Mercurial > repos > jdv > albacore

comparison 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
comparison
equal deleted inserted replaced
5:4d72adba794f 6:3870c546db18
119 if len(files) < 1: 119 if len(files) < 1:
120 raise ValueError('No FAST5 files found') 120 raise ValueError('No FAST5 files found')
121 test_file = files[0] 121 test_file = files[0]
122 122
123 f = h5py.File(test_file,"r") 123 f = h5py.File(test_file,"r")
124 flowcell = f["/UniqueGlobalKey/context_tags"].attrs["flowcell"].upper() 124 #TODO: clean up attribute checking
125 kit = f["/UniqueGlobalKey/context_tags"].attrs["sequencing_kit"].upper() 125 try:
126 flowcell = f["/UniqueGlobalKey/context_tags"].attrs["flowcell"].upper()
127 except:
128 try:
129 flowcell = f["/UniqueGlobalKey/context_tags"].attrs["flowcell_type"].upper()
130 except:
131 raise ValueError('No attribute found for flowcell type')
132 try:
133 kit = f["/UniqueGlobalKey/context_tags"].attrs["sequencing_kit"].upper()
134 except:
135 raise ValueError('No attribute found for sequencing kit')
136
126 except OSError as e: 137 except OSError as e:
127 print("Unexpected error:", e.strerror) 138 print("Unexpected error:", e.strerror)
128 raise 139 raise
129 140
130 except: 141 except: