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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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