s_mart: smart_toolShed/commons/core/seq/test/Utils_for_T

author	yufei-luo
date	Thu, 17 Jan 2013 10:52:14 -0500
parents
children

rev	line source
0 e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	1 # Copyright INRA (Institut National de la Recherche Agronomique)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	2 # http://www.inra.fr
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	3 # http://urgi.versailles.inra.fr
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	4 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	5 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	6 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	7 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	8 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	9 # "http://www.cecill.info".
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	10 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	11 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	12 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	13 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	14 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	15 # liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	16 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	17 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	18 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	19 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	20 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	21 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	22 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	23 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	24 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	25 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	26 # same conditions as regards security.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	27 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	28 # The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	29 # knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	30
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	31
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	32 class Utils_for_T_FastaUtils( object ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	33
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	34 def _createFastaFile_for_empty_file(fileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	35 f = open(fileName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	36 f.write("")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	37 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	38
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	39 _createFastaFile_for_empty_file = staticmethod ( _createFastaFile_for_empty_file )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	40
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	41
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	42 def _createFastaFile_one_sequence(fileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	43 f = open(fileName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	44 f.write(">seq 1\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	45 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	46 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	47 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	48 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	49
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	50 _createFastaFile_one_sequence = staticmethod ( _createFastaFile_one_sequence )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	51
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	52
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	53 def createFastaFile_twoSequences( fileName ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	54 f = open( fileName, "w" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	55 f.write( ">seq 1\n" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	56 f.write( "ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	57 f.write( "ATATTCG\n" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	58 f.write( ">seq 2\n" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	59 f.write( "ATATTCTTTCATCGATCGATCGGCGGCTATATGCTAGTGACGAAGCTAGTGTGAGTAGTA\n" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	60 f.write( "ATATTCG\n" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	61 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	62
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	63 createFastaFile_twoSequences = staticmethod ( createFastaFile_twoSequences )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	64
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	65
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	66 def createFastaFile_seq_1( fileName ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	67 f = open( fileName, "w" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	68 f.write( ">seq 1\n" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	69 f.write( "ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	70 f.write( "ATATTCG\n" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	71 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	72
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	73 createFastaFile_seq_1 = staticmethod( createFastaFile_seq_1 )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	74
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	75
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	76 def createFastaFile_seq_2( fileName ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	77 f = open( fileName, "w" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	78 f.write( ">seq 2\n" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	79 f.write( "ATATTCTTTCATCGATCGATCGGCGGCTATATGCTAGTGACGAAGCTAGTGTGAGTAGTA\n" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	80 f.write( "ATATTCG\n" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	81 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	82
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	83 createFastaFile_seq_2 = staticmethod( createFastaFile_seq_2 )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	84
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	85
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	86 def _createFastaFile_sequence_without_header(fileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	87 f = open(fileName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	88 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	89 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	90 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	91 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	92
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	93 _createFastaFile_sequence_without_header = staticmethod ( _createFastaFile_sequence_without_header )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	94
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	95
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	96 def _createFastaFile_four_sequences(fileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	97 f = open(fileName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	98 f.write(">seq 1\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	99 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	100 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	101 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	102 f.write(">seq 2\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	103 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	104 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	105 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	106 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	107 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	108 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	109 f.write(">seq 3\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	110 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	111 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	112 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	113 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	114 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	115 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	116 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	117 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	118 f.write(">seq 4\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	119 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	120 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	121 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	122 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	123 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	124 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	125 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	126
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	127 _createFastaFile_four_sequences = staticmethod ( _createFastaFile_four_sequences )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	128
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	129
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	130 def _createFastaFile_three_sequences(fileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	131 f = open(fileName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	132 f.write(">seq 1\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	133 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	134 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	135 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	136 f.write(">seq 2\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	137 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	138 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	139 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	140 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	141 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	142 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	143 f.write(">seq 4\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	144 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	145 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	146 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	147 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	148 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	149 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	150 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	151
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	152 _createFastaFile_three_sequences = staticmethod ( _createFastaFile_three_sequences )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	153
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	154
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	155 # ------------------ for dbSplit ---------------- #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	156
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	157 def _createBatch1_two_sequences(inFileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	158 f = open(inFileName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	159 f.write(">seq 1\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	160 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	161 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	162 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	163 f.write(">seq 2\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	164 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	165 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	166 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	167 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	168 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	169 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	170 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	171
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	172 _createBatch1_two_sequences = staticmethod ( _createBatch1_two_sequences )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	173
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	174
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	175 def _createBatch2_two_sequences(inFileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	176 f = open(inFileName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	177 f.write(">seq 3\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	178 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	179 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	180 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	181 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	182 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	183 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	184 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	185 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	186 f.write(">seq 4\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	187 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	188 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	189 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	190 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	191 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	192 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	193 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	194
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	195 _createBatch2_two_sequences = staticmethod ( _createBatch2_two_sequences )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	196
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	197
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	198 def _createBatch1_three_sequences(inFileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	199 f = open(inFileName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	200 f.write(">seq 1\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	201 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	202 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	203 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	204 f.write(">seq 2\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	205 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	206 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	207 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	208 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	209 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	210 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	211 f.write(">seq 3\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	212 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	213 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	214 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	215 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	216 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	217 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	218 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	219 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	220 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	221
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	222 _createBatch1_three_sequences = staticmethod ( _createBatch1_three_sequences )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	223
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	224
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	225 def _createBatch2_one_sequence(inFileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	226 f = open(inFileName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	227 f.write(">seq 4\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	228 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	229 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	230 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	231 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	232 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	233 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	234 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	235
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	236 _createBatch2_one_sequence = staticmethod ( _createBatch2_one_sequence )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	237
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	238
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	239 def _createFastaFile_ten_sequences(fileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	240 f = open(fileName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	241 f.write(">seq 1\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	242 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	243 f.write(">seq 2\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	244 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	245 f.write(">seq 3\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	246 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	247 f.write(">seq 4\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	248 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	249 f.write(">seq 5\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	250 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	251 f.write(">seq 6\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	252 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	253 f.write(">seq 7\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	254 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	255 f.write(">seq 8\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	256 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	257 f.write(">seq 9\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	258 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	259 f.write(">seq 10\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	260 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	261 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	262
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	263 _createFastaFile_ten_sequences = staticmethod ( _createFastaFile_ten_sequences )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	264
