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85 lines
2.5 KiB
Python
Executable File
85 lines
2.5 KiB
Python
Executable File
#!/usr/bin/env python2.4
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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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#tempfile, shutil
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BUFFER = 1048576
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uids = sys.argv[1].split(",")
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out_file1 = sys.argv[2]
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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 line in open( "/cache/encode_datasets/encode_datasets.loc" ):
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if line[0:1] == "#" : continue
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fields = line.split('\t')
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#read each line, if not enough fields, go to next line
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try:
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encode_group = fields[0]
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build = fields[1]
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description = fields[2]
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uid = fields[3]
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path = fields[4]
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path = path.replace("\n","")
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path = path.replace("\r","")
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try:
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file_type = fields[5]
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#remove newlines from file type
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file_type = file_type.replace("\n","")
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file_type = file_type.replace("\r","")
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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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print >>sys.stderr, "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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print >>sys.stderr, "There were no valid files requested."
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sys.exit()
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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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print >>sys.stderr, "The file specified is missing."
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continue
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#print >>sys.stderr, "The file specified is missing."
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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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