Mercurial > repos > rmarenco > hubarchivecreator

comparison util/subtools.py @ 10:acc233161f50 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
author rmarenco
date Thu, 21 Jul 2016 05:58:51 -0400
parents fb5e60d4d18a
children 25809f699cb3
comparison
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9:4f9847539a28 10:acc233161f50
37 array_call = ['twoBitInfo', two_bit_file_name, two_bit_info_file] 37 array_call = ['twoBitInfo', two_bit_file_name, two_bit_info_file]
38 p = _handleExceptionAndCheckCall(array_call) 38 p = _handleExceptionAndCheckCall(array_call)
39 return p 39 return p
40 40
41 41
42 def faToTwoBit(fasta_file_name, mySpecieFolder): 42 def faToTwoBit(fasta_file_name, twoBitFile):
43 """ 43 """
44 This function call faToTwoBit UCSC tool, and return the twoBitFile 44 This function call faToTwoBit UCSC tool, and return the twoBitFile
45 :param fasta_file_name: 45 :param fasta_file_name:
46 :param mySpecieFolder: 46 :param mySpecieFolder:
47 :return: 47 :return:
48 """ 48 """
49 baseNameFasta = os.path.basename(fasta_file_name)
50 suffixTwoBit, extensionTwoBit = os.path.splitext(baseNameFasta)
51 nameTwoBit = suffixTwoBit + '.2bit'
52 49
53 with open(os.path.join(mySpecieFolder, nameTwoBit), 'w') as twoBitFile: 50 array_call = ['faToTwoBit', fasta_file_name, twoBitFile]
54 array_call = ['faToTwoBit', fasta_file_name, twoBitFile.name] 51 _handleExceptionAndCheckCall(array_call)
55 _handleExceptionAndCheckCall(array_call)
56 52
57 return twoBitFile 53 return twoBitFile
58 54
59 55
60 def gtfToGenePred(input_gtf_file_name, gene_pred_file_name): 56 def gtfToGenePred(input_gtf_file_name, gene_pred_file_name):