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	265
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	266 def _createBatch_one_small_sequence(fileName, seqName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	267 f = open(fileName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	268 f.write(">" +seqName + "\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	269 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	270 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	271
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	272 _createBatch_one_small_sequence = staticmethod ( _createBatch_one_small_sequence )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	273
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	274
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	275 # ------------------ for dbChunks ------------------- #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	276
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	277 def _createFastaFile_big_sequence(fileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	278 f = open(fileName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	279 f.write(">sequence\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	280 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	281 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	282 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	283 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	284 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	285 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	286 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	287 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	288 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	289 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	290 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	291 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	292 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	293 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	294 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	295 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	296 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	297 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	298 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	299 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	300 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	301
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	302 _createFastaFile_big_sequence = staticmethod ( _createFastaFile_big_sequence )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	303
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	304
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	305 def _createFastaFile_of_Chunks(fileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	306 f = open(fileName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	307 f.write('>chunk01\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	308 f.write('ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	309 f.write('>chunk02\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	310 f.write('GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	311 f.write('>chunk03\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	312 f.write('GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	313 f.write('>chunk04\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	314 f.write('ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	315 f.write('>chunk05\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	316 f.write('CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	317 f.write('>chunk06\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	318 f.write('ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	319 f.write('>chunk07\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	320 f.write('ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	321 f.write('>chunk08\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	322 f.write('GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	323 f.write('>chunk09\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	324 f.write('GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	325 f.write('>chunk10\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	326 f.write('ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	327 f.write('>chunk11\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	328 f.write('CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	329 f.write('>chunk12\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	330 f.write('ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	331 f.write('>chunk13\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	332 f.write('ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	333 f.write('>chunk14\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	334 f.write('GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	335 f.write('>chunk15\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	336 f.write('GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	337 f.write('>chunk16\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	338 f.write('ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	339 f.write('>chunk17\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	340 f.write('CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	341 f.write('>chunk18\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	342 f.write('ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	343 f.write('>chunk19\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	344 f.write('ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	345 f.write('>chunk20\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	346 f.write('GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	347 f.write('>chunk21\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	348 f.write('GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	349 f.write('>chunk22\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	350 f.write('ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	351 f.write('>chunk23\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	352 f.write('CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCG\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	353 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	354
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	355 _createFastaFile_of_Chunks = staticmethod ( _createFastaFile_of_Chunks )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	356
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	357
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	358 def _createMapFile_of_Chunks(fileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	359 f = open(fileName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	360 f.write("chunk01\tsequence\t1\t60\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	361 f.write("chunk02\tsequence\t51\t110\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	362 f.write("chunk03\tsequence\t101\t160\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	363 f.write("chunk04\tsequence\t151\t210\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	364 f.write("chunk05\tsequence\t201\t260\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	365 f.write("chunk06\tsequence\t251\t310\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	366 f.write("chunk07\tsequence\t301\t360\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	367 f.write("chunk08\tsequence\t351\t410\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	368 f.write("chunk09\tsequence\t401\t460\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	369 f.write("chunk10\tsequence\t451\t510\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	370 f.write("chunk11\tsequence\t501\t560\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	371 f.write("chunk12\tsequence\t551\t610\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	372 f.write("chunk13\tsequence\t601\t660\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	373 f.write("chunk14\tsequence\t651\t710\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	374 f.write("chunk15\tsequence\t701\t760\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	375 f.write("chunk16\tsequence\t751\t810\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	376 f.write("chunk17\tsequence\t801\t860\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	377 f.write("chunk18\tsequence\t851\t910\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	378 f.write("chunk19\tsequence\t901\t960\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	379 f.write("chunk20\tsequence\t951\t1010\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	380 f.write("chunk21\tsequence\t1001\t1060\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	381 f.write("chunk22\tsequence\t1051\t1110\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	382 f.write("chunk23\tsequence\t1101\t1147\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	383 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	384
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	385 _createMapFile_of_Chunks = staticmethod ( _createMapFile_of_Chunks )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	386
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	387
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	388 def _createFastaFile_of_cut(fileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	389 f = open(fileName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	390 f.write(">1 sequence {Cut} 1..60\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	391 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	392 f.write(">2 sequence {Cut} 51..110\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	393 f.write("GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	394 f.write(">3 sequence {Cut} 101..160\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	395 f.write("GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	396 f.write(">4 sequence {Cut} 151..210\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	397 f.write("ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	398 f.write(">5 sequence {Cut} 201..260\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	399 f.write("CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	400 f.write(">6 sequence {Cut} 251..310\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	401 f.write("ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	402 f.write(">7 sequence {Cut} 301..360\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	403 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	404 f.write(">8 sequence {Cut} 351..410\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	405 f.write("GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	406 f.write(">9 sequence {Cut} 401..460\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	407 f.write("GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	408 f.write(">10 sequence {Cut} 451..510\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	409 f.write("ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	410 f.write(">11 sequence {Cut} 501..560\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	411 f.write("CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	412 f.write(">12 sequence {Cut} 551..610\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	413 f.write("ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	414 f.write(">13 sequence {Cut} 601..660\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	415 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	416 f.write(">14 sequence {Cut} 651..710\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	417 f.write("GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	418 f.write(">15 sequence {Cut} 701..760\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	419 f.write("GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	420 f.write(">16 sequence {Cut} 751..810\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	421 f.write("ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	422 f.write(">17 sequence {Cut} 801..860\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	423 f.write("CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	424 f.write(">18 sequence {Cut} 851..910\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	425 f.write("ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	426 f.write(">19 sequence {Cut} 901..960\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	427 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	428 f.write(">20 sequence {Cut} 951..1010\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	429 f.write("GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	430 f.write(">21 sequence {Cut} 1001..1060\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	431 f.write("GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	432 f.write(">22 sequence {Cut} 1051..1110\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	433 f.write("ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	434 f.write(">23 sequence {Cut} 1101..1147\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	435 f.write("CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	436 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	437
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	438 _createFastaFile_of_cut = staticmethod ( _createFastaFile_of_cut )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	439
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	440
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	441 def _createFastaFile_of_Nstretch(fileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	442 f = open(fileName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	443 f.write("")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	444 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	445
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	446 _createFastaFile_of_Nstretch = staticmethod ( _createFastaFile_of_Nstretch )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	447
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	448
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	449 # ------------------ for splitSeqPerCluster ------------------- #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	450
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	451 def _createFastaFile_of_four_sequences_with_specific_header(inFileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	452 f = open(inFileName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	453 f.write(">ReconCluster1Mb155 chunk183 {Fragment} 1..5506\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	454 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	455 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	456 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	457 f.write(">MbQ3Gr2Cl0 chunk440 {Fragment} 2678..3645\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	458 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	459 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	460 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	461 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	462 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	463 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	464 f.write(">MbS2Gr2Cl0 chunk622 {Fragment} 104..1078\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	465 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	466 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	467 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	468 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	469 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	470 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	471 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	472 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	473 f.write(">PilerCluster3.574Mb796 chunk0117 {Fragment} 51582..50819\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	474 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	475 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	476 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	477 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	478 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	479 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	480 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	481
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	482 _createFastaFile_of_four_sequences_with_specific_header = staticmethod ( _createFastaFile_of_four_sequences_with_specific_header )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	483
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	484
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	485 def _createFastaFile_of_four_sequences_with_specific_header_shuffle(inFileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	486 f = open(inFileName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	487 f.write(">MbQ3Gr2Cl0 chunk440 {Fragment} 2678..3645\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	488 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	489 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	490 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	491 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	492 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	493 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	494 f.write(">ReconCluster1Mb155 chunk183 {Fragment} 1..5506\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	495 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	496 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	497 f.write("ATATTCG\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	498 f.write(">MbS2Gr2Cl0 chunk622 {Fragment} 104..1078\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	499 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	500 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

