1:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
60 raise ValueError('No FAST5 output files found')
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
61 tar = tarfile.open(out, 'w:gz')
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
62 tar.add( d )
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
63 tar.close()
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
64
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
65 else:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
66 raise ValueError('Bad output format specified')
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
67
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
68 else:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
69 if out_fmt == 'fastq':
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
70 #check for single albacore output and copy to Galaxy output
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
71 files = glob.glob("out_dir/workspace/*.fastq")
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
72 if len(files) != 1:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
73 raise ValueError('No or multiple FASTQ output files found')
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
74 found_file = files[0]
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
75 shutil.copy(found_file, out_file)
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
76 elif out_fmt == 'fast5':
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
77 #check for single albacore output and copy to Galaxy output
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
78 files = glob.glob("out_dir/workspace/**/*.fast5", recursive=True)
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
79 if len(files) < 1:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
80 raise ValueError('No FAST5 output files found')
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
81 tar = tarfile.open(out_file, 'w:gz')
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
82 tar.add("out_dir/workspace")
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
83 tar.close()
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
84 else:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
85 raise ValueError('Bad output format specified')
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
jdv
parents: 0
diff changeset
86
0
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
87
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
88 def parse_meta(fn):
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
89
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
90 try:
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
91 in_dir = "in_dir"
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
92 if not os.path.exists(in_dir):
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
93 os.makedirs(in_dir)
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
94
3
d561e3f9ccbb planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
parents: 1
diff changeset
95 # python's tarfile interface does not sanitize file paths within
d561e3f9ccbb planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
parents: 1
diff changeset
96 # tarballs, which can be a big security risk. GNU tar does sanitize by
d561e3f9ccbb planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
parents: 1
diff changeset
97 # default, so it's easier/safer here just to call the system tar
d561e3f9ccbb planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
parents: 1
diff changeset
98 subprocess.call([
d561e3f9ccbb planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
parents: 1
diff changeset
99 "tar",
d561e3f9ccbb planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
parents: 1
diff changeset
100 "-xf",
d561e3f9ccbb planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
parents: 1
diff changeset
101 fn,
d561e3f9ccbb planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
parents: 1
diff changeset
102 "-C",
d561e3f9ccbb planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
parents: 1
diff changeset
103 in_dir])
0
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
104
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
105 files = glob.glob(
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
106 os.path.join(in_dir, "**", "*.fast5"),
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
107 recursive=True
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
108 )
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
109 if len(files) < 1:
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
110 raise ValueError('No FAST5 files found')
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
111 test_file = files[0]
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
112
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
113 f = h5py.File(test_file,"r")
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
114 flowcell = f["/UniqueGlobalKey/context_tags"].attrs["flowcell"].upper()
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
115 kit = f["/UniqueGlobalKey/context_tags"].attrs["sequencing_kit"].upper()
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
116 except OSError as e:
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
117 print("Unexpected error:", e.strerror)
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
118 raise
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
119
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
120 except:
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
121 print("Unexpected error:", sys.exc_info()[0])
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
122 raise
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
123
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
124 return flowcell, kit
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
125
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
126 if __name__ == "__main__" :
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
127 main()