[2] | 1 | #!/usr/bin/env python |
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| 2 | |
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| 3 | """ |
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| 4 | Script that imports locally stored data as a new dataset for the user |
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| 5 | Usage: import id outputfile |
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| 6 | """ |
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| 7 | import sys, os |
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| 8 | from shutil import copyfile |
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| 9 | |
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| 10 | assert sys.version_info[:2] >= ( 2, 4 ) |
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| 11 | |
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| 12 | BUFFER = 1048576 |
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| 13 | |
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| 14 | uids = sys.argv[1].split(",") |
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| 15 | out_file1 = sys.argv[2] |
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| 16 | |
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| 17 | #remove NONE from uids |
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| 18 | have_none = True |
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| 19 | while have_none: |
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| 20 | try: |
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| 21 | uids.remove('None') |
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| 22 | except: |
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| 23 | have_none = False |
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| 24 | |
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| 25 | |
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| 26 | #create dictionary keyed by uid of tuples of (displayName,filePath,build) for all files |
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| 27 | available_files = {} |
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| 28 | try: |
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| 29 | filename = sys.argv[-1] |
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| 30 | for i, line in enumerate( file( filename ) ): |
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| 31 | if not line or line[0:1] == "#" : continue |
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| 32 | fields = line.split('\t') |
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| 33 | try: |
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| 34 | info_type = fields.pop(0) |
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| 35 | |
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| 36 | if info_type.upper()=="DATA": |
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| 37 | uid = fields.pop(0) |
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| 38 | org_num = fields.pop(0) |
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| 39 | chr_acc = fields.pop(0) |
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| 40 | feature = fields.pop(0) |
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| 41 | filetype = fields.pop(0) |
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| 42 | path = fields.pop(0).replace("\r","").replace("\n","") |
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| 43 | |
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| 44 | file_type = filetype |
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| 45 | build = org_num |
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| 46 | description = uid |
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| 47 | else: |
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| 48 | continue |
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| 49 | except: |
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| 50 | continue |
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| 51 | |
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| 52 | available_files[uid]=(description,path,build,file_type,chr_acc) |
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| 53 | except: |
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| 54 | print >>sys.stderr, "It appears that the configuration file for this tool is missing." |
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| 55 | |
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| 56 | #create list of tuples of (displayName,FileName,build) for desired files |
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| 57 | desired_files = [] |
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| 58 | for uid in uids: |
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| 59 | try: |
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| 60 | desired_files.append(available_files[uid]) |
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| 61 | except: |
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| 62 | continue |
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| 63 | |
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| 64 | #copy first file to contents of given output file |
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| 65 | file1_copied = False |
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| 66 | while not file1_copied: |
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| 67 | try: |
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| 68 | first_file = desired_files.pop(0) |
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| 69 | except: |
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| 70 | print >>sys.stderr, "There were no valid files requested." |
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| 71 | sys.exit() |
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| 72 | file1_desc, file1_path, file1_build, file1_type,file1_chr_acc = first_file |
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| 73 | try: |
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| 74 | copyfile(file1_path,out_file1) |
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| 75 | print "#File1\t"+file1_desc+"\t"+file1_chr_acc+"\t"+file1_build+"\t"+file1_type |
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| 76 | file1_copied = True |
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| 77 | except: |
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| 78 | print >>sys.stderr, "The file specified is missing." |
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| 79 | continue |
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| 80 | #print >>sys.stderr, "The file specified is missing." |
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| 81 | |
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| 82 | |
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| 83 | #Tell post-process filter where remaining files reside |
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| 84 | for extra_output in desired_files: |
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| 85 | file_desc, file_path, file_build, file_type,file_chr_acc = extra_output |
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| 86 | print "#NewFile\t"+file_desc+"\t"+file_chr_acc+"\t"+file_build+"\t"+file_path+"\t"+file_type |
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