Mercurial > repos > jdv > albacore

annotate albacore_1D.py @ 7:ce1fa05ffb6c draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 00096785a6bc71027828388a53a61b9d22fdaadf
author jdv
date Sat, 10 Mar 2018 15:43:07 -0500
parents 3870c546db18
children 3dfde840119e
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f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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1 #!/usr/bin/env python3
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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2
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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3 import sys, os
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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4 import glob
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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5 import tarfile
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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6 import subprocess
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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7 import shutil
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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8 import h5py
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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9 import numpy as np
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10 from distutils.util import strtobool
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ce1fa05ffb6c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 00096785a6bc71027828388a53a61b9d22fdaadf
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11 from tempfile import mkdtemp
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f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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12
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13 def main():
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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14 tar_file = sys.argv[1]
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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15 out_file = sys.argv[2]
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16 out_fmt = sys.argv[3]
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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17 demux = strtobool( sys.argv[4] )
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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18 threads = sys.argv[5]
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f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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19
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20 tempdir = mkdtemp()
ce1fa05ffb6c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 00096785a6bc71027828388a53a61b9d22fdaadf
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ce1fa05ffb6c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 00096785a6bc71027828388a53a61b9d22fdaadf
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22 (flowcell, kit) = parse_meta(tar_file, tempdir)
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f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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23
1
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24 subprocess.call(
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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25 ["read_fast5_basecaller.py",
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ce1fa05ffb6c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 00096785a6bc71027828388a53a61b9d22fdaadf
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26 "--input", tempdir,
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27 "--worker_threads", threads,
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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28 "--save_path", "out_dir",
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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29 "--flowcell", flowcell,
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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30 "--kit", kit,
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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31 "--recursive",
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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32 "--files_per_batch_folder", "0",
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0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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33 "--output_format", out_fmt,
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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34 "--reads_per_fastq_batch", "999999999" ] +
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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35 ["--barcoding"] * demux )
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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36
4
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37 out_path = "out_dir/workspace"
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
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38 pass_path = os.path.join( out_path, "pass" )
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
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39 if os.path.exists( pass_path ):
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
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40 out_path = pass_path
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0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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41 if demux:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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42 #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
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43 final_dir = "final"
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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44 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
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45 os.makedirs(final_dir)
4
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
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46 dirs = glob.glob( os.path.join(out_path, "*") )
1
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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47 for d in dirs:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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48
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49 if out_fmt == 'fastq':
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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50 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
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51 print(d)
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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52 print(bc)
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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53 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
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54 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
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55 if len(files) != 1:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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56 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
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57 found_file = files[0]
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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58 shutil.copy(found_file, out)
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59
1
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60 elif out_fmt == 'fast5':
4
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61 if (os.path.isfile(d)):
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
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62 if (d.endswith('.fast5')):
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
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63 bc = os.path.basename( os.path.normpath(d) ) + ".tar.gz"
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
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64 files = [d]
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
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65 else:
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
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66 continue
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
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67 else:
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
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68 bc = os.path.basename( os.path.normpath( d ) ) + ".fast5.tar.gz"
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
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69 files = glob.glob( os.path.join( d, "**", "*.fast5"), recursive=True)
1
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70 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
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71 if len(files) < 1:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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72 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
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73 tar = tarfile.open(out, 'w:gz')
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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74 tar.add( d )
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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75 tar.close()
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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76
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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77 else:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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78 raise ValueError('Bad output format specified')
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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79
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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80 else:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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81 if out_fmt == 'fastq':
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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82 #check for single albacore output and copy to Galaxy output
4
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
