Mercurial > repos > yufei-luo > s_mart
diff commons/core/seq/test/Utils_for_T_FastaUtils.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/core/seq/test/Utils_for_T_FastaUtils.py Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,857 @@ +# Copyright INRA (Institut National de la Recherche Agronomique) +# http://www.inra.fr +# http://urgi.versailles.inra.fr +# +# This software is governed by the CeCILL license under French law and +# abiding by the rules of distribution of free software. You can use, +# modify and/ or redistribute the software under the terms of the CeCILL +# license as circulated by CEA, CNRS and INRIA at the following URL +# "http://www.cecill.info". +# +# As a counterpart to the access to the source code and rights to copy, +# modify and redistribute granted by the license, users are provided only +# with a limited warranty and the software's author, the holder of the +# economic rights, and the successive licensors have only limited +# liability. +# +# In this respect, the user's attention is drawn to the risks associated +# with loading, using, modifying and/or developing or reproducing the +# software by the user in light of its specific status of free software, +# that may mean that it is complicated to manipulate, and that also +# therefore means that it is reserved for developers and experienced +# professionals having in-depth computer knowledge. Users are therefore +# encouraged to load and test the software's suitability as regards their +# requirements in conditions enabling the security of their systems and/or +# data to be ensured and, more generally, to use and operate it in the +# same conditions as regards security. +# +# The fact that you are presently reading this means that you have had +# knowledge of the CeCILL license and that you accept its terms. + + +class Utils_for_T_FastaUtils( object ): + + def _createFastaFile_for_empty_file(fileName): + f = open(fileName, 'w') + f.write("") + f.close() + + _createFastaFile_for_empty_file = staticmethod ( _createFastaFile_for_empty_file ) + + + def _createFastaFile_one_sequence(fileName): + f = open(fileName, 'w') + f.write(">seq 1\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createFastaFile_one_sequence = staticmethod ( _createFastaFile_one_sequence ) + + + def createFastaFile_twoSequences( fileName ): + f = open( fileName, "w" ) + f.write( ">seq 1\n" ) + f.write( "ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n" ) + f.write( "ATATTCG\n" ) + f.write( ">seq 2\n" ) + f.write( "ATATTCTTTCATCGATCGATCGGCGGCTATATGCTAGTGACGAAGCTAGTGTGAGTAGTA\n" ) + f.write( "ATATTCG\n" ) + f.close() + + createFastaFile_twoSequences = staticmethod ( createFastaFile_twoSequences ) + + + def createFastaFile_seq_1( fileName ): + f = open( fileName, "w" ) + f.write( ">seq 1\n" ) + f.write( "ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n" ) + f.write( "ATATTCG\n" ) + f.close() + + createFastaFile_seq_1 = staticmethod( createFastaFile_seq_1 ) + + + def createFastaFile_seq_2( fileName ): + f = open( fileName, "w" ) + f.write( ">seq 2\n" ) + f.write( "ATATTCTTTCATCGATCGATCGGCGGCTATATGCTAGTGACGAAGCTAGTGTGAGTAGTA\n" ) + f.write( "ATATTCG\n" ) + f.close() + + createFastaFile_seq_2 = staticmethod( createFastaFile_seq_2 ) + + + def _createFastaFile_sequence_without_header(fileName): + f = open(fileName, 'w') + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createFastaFile_sequence_without_header = staticmethod ( _createFastaFile_sequence_without_header ) + + + def _createFastaFile_four_sequences(fileName): + f = open(fileName, 'w') + f.write(">seq 1\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">seq 2\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">seq 3\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">seq 4\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createFastaFile_four_sequences = staticmethod ( _createFastaFile_four_sequences ) + + + def _createFastaFile_three_sequences(fileName): + f = open(fileName, 'w') + f.write(">seq 1\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">seq 2\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">seq 4\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createFastaFile_three_sequences = staticmethod ( _createFastaFile_three_sequences ) + + +# ------------------ for dbSplit ---------------- # + + def _createBatch1_two_sequences(inFileName): + f = open(inFileName, 'w') + f.write(">seq 1\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">seq 2\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createBatch1_two_sequences = staticmethod ( _createBatch1_two_sequences ) + + + def _createBatch2_two_sequences(inFileName): + f = open(inFileName, 'w') + f.write(">seq 3\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">seq 4\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createBatch2_two_sequences = staticmethod ( _createBatch2_two_sequences ) + + + def _createBatch1_three_sequences(inFileName): + f = open(inFileName, 'w') + f.write(">seq 1\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">seq 2\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">seq 3\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createBatch1_three_sequences = staticmethod ( _createBatch1_three_sequences ) + + + def _createBatch2_one_sequence(inFileName): + f = open(inFileName, 'w') + f.write(">seq 4\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createBatch2_one_sequence = staticmethod ( _createBatch2_one_sequence ) + + + def _createFastaFile_ten_sequences(fileName): + f = open(fileName, 'w') + f.write(">seq 1\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write(">seq 2\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write(">seq 3\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write(">seq 4\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write(">seq 5\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write(">seq 6\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write(">seq 7\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write(">seq 8\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write(">seq 9\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write(">seq 10\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.close() + + _createFastaFile_ten_sequences = staticmethod ( _createFastaFile_ten_sequences ) + + + def _createBatch_one_small_sequence(fileName, seqName): + f = open(fileName, 'w') + f.write(">" +seqName + "\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.close() + + _createBatch_one_small_sequence = staticmethod ( _createBatch_one_small_sequence ) + + +# ------------------ for dbChunks ------------------- # + + def _createFastaFile_big_sequence(fileName): + f = open(fileName, 'w') + f.write(">sequence\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createFastaFile_big_sequence = staticmethod ( _createFastaFile_big_sequence ) + + + def _createFastaFile_of_Chunks(fileName): + f = open(fileName, 'w') + f.write('>chunk01\n') + f.write('ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n') + f.write('>chunk02\n') + f.write('GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n') + f.write('>chunk03\n') + f.write('GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n') + f.write('>chunk04\n') + f.write('ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n') + f.write('>chunk05\n') + f.write('CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n') + f.write('>chunk06\n') + f.write('ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n') + f.write('>chunk07\n') + f.write('ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n') + f.write('>chunk08\n') + f.write('GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n') + f.write('>chunk09\n') + f.write('GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n') + f.write('>chunk10\n') + f.write('ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n') + f.write('>chunk11\n') + f.write('CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n') + f.write('>chunk12\n') + f.write('ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n') + f.write('>chunk13\n') + f.write('ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n') + f.write('>chunk14\n') + f.write('GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n') + f.write('>chunk15\n') + f.write('GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n') + f.write('>chunk16\n') + f.write('ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n') + f.write('>chunk17\n') + f.write('CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n') + f.write('>chunk18\n') + f.write('ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n') + f.write('>chunk19\n') + f.write('ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n') + f.write('>chunk20\n') + f.write('GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n') + f.write('>chunk21\n') + f.write('GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n') + f.write('>chunk22\n') + f.write('ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n') + f.write('>chunk23\n') + f.write('CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCG\n') + f.close() + + _createFastaFile_of_Chunks = staticmethod ( _createFastaFile_of_Chunks ) + + + def _createMapFile_of_Chunks(fileName): + f = open(fileName, 'w') + f.write("chunk01\tsequence\t1\t60\n") + f.write("chunk02\tsequence\t51\t110\n") + f.write("chunk03\tsequence\t101\t160\n") + f.write("chunk04\tsequence\t151\t210\n") + f.write("chunk05\tsequence\t201\t260\n") + f.write("chunk06\tsequence\t251\t310\n") + f.write("chunk07\tsequence\t301\t360\n") + f.write("chunk08\tsequence\t351\t410\n") + f.write("chunk09\tsequence\t401\t460\n") + f.write("chunk10\tsequence\t451\t510\n") + f.write("chunk11\tsequence\t501\t560\n") + f.write("chunk12\tsequence\t551\t610\n") + f.write("chunk13\tsequence\t601\t660\n") + f.write("chunk14\tsequence\t651\t710\n") + f.write("chunk15\tsequence\t701\t760\n") + f.write("chunk16\tsequence\t751\t810\n") + f.write("chunk17\tsequence\t801\t860\n") + f.write("chunk18\tsequence\t851\t910\n") + f.write("chunk19\tsequence\t901\t960\n") + f.write("chunk20\tsequence\t951\t1010\n") + f.write("chunk21\tsequence\t1001\t1060\n") + f.write("chunk22\tsequence\t1051\t1110\n") + f.write("chunk23\tsequence\t1101\t1147\n") + f.close() + + _createMapFile_of_Chunks = staticmethod ( _createMapFile_of_Chunks ) + + + def _createFastaFile_of_cut(fileName): + f = open(fileName, 'w') + f.write(">1 sequence {Cut} 1..60\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write(">2 sequence {Cut} 51..110\n") + f.write("GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n") + f.write(">3 sequence {Cut} 101..160\n") + f.write("GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n") + f.write(">4 sequence {Cut} 