0

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

1 # Copyright INRA (Institut National de la Recherche Agronomique)

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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2 # http://www.inra.fr

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

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3 # http://urgi.versailles.inra.fr

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

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4 #

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

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5 # This software is governed by the CeCILL license under French law and

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

6 # abiding by the rules of distribution of free software. You can use,

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

7 # modify and/ or redistribute the software under the terms of the CeCILL

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

8 # license as circulated by CEA, CNRS and INRIA at the following URL

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

9 # "http://www.cecill.info".

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

10 #

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

11 # As a counterpart to the access to the source code and rights to copy,

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

12 # modify and redistribute granted by the license, users are provided only

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

13 # with a limited warranty and the software's author, the holder of the

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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diff changeset

14 # economic rights, and the successive licensors have only limited

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

15 # liability.

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

16 #

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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diff changeset

17 # In this respect, the user's attention is drawn to the risks associated

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

18 # with loading, using, modifying and/or developing or reproducing the

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

19 # software by the user in light of its specific status of free software,

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

20 # that may mean that it is complicated to manipulate, and that also

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

21 # therefore means that it is reserved for developers and experienced

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

22 # professionals having in-depth computer knowledge. Users are therefore

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

23 # encouraged to load and test the software's suitability as regards their

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

24 # requirements in conditions enabling the security of their systems and/or

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

25 # data to be ensured and, more generally, to use and operate it in the

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

26 # same conditions as regards security.

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

27 #

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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28 # The fact that you are presently reading this means that you have had

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

29 # knowledge of the CeCILL license and that you accept its terms.

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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diff changeset

30

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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31

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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32 class Utils_for_T_FastaUtils( object ):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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33

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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34 def _createFastaFile_for_empty_file(fileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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35 f = open(fileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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36 f.write("")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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37 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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38

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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39 _createFastaFile_for_empty_file = staticmethod ( _createFastaFile_for_empty_file )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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40

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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41

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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42 def _createFastaFile_one_sequence(fileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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43 f = open(fileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

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44 f.write(">seq 1\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

45 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

46 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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47 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

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48 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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49

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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50 _createFastaFile_one_sequence = staticmethod ( _createFastaFile_one_sequence )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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51

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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52

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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53 def createFastaFile_twoSequences( fileName ):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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54 f = open( fileName, "w" )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

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55 f.write( ">seq 1\n" )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

56 f.write( "ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n" )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

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57 f.write( "ATATTCG\n" )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

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58 f.write( ">seq 2\n" )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

59 f.write( "ATATTCTTTCATCGATCGATCGGCGGCTATATGCTAGTGACGAAGCTAGTGTGAGTAGTA\n" )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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60 f.write( "ATATTCG\n" )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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61 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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62

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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63 createFastaFile_twoSequences = staticmethod ( createFastaFile_twoSequences )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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64

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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65

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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66 def createFastaFile_seq_1( fileName ):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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67 f = open( fileName, "w" )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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68 f.write( ">seq 1\n" )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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69 f.write( "ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n" )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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70 f.write( "ATATTCG\n" )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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71 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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72

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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73 createFastaFile_seq_1 = staticmethod( createFastaFile_seq_1 )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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74

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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75

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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76 def createFastaFile_seq_2( fileName ):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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77 f = open( fileName, "w" )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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78 f.write( ">seq 2\n" )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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79 f.write( "ATATTCTTTCATCGATCGATCGGCGGCTATATGCTAGTGACGAAGCTAGTGTGAGTAGTA\n" )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

80 f.write( "ATATTCG\n" )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

81 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

82

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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83 createFastaFile_seq_2 = staticmethod( createFastaFile_seq_2 )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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diff changeset

84

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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85

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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86 def _createFastaFile_sequence_without_header(fileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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87 f = open(fileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

88 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

89 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

90 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

91 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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parents:

diff changeset

92

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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93 _createFastaFile_sequence_without_header = staticmethod ( _createFastaFile_sequence_without_header )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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diff changeset

94

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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95

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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96 def _createFastaFile_four_sequences(fileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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97 f = open(fileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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98 f.write(">seq 1\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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parents:

diff changeset

99 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

100 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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diff changeset

101 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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102 f.write(">seq 2\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

103 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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104 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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diff changeset

105 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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106 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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diff changeset

107 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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108 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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109 f.write(">seq 3\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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110 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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111 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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diff changeset

112 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

113 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

114 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

115 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

116 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

117 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

118 f.write(">seq 4\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

119 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

120 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

121 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

122 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

123 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

124 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

125 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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diff changeset

126

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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127 _createFastaFile_four_sequences = staticmethod ( _createFastaFile_four_sequences )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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diff changeset

128

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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129

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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130 def _createFastaFile_three_sequences(fileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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131 f = open(fileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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132 f.write(">seq 1\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

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133 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

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134 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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135 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

136 f.write(">seq 2\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

137 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

138 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

139 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

140 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

141 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

142 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

143 f.write(">seq 4\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

144 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

145 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

146 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

147 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

148 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

149 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

150 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

151

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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152 _createFastaFile_three_sequences = staticmethod ( _createFastaFile_three_sequences )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

153

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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154

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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diff changeset

155 # ------------------ for dbSplit ---------------- #

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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156

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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157 def _createBatch1_two_sequences(inFileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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158 f = open(inFileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