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83 files = glob.glob( os.path.join(out_path, "*.fastq") )
1
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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84 if len(files) != 1:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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85 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
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parents: 0
diff changeset
86 found_file = files[0]
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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parents: 0
diff changeset
87 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
88 elif out_fmt == 'fast5':
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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parents: 0
diff changeset
89 #check for single albacore output and copy to Galaxy output
4
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
jdv
parents: 3
diff changeset
90 files = glob.glob( os.path.join(out_path,"**","*.fast5"), recursive=True )
1
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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parents: 0
diff changeset
91 if len(files) < 1:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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parents: 0
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92 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
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93 tar = tarfile.open(out_file, 'w:gz')
4
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
jdv
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94 tar.add(out_path)
1
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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parents: 0
diff changeset
95 tar.close()
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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parents: 0
diff changeset
96 else:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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parents: 0
diff changeset
97 raise ValueError('Bad output format specified')
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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98
7
ce1fa05ffb6c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 00096785a6bc71027828388a53a61b9d22fdaadf
jdv
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diff changeset
99 try:
ce1fa05ffb6c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 00096785a6bc71027828388a53a61b9d22fdaadf
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100 shutil.rmtree(tempdir)
ce1fa05ffb6c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 00096785a6bc71027828388a53a61b9d22fdaadf
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diff changeset
101 except:
ce1fa05ffb6c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 00096785a6bc71027828388a53a61b9d22fdaadf
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102 print("Unable to remove temp directory:", sys.exc_info()[0])
ce1fa05ffb6c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 00096785a6bc71027828388a53a61b9d22fdaadf
jdv
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diff changeset
103 raise
0
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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104
7
ce1fa05ffb6c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 00096785a6bc71027828388a53a61b9d22fdaadf
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parents: 6
diff changeset
105
ce1fa05ffb6c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 00096785a6bc71027828388a53a61b9d22fdaadf
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106 def parse_meta(fn, in_dir):
0
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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diff changeset
107
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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diff changeset
108 try:
3
d561e3f9ccbb planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
parents: 1
diff changeset
109 # 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
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diff changeset
110 # 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
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111 # 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
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112 subprocess.call([
d561e3f9ccbb planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
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diff changeset
113 "tar",
4
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
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diff changeset
114 "--warning=no-unknown-keyword",
3
d561e3f9ccbb planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
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diff changeset
115 "-xf",
d561e3f9ccbb planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
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parents: 1
diff changeset
116 fn,
d561e3f9ccbb planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
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117 "-C",
d561e3f9ccbb planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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diff changeset
118 in_dir])
0
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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119
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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diff changeset
120 files = glob.glob(
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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121 os.path.join(in_dir, "**", "*.fast5"),
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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122 recursive=True
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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diff changeset
123 )
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
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124 if len(files) < 1:
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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125 raise ValueError('No FAST5 files found')
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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126 test_file = files[0]
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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127
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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128 f = h5py.File(test_file,"r")
6
3870c546db18 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 1514f4060da0b3a7866ac36d8a389828cbf48bd7
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129 #TODO: clean up attribute checking
3870c546db18 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 1514f4060da0b3a7866ac36d8a389828cbf48bd7
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130 try:
3870c546db18 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 1514f4060da0b3a7866ac36d8a389828cbf48bd7
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131 flowcell = f["/UniqueGlobalKey/context_tags"].attrs["flowcell"].upper()
3870c546db18 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 1514f4060da0b3a7866ac36d8a389828cbf48bd7
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132 except:
3870c546db18 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 1514f4060da0b3a7866ac36d8a389828cbf48bd7
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diff changeset
133 try:
3870c546db18 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 1514f4060da0b3a7866ac36d8a389828cbf48bd7
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134 flowcell = f["/UniqueGlobalKey/context_tags"].attrs["flowcell_type"].upper()
3870c546db18 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 1514f4060da0b3a7866ac36d8a389828cbf48bd7
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diff changeset
135 except:
3870c546db18 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 1514f4060da0b3a7866ac36d8a389828cbf48bd7
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136 raise ValueError('No attribute found for flowcell type')
3870c546db18 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 1514f4060da0b3a7866ac36d8a389828cbf48bd7
jdv
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diff changeset
137 try:
3870c546db18 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 1514f4060da0b3a7866ac36d8a389828cbf48bd7
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diff changeset
138 kit = f["/UniqueGlobalKey/context_tags"].attrs["sequencing_kit"].upper()
3870c546db18 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 1514f4060da0b3a7866ac36d8a389828cbf48bd7
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diff changeset
139 except:
3870c546db18 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 1514f4060da0b3a7866ac36d8a389828cbf48bd7
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diff changeset
140 raise ValueError('No attribute found for sequencing kit')
3870c546db18 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 1514f4060da0b3a7866ac36d8a389828cbf48bd7
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diff changeset
141
0
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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142 except OSError as e:
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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parents:
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143 print("Unexpected error:", e.strerror)
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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diff changeset
144 raise
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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diff changeset
145
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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146 except:
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
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147 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
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diff changeset
148 raise
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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149
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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diff changeset
150 return flowcell, kit
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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151
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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152 if __name__ == "__main__" :
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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153 main()