151..210\n") + f.write("ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n") + f.write(">5 sequence {Cut} 201..260\n") + f.write("CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n") + f.write(">6 sequence {Cut} 251..310\n") + f.write("ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n") + f.write(">7 sequence {Cut} 301..360\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write(">8 sequence {Cut} 351..410\n") + f.write("GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n") + f.write(">9 sequence {Cut} 401..460\n") + f.write("GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n") + f.write(">10 sequence {Cut} 451..510\n") + f.write("ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n") + f.write(">11 sequence {Cut} 501..560\n") + f.write("CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n") + f.write(">12 sequence {Cut} 551..610\n") + f.write("ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n") + f.write(">13 sequence {Cut} 601..660\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write(">14 sequence {Cut} 651..710\n") + f.write("GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n") + f.write(">15 sequence {Cut} 701..760\n") + f.write("GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n") + f.write(">16 sequence {Cut} 751..810\n") + f.write("ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n") + f.write(">17 sequence {Cut} 801..860\n") + f.write("CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n") + f.write(">18 sequence {Cut} 851..910\n") + f.write("ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n") + f.write(">19 sequence {Cut} 901..960\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write(">20 sequence {Cut} 951..1010\n") + f.write("GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n") + f.write(">21 sequence {Cut} 1001..1060\n") + f.write("GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n") + f.write(">22 sequence {Cut} 1051..1110\n") + f.write("ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n") + f.write(">23 sequence {Cut} 1101..1147\n") + f.write("CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCG\n") + f.close() + + _createFastaFile_of_cut = staticmethod ( _createFastaFile_of_cut ) + + + def _createFastaFile_of_Nstretch(fileName): + f = open(fileName, 'w') + f.write("") + f.close() + + _createFastaFile_of_Nstretch = staticmethod ( _createFastaFile_of_Nstretch ) + + +# ------------------ for splitSeqPerCluster ------------------- # + + def _createFastaFile_of_four_sequences_with_specific_header(inFileName): + f = open(inFileName, 'w') + f.write(">ReconCluster1Mb155 chunk183 {Fragment} 1..5506\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">MbQ3Gr2Cl0 chunk440 {Fragment} 2678..3645\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">MbS2Gr2Cl0 chunk622 {Fragment} 104..1078\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">PilerCluster3.574Mb796 chunk0117 {Fragment} 51582..50819\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createFastaFile_of_four_sequences_with_specific_header = staticmethod ( _createFastaFile_of_four_sequences_with_specific_header ) + + + def _createFastaFile_of_four_sequences_with_specific_header_shuffle(inFileName): + f = open(inFileName, 'w') + f.write(">MbQ3Gr2Cl0 chunk440 {Fragment} 2678..3645\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">ReconCluster1Mb155 chunk183 {Fragment} 1..5506\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">MbS2Gr2Cl0 chunk622 {Fragment} 104..1078\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">PilerCluster3.574Mb796 chunk0117 {Fragment} 