159 f.write(">seq 1\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

160 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

161 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

162 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

163 f.write(">seq 2\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

164 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

165 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

166 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

167 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

168 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

169 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

170 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

171

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

172 _createBatch1_two_sequences = staticmethod ( _createBatch1_two_sequences )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

173

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

174

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

175 def _createBatch2_two_sequences(inFileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

176 f = open(inFileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

177 f.write(">seq 3\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

178 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

179 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

180 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

181 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

182 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

183 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

184 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

185 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

186 f.write(">seq 4\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

187 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

188 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

189 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

190 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

191 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

192 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

193 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

194

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

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195 _createBatch2_two_sequences = staticmethod ( _createBatch2_two_sequences )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

196

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

197

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

198 def _createBatch1_three_sequences(inFileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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199 f = open(inFileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

200 f.write(">seq 1\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

201 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

202 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

203 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

204 f.write(">seq 2\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

205 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

206 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

207 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

208 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

209 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

210 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

211 f.write(">seq 3\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

212 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

213 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

214 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

215 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

216 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

217 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

218 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

219 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

220 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

221

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

222 _createBatch1_three_sequences = staticmethod ( _createBatch1_three_sequences )

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223

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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224

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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225 def _createBatch2_one_sequence(inFileName):

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226 f = open(inFileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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227 f.write(">seq 4\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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228 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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229 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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230 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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231 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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232 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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233 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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234 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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235

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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236 _createBatch2_one_sequence = staticmethod ( _createBatch2_one_sequence )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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237

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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238

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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239 def _createFastaFile_ten_sequences(fileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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240 f = open(fileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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241 f.write(">seq 1\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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parents:

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242 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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243 f.write(">seq 2\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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244 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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245 f.write(">seq 3\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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parents:

diff changeset

246 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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diff changeset

247 f.write(">seq 4\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

248 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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249 f.write(">seq 5\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

250 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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251 f.write(">seq 6\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

252 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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253 f.write(">seq 7\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

254 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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diff changeset

255 f.write(">seq 8\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

256 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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diff changeset

257 f.write(">seq 9\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

258 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

259 f.write(">seq 10\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

260 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

261 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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diff changeset

262

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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263 _createFastaFile_ten_sequences = staticmethod ( _createFastaFile_ten_sequences )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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diff changeset

264

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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265

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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266 def _createBatch_one_small_sequence(fileName, seqName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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267 f = open(fileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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268 f.write(">" +seqName + "\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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269 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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diff changeset

270 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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271

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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272 _createBatch_one_small_sequence = staticmethod ( _createBatch_one_small_sequence )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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diff changeset

273

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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274

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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275 # ------------------ for dbChunks ------------------- #

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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276

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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277 def _createFastaFile_big_sequence(fileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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278 f = open(fileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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279 f.write(">sequence\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

280 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

281 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

282 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

283 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

284 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

285 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

286 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

287 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

288 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

289 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

290 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

291 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

292 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

293 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

294 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

295 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

296 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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diff changeset

297 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

298 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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diff changeset

299 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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diff changeset

300 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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diff changeset

301

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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302 _createFastaFile_big_sequence = staticmethod ( _createFastaFile_big_sequence )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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diff changeset

303

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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diff changeset

304

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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diff changeset

305 def _createFastaFile_of_Chunks(fileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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306 f = open(fileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

307 f.write('>chunk01\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

308 f.write('ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

309 f.write('>chunk02\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

310 f.write('GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

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diff changeset

311 f.write('>chunk03\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

312 f.write('GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

313 f.write('>chunk04\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

314 f.write('ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

315 f.write('>chunk05\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

316 f.write('CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

317 f.write('>chunk06\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

318 f.write('ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

319 f.write('>chunk07\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

320 f.write('ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

321 f.write('>chunk08\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

322 f.write('GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

323 f.write('>chunk09\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

324 f.write('GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

325 f.write('>chunk10\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

326 f.write('ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

327 f.write('>chunk11\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

328 f.write('CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

329 f.write('>chunk12\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

330 f.write('ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

331 f.write('>chunk13\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

332 f.write('ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

333 f.write('>chunk14\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

334 f.write('GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

335 f.write('>chunk15\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

336 f.write('GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

337 f.write('>chunk16\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

338 f.write('ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

339 f.write('>chunk17\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

340 f.write('CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

341 f.write('>chunk18\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

342 f.write('ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

343 f.write('>chunk19\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

344 f.write('ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

345 f.write('>chunk20\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

346 f.write('GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

347 f.write('>chunk21\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

348 f.write('GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

349 f.write('>chunk22\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

350 f.write('ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

351 f.write('>chunk23\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

352 f.write('CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCG\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

353 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

354

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

355 _createFastaFile_of_Chunks = staticmethod ( _createFastaFile_of_Chunks )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

356

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

357

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

358 def _createMapFile_of_Chunks(fileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

359 f = open(fileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

360 f.write("chunk01\tsequence\t1\t60\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

361 f.write("chunk02\tsequence\t51\t110\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

362 f.write("chunk03\tsequence\t101\t160\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

363 f.write("chunk04\tsequence\t151\t210\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

364 f.write("chunk05\tsequence\t201\t260\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

365 f.write("chunk06\tsequence\t251\t310\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

366 f.write("chunk07\tsequence\t301\t360\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

367 f.write("chunk08\tsequence\t351\t410\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

368 f.write("chunk09\tsequence\t401\t460\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

369 f.write("chunk10\tsequence\t451\t510\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

370 f.write("chunk11\tsequence\t501\t560\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

371 f.write("chunk12\tsequence\t551\t610\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

372 f.write("chunk13\tsequence\t601\t660\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

373 f.write("chunk14\tsequence\t651\t710\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

374 f.write("chunk15\tsequence\t701\t760\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

375 f.write("chunk16\tsequence\t751\t810\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

376 f.write("chunk17\tsequence\t801\t860\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

377 f.write("chunk18\tsequence\t851\t910\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

378 f.write("chunk19\tsequence\t901\t960\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

379 f.write("chunk20\tsequence\t951\t1010\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

380 f.write("chunk21\tsequence\t1001\t1060\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

381 f.write("chunk22\tsequence\t1051\t1110\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

382 f.write("chunk23\tsequence\t1101\t1147\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

383 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

384

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

385 _createMapFile_of_Chunks = staticmethod ( _createMapFile_of_Chunks )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

386

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

387

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

388 def _createFastaFile_of_cut(fileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

389 f = open(fileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

390 f.write(">1 sequence {Cut} 1..60\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

391 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

392 f.write(">2 sequence {Cut} 51..110\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

393 f.write("GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

394 f.write(">3 sequence {Cut} 101..160\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

