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83 lines
2.6 KiB
Python
Executable File
83 lines
2.6 KiB
Python
Executable File
#!/usr/bin/env python
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"""
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Script that imports locally stored data as a new dataset for the user
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Usage: import id outputfile
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"""
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import sys, os
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from shutil import copyfile
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assert sys.version_info[:2] >= ( 2, 4 )
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BUFFER = 1048576
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def stop_err( msg ):
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sys.stderr.write( msg )
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sys.exit()
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def main():
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uids = sys.argv[1].split(",")
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out_file1 = sys.argv[2]
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file_name = "%s/encode_datasets.loc" % sys.argv[3]
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#remove NONE from uids
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have_none = True
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while have_none:
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try:
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uids.remove('None')
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except:
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have_none = False
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#create dictionary keyed by uid of tuples of (displayName,filePath,build) for all files
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available_files = {}
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try:
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for i, line in enumerate( file ( file_name ) ):
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line = line.rstrip( '\r\n' )
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if line and not line.startswith( '#' ):
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fields = line.split( '\t' )
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try:
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encode_group = fields[0].strip()
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build = fields[1].strip()
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description = fields[2].strip()
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uid = fields[3].strip()
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path = fields[4].strip()
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try:
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file_type = fields[5].strip()
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except:
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file_type = "bed"
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except:
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continue
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available_files[uid] = ( description, path, build, file_type )
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except:
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stop_err( "It appears that the configuration file for this tool is missing." )
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#create list of tuples of ( displayName, FileName, build ) for desired files
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desired_files = []
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for uid in uids:
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try:
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desired_files.append( available_files[uid] )
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except:
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continue
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#copy first file to contents of given output file
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file1_copied = False
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while not file1_copied:
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try:
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first_file = desired_files.pop(0)
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except:
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stop_err( "There were no valid files requested." )
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file1_desc, file1_path, file1_build, file1_type = first_file
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try:
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copyfile( file1_path, out_file1 )
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print "#File1\t" + file1_desc + "\t" + file1_build + "\t" + file1_type
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file1_copied = True
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except:
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stop_err( "The file '%s' is missing." %str( file1_path ) )
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#Tell post-process filter where remaining files reside
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for extra_output in desired_files:
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file_desc, file_path, file_build, file_type = extra_output
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print "#NewFile\t" + file_desc + "\t" + file_build + "\t" + file_path + "\t" + file_type
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if __name__ == "__main__": main()
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