Mercurial > repos > jdv > albacore

annotate albacore_1D.py @ 6:3870c546db18 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 1514f4060da0b3a7866ac36d8a389828cbf48bd7
author jdv
date Tue, 23 Jan 2018 14:24:39 -0500
parents 8a9f61d08201
children ce1fa05ffb6c
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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
1
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10 from distutils.util import strtobool
0
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12 def main():
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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13 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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14 out_file = sys.argv[2]
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15 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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16 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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17 threads = sys.argv[5]
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18
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19 (flowcell, kit) = parse_meta(tar_file)
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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20
1
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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21 subprocess.call(
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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22 ["read_fast5_basecaller.py",
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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 "--input", "in_dir",
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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24 "--worker_threads", threads,
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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25 "--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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26 "--flowcell", flowcell,
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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27 "--kit", kit,
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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28 "--recursive",
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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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
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30 "--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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31 "--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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32 ["--barcoding"] * demux )
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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33
4
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34 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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35 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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36 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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37 out_path = pass_path
1
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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38 if demux:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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39 #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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40 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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41 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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42 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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43 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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44 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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45
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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46 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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47 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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48 print(d)
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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49 print(bc)
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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50 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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51 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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52 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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53 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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54 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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55 shutil.copy(found_file, out)
0
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56
1
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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57 elif out_fmt == 'fast5':
4
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58 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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59 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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60 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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61 files = [d]
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
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62 else:
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
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63 continue
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
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64 else:
8a9f61d08201 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 9a7fa5134243f712595bef72121b8006be8a318b
jdv
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65 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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66 files = glob.glob( os.path.join( d, "**", "*.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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67 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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68 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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69 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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70 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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71 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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72 tar.close()
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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73
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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74 else:
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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75 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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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 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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79 #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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80 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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81 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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82 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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83 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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84 shutil.copy(found_file, out_file)
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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85 elif out_fmt == 'fast5':
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86 #check for single albacore output and copy to Galaxy output
4
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87 files = glob.glob( os.path.join(out_path,"**","*.fast5"), recursive=True )
1
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88 if len(files) < 1:
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89 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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90 tar = tarfile.open(out_file, 'w:gz')
4
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91 tar.add(out_path)
1
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92 tar.close()
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93 else:
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94 raise ValueError('Bad output format specified')
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95
0
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96
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97 def parse_meta(fn):
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98
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99 try:
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100 in_dir = "in_dir"
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101 if not os.path.exists(in_dir):
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102 os.makedirs(in_dir)
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103
3
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104 # python's tarfile interface does not sanitize file paths within
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105 # 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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106 # default, so it's easier/safer here just to call the system tar
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107 subprocess.call([
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108 "tar",
4
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109 "--warning=no-unknown-keyword",
3
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110 "-xf",
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111 fn,
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112 "-C",
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113 in_dir])
0
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114
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115 files = glob.glob(
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116 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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117 recursive=True
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118 )
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119 if len(files) < 1:
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120 raise ValueError('No FAST5 files found')
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121 test_file = files[0]
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122
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123 f = h5py.File(test_file,"r")
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124 #TODO: clean up attribute checking
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125 try:
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126 flowcell = f["/UniqueGlobalKey/context_tags"].attrs["flowcell"].upper()
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127 except:
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128 try:
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129 flowcell = f["/UniqueGlobalKey/context_tags"].attrs["flowcell_type"].upper()
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130 except:
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131 raise ValueError('No attribute found for flowcell type')
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132 try:
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133 kit = f["/UniqueGlobalKey/context_tags"].attrs["sequencing_kit"].upper()
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134 except:
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135 raise ValueError('No attribute found for sequencing kit')
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136
0
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137 except OSError as e:
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138 print("Unexpected error:", e.strerror)
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139 raise
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140
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141 except:
f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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142 print("Unexpected error:", sys.exc_info()[0])
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143 raise
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144
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145 return flowcell, kit
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146
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147 if __name__ == "__main__" :
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148 main()