395 f.write("GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

396 f.write(">4 sequence {Cut} 151..210\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

397 f.write("ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

398 f.write(">5 sequence {Cut} 201..260\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

399 f.write("CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

400 f.write(">6 sequence {Cut} 251..310\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

401 f.write("ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

402 f.write(">7 sequence {Cut} 301..360\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

403 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

404 f.write(">8 sequence {Cut} 351..410\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

405 f.write("GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

406 f.write(">9 sequence {Cut} 401..460\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

407 f.write("GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

408 f.write(">10 sequence {Cut} 451..510\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

409 f.write("ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

410 f.write(">11 sequence {Cut} 501..560\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

411 f.write("CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

412 f.write(">12 sequence {Cut} 551..610\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

413 f.write("ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

414 f.write(">13 sequence {Cut} 601..660\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

415 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

416 f.write(">14 sequence {Cut} 651..710\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

417 f.write("GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

418 f.write(">15 sequence {Cut} 701..760\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

419 f.write("GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

420 f.write(">16 sequence {Cut} 751..810\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

421 f.write("ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

422 f.write(">17 sequence {Cut} 801..860\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

423 f.write("CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

424 f.write(">18 sequence {Cut} 851..910\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

425 f.write("ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

426 f.write(">19 sequence {Cut} 901..960\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

427 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

428 f.write(">20 sequence {Cut} 951..1010\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

429 f.write("GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

430 f.write(">21 sequence {Cut} 1001..1060\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

431 f.write("GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

432 f.write(">22 sequence {Cut} 1051..1110\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

433 f.write("ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

434 f.write(">23 sequence {Cut} 1101..1147\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

435 f.write("CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

436 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

437

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

438 _createFastaFile_of_cut = staticmethod ( _createFastaFile_of_cut )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

439

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

440

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

441 def _createFastaFile_of_Nstretch(fileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

442 f = open(fileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

443 f.write("")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

444 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

445

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

446 _createFastaFile_of_Nstretch = staticmethod ( _createFastaFile_of_Nstretch )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

447

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

448

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

449 # ------------------ for splitSeqPerCluster ------------------- #

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

450

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

451 def _createFastaFile_of_four_sequences_with_specific_header(inFileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

452 f = open(inFileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

453 f.write(">ReconCluster1Mb155 chunk183 {Fragment} 1..5506\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

454 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

455 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

456 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

457 f.write(">MbQ3Gr2Cl0 chunk440 {Fragment} 2678..3645\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

458 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

459 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

460 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

461 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

462 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

463 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

464 f.write(">MbS2Gr2Cl0 chunk622 {Fragment} 104..1078\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

465 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

466 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

467 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

468 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

469 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

470 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

471 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

472 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

473 f.write(">PilerCluster3.574Mb796 chunk0117 {Fragment} 51582..50819\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

474 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

475 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

476 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

477 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

478 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

479 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

480 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

481

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

482 _createFastaFile_of_four_sequences_with_specific_header = staticmethod ( _createFastaFile_of_four_sequences_with_specific_header )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

483

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

484

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

485 def _createFastaFile_of_four_sequences_with_specific_header_shuffle(inFileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

486 f = open(inFileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

487 f.write(">MbQ3Gr2Cl0 chunk440 {Fragment} 2678..3645\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

488 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

489 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

490 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

491 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

492 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

493 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

494 f.write(">ReconCluster1Mb155 chunk183 {Fragment} 1..5506\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

495 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

496 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

497 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

498 f.write(">MbS2Gr2Cl0 chunk622 {Fragment} 104..1078\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

499 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

500 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

501 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

502 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

503 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

504 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

505 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

506 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

507 f.write(">PilerCluster3.574Mb796 chunk0117 {Fragment} 51582..50819\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

508 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

509 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

510 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

511 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

512 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

513 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

514 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

515

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

516 _createFastaFile_of_four_sequences_with_specific_header_shuffle = staticmethod ( _createFastaFile_of_four_sequences_with_specific_header_shuffle )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

517

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

518

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

519 def _createFastaFile_of_four_sequences_with_specific_header_in_same_cluster(inFileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

520 f = open(inFileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

521 f.write(">ReconCluster1Mb155 chunk1 {Fragment} 1..5506\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

522 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

523 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

524 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

525 f.write(">ReconCluster1Mb155 chunk2 {Fragment} 1..5506\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

526 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

527 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

528 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

529 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

530 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

531 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

532 f.write(">ReconCluster1Mb155 chunk3 {Fragment} 1..5506\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

533 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

534 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

535 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

536 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

537 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

538 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

539 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

540 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

541 f.write(">ReconCluster1Mb155 chunk4 {Fragment} 1..5506\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

542 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

543 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

544 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

545 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

546 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

547 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

548 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

549

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

550 _createFastaFile_of_four_sequences_with_specific_header_in_same_cluster = staticmethod ( _createFastaFile_of_four_sequences_with_specific_header_in_same_cluster )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

551

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

552

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

553 def _createFastaFile_of_first_cluster_result(inFileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

554 f = open(inFileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

555 f.write(">ReconCluster1Mb155 chunk183 {Fragment} 1..5506\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

556 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

557 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

558 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

559 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

560

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

561 _createFastaFile_of_first_cluster_result = staticmethod ( _createFastaFile_of_first_cluster_result )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

562

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

563

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

564 def _createFastaFile_of_second_cluster_result(inFileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

565 f = open(inFileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

566 f.write(">MbQ3Gr2Cl0 chunk440 {Fragment} 2678..3645\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

567 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

568 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

569 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

570 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

571 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

572 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

573 f.write(">MbS2Gr2Cl0 chunk622 {Fragment} 104..1078\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

574 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

575 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

576 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

577 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

578 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

579 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

580 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

581 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

582 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

583

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

584 _createFastaFile_of_second_cluster_result = staticmethod ( _createFastaFile_of_second_cluster_result )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

585

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

586

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

587 def _createFastaFile_of_third_cluster_result(inFileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

588 f = open(inFileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

589 f.write(">PilerCluster3.574Mb796 chunk0117 {Fragment} 51582..50819\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

590 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

591 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

592 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

593 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

594 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

595 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

596 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

597

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

598 _createFastaFile_of_third_cluster_result = staticmethod ( _createFastaFile_of_third_cluster_result )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

599

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

600

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

601 def _createFastaFile_of_first_cluster_result_with_simplify_header(inFileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

602 f = open(inFileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

603 f.write(">Piler_Cluster1_Seq155\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

604 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

605 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

606 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

607 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

608

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

609 _createFastaFile_of_first_cluster_result_with_simplify_header = staticmethod ( _createFastaFile_of_first_cluster_result_with_simplify_header )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

610

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

611

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

612 def _createFastaFile_of_second_cluster_result_with_simplify_header(inFileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

613 f = open(inFileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

614 f.write(">Piler_Cluster2_Seq3\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

615 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

616 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

617 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

618 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

619 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

620 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

621 f.write(">Piler_Cluster2_Seq2\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

622 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

623 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

624 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

625 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

626 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

627 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

628 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

629 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

630 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

631

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

632 _createFastaFile_of_second_cluster_result_with_simplify_header = staticmethod ( _createFastaFile_of_second_cluster_result_with_simplify_header )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

633

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

634

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

635 def _createFastaFile_of_third_cluster_result_with_simplify_header(inFileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

636 f = open(inFileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

637 f.write(">Piler_Cluster3.574_Seq796\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

638 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

639 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

640 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

641 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

642 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

643 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

644 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

645

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

646 _createFastaFile_of_third_cluster_result_with_simplify_header = staticmethod ( _createFastaFile_of_third_cluster_result_with_simplify_header )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

647

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

648 # ---------------------------------- #

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

649

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

650 def _createPatternFile(fileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

651 f = open(fileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

652 f.write('seq 3\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

653 f.write('f\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

654 f.write('s.q 1\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

655 f.write('q 8\n')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

656

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

657 _createPatternFile = staticmethod ( _createPatternFile )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

658

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

659

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

660 def _createResult_of_dbLengthFilter_sup(inFileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

661 f = open(inFileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

662 f.write(">seq 2\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

663 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

664 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

665 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

666 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

667 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

668 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

669 f.write(">seq 3\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

670 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

671 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

672 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

673 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

674 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

675 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

676 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

677 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

678 f.write(">seq 4\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

679 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

680 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

681 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

682 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

683 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

684 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

685 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

686

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

687 _createResult_of_dbLengthFilter_sup = staticmethod ( _createResult_of_dbLengthFilter_sup )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

688

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

689

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

690 def _createFastaFile_four_sequences_for_header_filtering(fileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

691 f = open(fileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

692 f.write(">seq1_HostGene\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

693 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

694 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

695 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

696 f.write(">seq2_SSR\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

697 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

698 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

699 f.write(">seq3_Map2_NoCat\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

700 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

701 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

702 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

703 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

704 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

705 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

706 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

707 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

708 f.write(">seq4_confused\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

709 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

710 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

711 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

712 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

713 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

714 f.write("ATATTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

715 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

716

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

717 _createFastaFile_four_sequences_for_header_filtering = staticmethod ( _createFastaFile_four_sequences_for_header_filtering )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

718

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

719

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

720 def _createFastaFile_three_sequences_with_ORFs(fileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

721 f = open(fileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

722 f.write(">Mivi_sl_Blaster_Grouper_1_Map_3\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

723 f.write("TACAGTCAAACCTGAGAAAATTTATATCGCCCAATCTTATACCTGGCAAAATTTATGGAC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

724 f.write("TTTTCAATCTCCCGACTTTTTTGGCTGACAGAACCTGTCCAATCTTATACCTTATAATTT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

725 f.write("ATGGGTTTACAGGTCAAATTATAAGATAAGAGAGAGCCGGAAATGAGCGATTGATCAGGA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

726 f.write("ATTGGCCTCTCCTTCGGCGTTCTTGTTGACGAGCCGCCTGCTGGAACAGTCCGAAATGCC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

727 f.write("CCGAAACAGCCGAGAAGCGAGCACAGTAGAGCAAAGGCGGCGGTTGACACGTTGACAGGC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

728 f.write("TATTAGTCGCGACGTGCTTCTCTCTCCTCTTCCGCCGACAACGACGCCGAAATGAACATC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

729 f.write("TTCACAATTCGAGAAGCCCTCATCAGAAATTCCTCTTCATATCATCATGGTCTCATTCCC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

730 f.write("TTCCCGGAATTCAACTGCTGGCGCCACGCTCAAATCTTGTCTGATCGCAAGAACAAAGGA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

731 f.write("TCGACCGACCATACACCTCTTCCCAACGGTCGCGGGCCTCTCGATGGCGATCGCGGCATC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

732 f.write("ATCAACGCGATGAACGCTCTGAAGACGGCGAACGATGAGCTGGTCGAAAAGGGGATAGTT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

733 f.write("ACGAGCAACGAGAAGATGAGTATCCACTTTCTCGTCGATGTGGAGGAGGAGAACCTTGCT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

734 f.write("GGTGGGGCTGAAATGACCGATCAGGAGATTGTGGACCTGGTCATTGCCGAAGAGTTGGAG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

735 f.write("GAGAATTGCGAGGGAGAAGGAGGAGAGGAGGAAGCGGAGATAGAGCTCCGACCGGCGGAG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

736 f.write("CGAACGACGCTGAAGGAGGCAATCTCAGCGCTTGATGTTTTCCTTAGGTTTGCTATGAAT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

737 f.write("GGGTACTCAGGTCCAACGGATTTGATTTCTTTTGAGGACGAGGCTAGGAGGATTCGCAGG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

738 f.write("ACTCTTGTTGCCGAGCAGGATGCCGCGAGGATTCAGACGACAATGACTTCGTATTTCCAG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

739 f.write("CGTCAGTAG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

740 f.write(">Mivi_sl_Blaster_Grouper_2_Map_3\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

741 f.write("TACAGTCAGACCTGAGAAAATTTATATCGCCCAATCTTATACCTGTCAAAATTTATGGAC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

742 f.write("TTTTCAATCTCCCGACTTTTTTGGCTGACAGAACCTGTCCAATCTTATACCTTATAATTT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

743 f.write("ATGGGTTTACAGGTCAAATTATAAGATAAGAGAGAGCCGGAAATGAGCGATTGATCAGGA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

744 f.write("ATTGGCCTCTCCTTCGGCGTTCTTGTTGACGAGCCGCCTGCTGGAAGAGTCCGAAATGCC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

745 f.write("CCGAAACAGCCAAGAAGCGAGCACAGTAGAGCAAAGGCGGCGGTTGACACGTTGACAGGC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

746 f.write("TAGTCGCGACGTGCTTCTCTCTCCTCTTCCGCCGACAACGACGCCGAAATGAACATCTTC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

747 f.write("ACAATCCGAGAAGCCCTCATCAGAAATTCCTCTTCATATCATCATGGTCTCATTCCCTTC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

748 f.write("CCGGAATTCAACTGCTGGCGCCACGCTCAAATCTTGTCTGATCGCAAGAACAAAGGATCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

749 f.write("ACCGACCATACACCTCTTCCCAACGGTCGCGGGCCTCTCGATGGCGATCGCGGCATCATC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

750 f.write("AACGCGATGAACGCTCTGAAGACGGCGAACGATGAGCTGGTCGAAAAGGGGATAGTTACG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

751 f.write("AGCAACGAGAAGATGAGTATCCACTTTCTCGTCGATGTGGAGGAGGAGAACCTTGCTGGT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

752 f.write("GGGGCTGAAATGACCGATCAGGAGATTGTGGACCTGGGGTCATTGCCGAAGAGTTGGAGG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

753 f.write("AGAATTGCGAGGGAGAACTTGAAGGAGGAGAGGAGGAAGCGGAGATAGAGCTCCGACCGG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

754 f.write("CGGAGCGAACGACGCTGAAGGAGGCAATCTCAGCGCTTGGTGTTTTCCTTAGGTTTGCTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

755 f.write("TGAATGGGTACTCAGGTCCAACGAATTTGATTTCTTTTGAGGACGAGGCTAGGAGGATTC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

756 f.write("GCAGGACTCTTGTTGCCGAGCAGGATGCCGCGAGGATTCAGACGACAATGACTTCGTATT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

757 f.write("TCCAGCGTCAGTAGGTCAAGATATTTTTTCTTGGAGCTTTCATAACTTGTTAGATGTCAT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

758 f.write("CATGCCTCAGTAGAGGCCGTACATTGGCTGCAATTCAGTAATTCGGGCCTTCTGAATTTC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

759 f.write("CTCCCCCTCAAAAGTCAATGTATCGACTCAAACGATGCACGAAAATTCTTGATTTGATGT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

760 f.write("AGGAAGCTCAAAAACGGAGTTTCAGGTCATAATGTAGTGATCTGAAGCCGAACTCTCCAA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

761 f.write("GCTTATACCTGTCTTAATTTATGGGAAAATCCGTCCACCGAAAATATAAATTTTCTCAGG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

762 f.write("TCTGACTGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

763 f.write(">Mivi_sl_Blaster_Grouper_3_Map_3\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

764 f.write("CAACACAAAGATAAGGCACCTTCATCCAGTGGCTCGCACGAACTTTCAATTGCAAGTCGT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

765 f.write("TGGCGTGCGCTGGGCGGGATCAAAACCGGGTCTGGGAGTCGCGTAACCCACTGGAGCAAG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

766 f.write("TAGGTGGTAGCCTGGACTGACAACGTGGACGTCAGCGACTTGAAATAGGTATTCGCGGCT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

767 f.write("TTCGTGGTCGGTGTACCCCTGTGTGTCCGGCATCGGCTGTCCAGAGTCGCCAGCCTGCCC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

768 f.write("GGTGCGAATGTGGGGGGCAGTCTCGGTCGCGCACGTGCGATGTCCCTCTCCCCACACGGG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

769 f.write("CCTGTCGGCTGCGGCTAACGGCCCCTGCAATGAGTCCTATCGACAGAAGTCCACCCAAGC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

770 f.write("TCAGCCTTCCCTCCACCAACACCAACATCGCAAGCCTCTCAAAAATTCACATCTCTTACA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

771 f.write("TCCCCTCGAAACACCCACTAAATGGATCCCTACCCTATCACTTGGCGGCAGTACTAGTAG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

772 f.write("CACGGGCCCAACTTCGACGGATCTCGAACGGACTTCCCACGGGTTCTCGGTGTGCAAGCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

773 f.write("TCTCAGGTCAAGGTTTTGGTTGGTGGGCTTTCTGGGTGTGCAAAGGGGATTATTATAGAG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

774 f.write("GGAAGAAGAAGAAGGATGGGACCAGGGAGGCAGAGACGTGCGGGGTCAGGTTGATGGGGG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

775 f.write("AAGGTCGTGGAAGCGAAGAACGAGAGGCGAGCTTGTCGTTTGAGGAGAAAGGGGCCTCGC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

776 f.write("TGCCTGCAGAGAAAGGCGGTAAGTTGACCGGCGCAAAGTTATCATGAGACCGTAGCTCAG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

777 f.write("TATCGTTTCCTGTCGAGGGCATGGGTTACAGTCCGTCGAACTATGCGCGAGATCATCTGG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

778 f.write("TAGTAAAGAATCCCGCCGCCACTGACCAGATCTCCTGTGTCCTCTCAGCTCTCACAAAAC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

779 f.write("CTAGAAAAGCTTCGCATGGAGCCAAACGAATACTCCAATCCGACATTGAGCAAGACCCTT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

780 f.write("CCCTCTCGCCTCATAGGAACGAAACGGCCCATCTTCGAAGGGACAACTCTCTGTCGGCCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

781 f.write("AGGAGATGACTTTTCTGACCGAGCGTAAGAGGAGATCGCACAGAGTCAGGGGTTGGTCGA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

782 f.write("GCTTTTGGGATTGGAGGAAGGGGGAGAGATTGATGAACGAGACGTCCCAATAGTGAGTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

783 f.write("CTCCGCACTGGAGCAATGATGGCAAACCGTGGAGTTGAAGAGTCTTGAACGCTATCAGAT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

784 f.write("CGGGCTAGGAGGGTCGGGAGGCGGTTGAATGCGTGCCAACCTTGGCTTCCTGTCAACGAT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

785 f.write("CCTCGCCTTTCAAGAGCTCGATCTATGGCAGTTGTTGACCTACACAGCGGGGGTATCCGG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

786 f.write("GTCCTGTTGGGCTCTGGCGAGTTTATATACGCTACCGATCGCACGTCCGCTCACACCATC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

787 f.write("CATCACTCAACGCCGCTGCGGTGATTGAGCACTTTATGTCCGTCTCAGGGGATCACCGTC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

788 f.write("TGAGTACAAAATCGGTCAACCGAGTCAGGGAGGCACACGGAGGGTACCAATCGCTTTTCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

789 f.write("GACCTTTGATTTCAAAGTCTAAGAACAGTCAAAAGATCTGTAGTGAGTACAGACCACTGA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

790 f.write("CCCTCACTTGAGTAGATATTGACACTGACGAAGATCGCTACACTGCGGGCCTTGACAGTG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

791 f.write("ATTGATCTGTACTCGACACTGGTCTCATCGTACTTCTGGATGATGCCCAGAAAAGATGGG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

792 f.write("AAGGATCAGGTTGATCCGTATGTACCCCTGCGTCGGCTCGTGAGGTCCAGAGAGGGTCAT\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

793 f.write("TCCACTGACTGTCCCGAACCCCCCCTGGCTGATCGTCAGCGCCTCGATGAAATGGTCGCG\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

794 f.write("CGCGTACGATAATGCGGGCCTGGCTCACGGATGCGCGCCTTTCCCTATCGTCAGTCACGC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

795 f.write("AAATGTAGGCTTCCATCTGGAACGCTGCTTGATGGCCTAAGAATGGGCCGTCACGGAACA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

796 f.write("GCTCACCGCCTGCAGACACGAACGGCCGTGGCGGTCATGGAAGGATCTGAACGTGTCGCC\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

797 f.write("CCATACGATTGACGAAGAGATGTAAGCTCCCTTGGTA\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

798 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

799

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

800 _createFastaFile_three_sequences_with_ORFs = staticmethod ( _createFastaFile_three_sequences_with_ORFs )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

801

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

802

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

803 def _createFastaFile_three_sequences_with_ORFs_expected(fileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

804 f = open(fileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

805 f.write("ORF|1|662\tMivi_sl_Blaster_Grouper_1_Map_3\t307\t969\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

806 f.write("ORF|-3|254\tMivi_sl_Blaster_Grouper_1_Map_3\t793\t539\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

807 f.write("ORF|2|197\tMivi_sl_Blaster_Grouper_1_Map_3\t356\t553\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

808 f.write("ORF|3|176\tMivi_sl_Blaster_Grouper_1_Map_3\t288\t464\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

809 f.write("ORF|-1|176\tMivi_sl_Blaster_Grouper_1_Map_3\t786\t610\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

810 f.write("ORF|3|143\tMivi_sl_Blaster_Grouper_1_Map_3\t672\t815\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

811 f.write("ORF|1|131\tMivi_sl_Blaster_Grouper_1_Map_3\t175\t306\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

812 f.write("ORF|-2|131\tMivi_sl_Blaster_Grouper_1_Map_3\t797\t666\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

813 f.write("ORF|2|128\tMivi_sl_Blaster_Grouper_1_Map_3\t167\t295\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

814 f.write("ORF|-2|119\tMivi_sl_Blaster_Grouper_1_Map_3\t242\t123\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

815 f.write("ORF|1|464\tMivi_sl_Blaster_Grouper_2_Map_3\t304\t768\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

816 f.write("ORF|3|305\tMivi_sl_Blaster_Grouper_2_Map_3\t669\t974\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

817 f.write("ORF|-3|251\tMivi_sl_Blaster_Grouper_2_Map_3\t1094\t843\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

818 f.write("ORF|-2|245\tMivi_sl_Blaster_Grouper_2_Map_3\t531\t286\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

819 f.write("ORF|-3|224\tMivi_sl_Blaster_Grouper_2_Map_3\t791\t567\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

820 f.write("ORF|-2|215\tMivi_sl_Blaster_Grouper_2_Map_3\t1098\t883\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

821 f.write("ORF|2|197\tMivi_sl_Blaster_Grouper_2_Map_3\t353\t550\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

822 f.write("ORF|3|173\tMivi_sl_Blaster_Grouper_2_Map_3\t288\t461\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

823 f.write("ORF|-1|173\tMivi_sl_Blaster_Grouper_2_Map_3\t1087\t914\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

824 f.write("ORF|-1|143\tMivi_sl_Blaster_Grouper_2_Map_3\t310\t167\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

825 f.write("ORF|3|626\tMivi_sl_Blaster_Grouper_3_Map_3\t141\t767\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

826 f.write("ORF|2|434\tMivi_sl_Blaster_Grouper_3_Map_3\t164\t598\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

827 f.write("ORF|3|365\tMivi_sl_Blaster_Grouper_3_Map_3\t768\t1133\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

828 f.write("ORF|-3|359\tMivi_sl_Blaster_Grouper_3_Map_3\t1514\t1155\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

829 f.write("ORF|-1|320\tMivi_sl_Blaster_Grouper_3_Map_3\t1879\t1559\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

830 f.write("ORF|3|272\tMivi_sl_Blaster_Grouper_3_Map_3\t1299\t1571\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

831 f.write("ORF|-2|248\tMivi_sl_Blaster_Grouper_3_Map_3\t1503\t1255\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

832 f.write("ORF|1|236\tMivi_sl_Blaster_Grouper_3_Map_3\t1576\t1812\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

833 f.write("ORF|-1|227\tMivi_sl_Blaster_Grouper_3_Map_3\t1423\t1196\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

834 f.write("ORF|-3|227\tMivi_sl_Blaster_Grouper_3_Map_3\t368\t141\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

835 f.close()

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

836

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

837 _createFastaFile_three_sequences_with_ORFs_expected = staticmethod ( _createFastaFile_three_sequences_with_ORFs_expected )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

838

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

839

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

840 def _createLinkFile_four_sequences_with_new_headers(fileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

841 f = open(fileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

842 f.write("seq 1\tReconCluster1Mb155 chunk183 {Fragment} 1..5506\t1\t127\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

843 f.write("seq 2\tMbQ3Gr2Cl0 chunk440 {Fragment} 2678..3645\t1\t307\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

844 f.write("seq 3\tMbS2Gr2Cl0 chunk622 {Fragment} 104..1078\t1\t427\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

845 f.write("seq 4\tPilerCluster3.574Mb796 chunk0117 {Fragment} 51582..50819\t1\t307\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

846

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

847 _createLinkFile_four_sequences_with_new_headers = staticmethod ( _createLinkFile_four_sequences_with_new_headers )

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

848

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

849

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

850 def _createLinkFile_four_sequences_same_headers(fileName):

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

851 f = open(fileName, 'w')

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

852 f.write("seq 1\tseq 1\t1\t127\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

853 f.write("seq 2\tseq 2\t1\t307\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

854 f.write("seq 3\tseq 3\t1\t427\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

855 f.write("seq 4\tseq 4\t1\t307\n")

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

856

e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

yufei-luo

parents:

diff changeset

857 _createLinkFile_four_sequences_same_headers = staticmethod ( _createLinkFile_four_sequences_same_headers )

Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/seq/test/Utils_for_T_FastaUtils.py @ 0:e0f8dcca02ed