51582..50819\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createFastaFile_of_four_sequences_with_specific_header_shuffle = staticmethod ( _createFastaFile_of_four_sequences_with_specific_header_shuffle ) + + + def _createFastaFile_of_four_sequences_with_specific_header_in_same_cluster(inFileName): + f = open(inFileName, 'w') + f.write(">ReconCluster1Mb155 chunk1 {Fragment} 1..5506\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">ReconCluster1Mb155 chunk2 {Fragment} 1..5506\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">ReconCluster1Mb155 chunk3 {Fragment} 1..5506\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">ReconCluster1Mb155 chunk4 {Fragment} 1..5506\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createFastaFile_of_four_sequences_with_specific_header_in_same_cluster = staticmethod ( _createFastaFile_of_four_sequences_with_specific_header_in_same_cluster ) + + + def _createFastaFile_of_first_cluster_result(inFileName): + f = open(inFileName, 'w') + f.write(">ReconCluster1Mb155 chunk183 {Fragment} 1..5506\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createFastaFile_of_first_cluster_result = staticmethod ( _createFastaFile_of_first_cluster_result ) + + + def _createFastaFile_of_second_cluster_result(inFileName): + f = open(inFileName, 'w') + f.write(">MbQ3Gr2Cl0 chunk440 {Fragment} 2678..3645\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">MbS2Gr2Cl0 chunk622 {Fragment} 104..1078\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createFastaFile_of_second_cluster_result = staticmethod ( _createFastaFile_of_second_cluster_result ) + + + def _createFastaFile_of_third_cluster_result(inFileName): + f = open(inFileName, 'w') + f.write(">PilerCluster3.574Mb796 chunk0117 {Fragment} 51582..50819\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createFastaFile_of_third_cluster_result = staticmethod ( _createFastaFile_of_third_cluster_result ) + + + def _createFastaFile_of_first_cluster_result_with_simplify_header(inFileName): + f = open(inFileName, 'w') + f.write(">Piler_Cluster1_Seq155\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createFastaFile_of_first_cluster_result_with_simplify_header = staticmethod ( _createFastaFile_of_first_cluster_result_with_simplify_header ) + + + def _createFastaFile_of_second_cluster_result_with_simplify_header(inFileName): + f = open(inFileName, 'w') + f.write(">Piler_Cluster2_Seq3\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">Piler_Cluster2_Seq2\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createFastaFile_of_second_cluster_result_with_simplify_header = staticmethod ( _createFastaFile_of_second_cluster_result_with_simplify_header ) + + + def _createFastaFile_of_third_cluster_result_with_simplify_header(inFileName): + f = open(inFileName, 'w') + f.write(">Piler_Cluster3.574_Seq796\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createFastaFile_of_third_cluster_result_with_simplify_header = staticmethod ( _createFastaFile_of_third_cluster_result_with_simplify_header ) + +# ---------------------------------- # + + def _createPatternFile(fileName): + f = open(fileName, 'w') + f.write('seq 3\n') + f.write('f\n') + f.write('s.q 1\n') + f.write('q 8\n') + + _createPatternFile = staticmethod ( _createPatternFile ) + + + def _createResult_of_dbLengthFilter_sup(inFileName): + f = open(inFileName, 'w') + f.write(">seq 2\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">seq 3\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">seq 4\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createResult_of_dbLengthFilter_sup = staticmethod ( _createResult_of_dbLengthFilter_sup ) + + + def _createFastaFile_four_sequences_for_header_filtering(fileName): + f = open(fileName, 'w') + f.write(">seq1_HostGene\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">seq2_SSR\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">seq3_Map2_NoCat\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.write(">seq4_confused\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n") + f.write("ATATTCG\n") + f.close() + + _createFastaFile_four_sequences_for_header_filtering = staticmethod ( _createFastaFile_four_sequences_for_header_filtering ) + + + def _createFastaFile_three_sequences_with_ORFs(fileName): + f = open(fileName, 'w') + f.write(">Mivi_sl_Blaster_Grouper_1_Map_3\n") + f.write("TACAGTCAAACCTGAGAAAATTTATATCGCCCAATCTTATACCTGGCAAAATTTATGGAC\n") + f.write("TTTTCAATCTCCCGACTTTTTTGGCTGACAGAACCTGTCCAATCTTATACCTTATAATTT\n") + f.write("ATGGGTTTACAGGTCAAATTATAAGATAAGAGAGAGCCGGAAATGAGCGATTGATCAGGA\n") + f.write("ATTGGCCTCTCCTTCGGCGTTCTTGTTGACGAGCCGCCTGCTGGAACAGTCCGAAATGCC\n") + f.write("CCGAAACAGCCGAGAAGCGAGCACAGTAGAGCAAAGGCGGCGGTTGACACGTTGACAGGC\n") + f.write("TATTAGTCGCGACGTGCTTCTCTCTCCTCTTCCGCCGACAACGACGCCGAAATGAACATC\n") + f.write("TTCACAATTCGAGAAGCCCTCATCAGAAATTCCTCTTCATATCATCATGGTCTCATTCCC\n") + f.write("TTCCCGGAATTCAACTGCTGGCGCCACGCTCAAATCTTGTCTGATCGCAAGAACAAAGGA\n") + f.write("TCGACCGACCATACACCTCTTCCCAACGGTCGCGGGCCTCTCGATGGCGATCGCGGCATC\n") + f.write("ATCAACGCGATGAACGCTCTGAAGACGGCGAACGATGAGCTGGTCGAAAAGGGGATAGTT\n") + f.write("ACGAGCAACGAGAAGATGAGTATCCACTTTCTCGTCGATGTGGAGGAGGAGAACCTTGCT\n") + f.write("GGTGGGGCTGAAATGACCGATCAGGAGATTGTGGACCTGGTCATTGCCGAAGAGTTGGAG\n") + f.write("GAGAATTGCGAGGGAGAAGGAGGAGAGGAGGAAGCGGAGATAGAGCTCCGACCGGCGGAG\n") + f.write("CGAACGACGCTGAAGGAGGCAATCTCAGCGCTTGATGTTTTCCTTAGGTTTGCTATGAAT\n") + f.write("GGGTACTCAGGTCCAACGGATTTGATTTCTTTTGAGGACGAGGCTAGGAGGATTCGCAGG\n") + f.write("ACTCTTGTTGCCGAGCAGGATGCCGCGAGGATTCAGACGACAATGACTTCGTATTTCCAG\n") + f.write("CGTCAGTAG\n") + f.write(">Mivi_sl_Blaster_Grouper_2_Map_3\n") + f.write("TACAGTCAGACCTGAGAAAATTTATATCGCCCAATCTTATACCTGTCAAAATTTATGGAC\n") + f.write("TTTTCAATCTCCCGACTTTTTTGGCTGACAGAACCTGTCCAATCTTATACCTTATAATTT\n") + f.write("ATGGGTTTACAGGTCAAATTATAAGATAAGAGAGAGCCGGAAATGAGCGATTGATCAGGA\n") + f.write("ATTGGCCTCTCCTTCGGCGTTCTTGTTGACGAGCCGCCTGCTGGAAGAGTCCGAAATGCC\n") + f.write("CCGAAACAGCCAAGAAGCGAGCACAGTAGAGCAAAGGCGGCGGTTGACACGTTGACAGGC\n") + f.write("TAGTCGCGACGTGCTTCTCTCTCCTCTTCCGCCGACAACGACGCCGAAATGAACATCTTC\n") + f.write("ACAATCCGAGAAGCCCTCATCAGAAATTCCTCTTCATATCATCATGGTCTCATTCCCTTC\n") + f.write("CCGGAATTCAACTGCTGGCGCCACGCTCAAATCTTGTCTGATCGCAAGAACAAAGGATCG\n") + f.write("ACCGACCATACACCTCTTCCCAACGGTCGCGGGCCTCTCGATGGCGATCGCGGCATCATC\n") + f.write("AACGCGATGAACGCTCTGAAGACGGCGAACGATGAGCTGGTCGAAAAGGGGATAGTTACG\n") + f.write("AGCAACGAGAAGATGAGTATCCACTTTCTCGTCGATGTGGAGGAGGAGAACCTTGCTGGT\n") + f.write("GGGGCTGAAATGACCGATCAGGAGATTGTGGACCTGGGGTCATTGCCGAAGAGTTGGAGG\n") + f.write("AGAATTGCGAGGGAGAACTTGAAGGAGGAGAGGAGGAAGCGGAGATAGAGCTCCGACCGG\n") + f.write("CGGAGCGAACGACGCTGAAGGAGGCAATCTCAGCGCTTGGTGTTTTCCTTAGGTTTGCTA\n") + f.write("TGAATGGGTACTCAGGTCCAACGAATTTGATTTCTTTTGAGGACGAGGCTAGGAGGATTC\n") + f.write("GCAGGACTCTTGTTGCCGAGCAGGATGCCGCGAGGATTCAGACGACAATGACTTCGTATT\n") + f.write("TCCAGCGTCAGTAGGTCAAGATATTTTTTCTTGGAGCTTTCATAACTTGTTAGATGTCAT\n") + f.write("CATGCCTCAGTAGAGGCCGTACATTGGCTGCAATTCAGTAATTCGGGCCTTCTGAATTTC\n") + f.write("CTCCCCCTCAAAAGTCAATGTATCGACTCAAACGATGCACGAAAATTCTTGATTTGATGT\n") + f.write("AGGAAGCTCAAAAACGGAGTTTCAGGTCATAATGTAGTGATCTGAAGCCGAACTCTCCAA\n") + f.write("GCTTATACCTGTCTTAATTTATGGGAAAATCCGTCCACCGAAAATATAAATTTTCTCAGG\n") + f.write("TCTGACTGTA\n") + f.write(">Mivi_sl_Blaster_Grouper_3_Map_3\n") + f.write("CAACACAAAGATAAGGCACCTTCATCCAGTGGCTCGCACGAACTTTCAATTGCAAGTCGT\n") + f.write("TGGCGTGCGCTGGGCGGGATCAAAACCGGGTCTGGGAGTCGCGTAACCCACTGGAGCAAG\n") + f.write("TAGGTGGTAGCCTGGACTGACAACGTGGACGTCAGCGACTTGAAATAGGTATTCGCGGCT\n") + f.write("TTCGTGGTCGGTGTACCCCTGTGTGTCCGGCATCGGCTGTCCAGAGTCGCCAGCCTGCCC\n") + f.write("GGTGCGAATGTGGGGGGCAGTCTCGGTCGCGCACGTGCGATGTCCCTCTCCCCACACGGG\n") + f.write("CCTGTCGGCTGCGGCTAACGGCCCCTGCAATGAGTCCTATCGACAGAAGTCCACCCAAGC\n") + f.write("TCAGCCTTCCCTCCACCAACACCAACATCGCAAGCCTCTCAAAAATTCACATCTCTTACA\n") + f.write("TCCCCTCGAAACACCCACTAAATGGATCCCTACCCTATCACTTGGCGGCAGTACTAGTAG\n") + f.write("CACGGGCCCAACTTCGACGGATCTCGAACGGACTTCCCACGGGTTCTCGGTGTGCAAGCG\n") + f.write("TCTCAGGTCAAGGTTTTGGTTGGTGGGCTTTCTGGGTGTGCAAAGGGGATTATTATAGAG\n") + f.write("GGAAGAAGAAGAAGGATGGGACCAGGGAGGCAGAGACGTGCGGGGTCAGGTTGATGGGGG\n") + f.write("AAGGTCGTGGAAGCGAAGAACGAGAGGCGAGCTTGTCGTTTGAGGAGAAAGGGGCCTCGC\n") + f.write("TGCCTGCAGAGAAAGGCGGTAAGTTGACCGGCGCAAAGTTATCATGAGACCGTAGCTCAG\n") + f.write("TATCGTTTCCTGTCGAGGGCATGGGTTACAGTCCGTCGAACTATGCGCGAGATCATCTGG\n") + f.write("TAGTAAAGAATCCCGCCGCCACTGACCAGATCTCCTGTGTCCTCTCAGCTCTCACAAAAC\n") + f.write("CTAGAAAAGCTTCGCATGGAGCCAAACGAATACTCCAATCCGACATTGAGCAAGACCCTT\n") + f.write("CCCTCTCGCCTCATAGGAACGAAACGGCCCATCTTCGAAGGGACAACTCTCTGTCGGCCG\n") + f.write("AGGAGATGACTTTTCTGACCGAGCGTAAGAGGAGATCGCACAGAGTCAGGGGTTGGTCGA\n") + f.write("GCTTTTGGGATTGGAGGAAGGGGGAGAGATTGATGAACGAGACGTCCCAATAGTGAGTCG\n") + f.write("CTCCGCACTGGAGCAATGATGGCAAACCGTGGAGTTGAAGAGTCTTGAACGCTATCAGAT\n") + f.write("CGGGCTAGGAGGGTCGGGAGGCGGTTGAATGCGTGCCAACCTTGGCTTCCTGTCAACGAT\n") + f.write("CCTCGCCTTTCAAGAGCTCGATCTATGGCAGTTGTTGACCTACACAGCGGGGGTATCCGG\n") + f.write("GTCCTGTTGGGCTCTGGCGAGTTTATATACGCTACCGATCGCACGTCCGCTCACACCATC\n") + f.write("CATCACTCAACGCCGCTGCGGTGATTGAGCACTTTATGTCCGTCTCAGGGGATCACCGTC\n") + f.write("TGAGTACAAAATCGGTCAACCGAGTCAGGGAGGCACACGGAGGGTACCAATCGCTTTTCG\n") + f.write("GACCTTTGATTTCAAAGTCTAAGAACAGTCAAAAGATCTGTAGTGAGTACAGACCACTGA\n") + f.write("CCCTCACTTGAGTAGATATTGACACTGACGAAGATCGCTACACTGCGGGCCTTGACAGTG\n") + f.write("ATTGATCTGTACTCGACACTGGTCTCATCGTACTTCTGGATGATGCCCAGAAAAGATGGG\n") + f.write("AAGGATCAGGTTGATCCGTATGTACCCCTGCGTCGGCTCGTGAGGTCCAGAGAGGGTCAT\n") + f.write("TCCACTGACTGTCCCGAACCCCCCCTGGCTGATCGTCAGCGCCTCGATGAAATGGTCGCG\n") + f.write("CGCGTACGATAATGCGGGCCTGGCTCACGGATGCGCGCCTTTCCCTATCGTCAGTCACGC\n") + f.write("AAATGTAGGCTTCCATCTGGAACGCTGCTTGATGGCCTAAGAATGGGCCGTCACGGAACA\n") + f.write("GCTCACCGCCTGCAGACACGAACGGCCGTGGCGGTCATGGAAGGATCTGAACGTGTCGCC\n") + f.write("CCATACGATTGACGAAGAGATGTAAGCTCCCTTGGTA\n") + f.close() + + _createFastaFile_three_sequences_with_ORFs = staticmethod ( _createFastaFile_three_sequences_with_ORFs ) + + + def _createFastaFile_three_sequences_with_ORFs_expected(fileName): + f = open(fileName, 'w') + f.write("ORF|1|662\tMivi_sl_Blaster_Grouper_1_Map_3\t307\t969\n") + f.write("ORF|-3|254\tMivi_sl_Blaster_Grouper_1_Map_3\t793\t539\n") + f.write("ORF|2|197\tMivi_sl_Blaster_Grouper_1_Map_3\t356\t553\n") + f.write("ORF|3|176\tMivi_sl_Blaster_Grouper_1_Map_3\t288\t464\n") + f.write("ORF|-1|176\tMivi_sl_Blaster_Grouper_1_Map_3\t786\t610\n") + f.write("ORF|3|143\tMivi_sl_Blaster_Grouper_1_Map_3\t672\t815\n") + f.write("ORF|1|131\tMivi_sl_Blaster_Grouper_1_Map_3\t175\t306\n") + f.write("ORF|-2|131\tMivi_sl_Blaster_Grouper_1_Map_3\t797\t666\n") + f.write("ORF|2|128\tMivi_sl_Blaster_Grouper_1_Map_3\t167\t295\n") + f.write("ORF|-2|119\tMivi_sl_Blaster_Grouper_1_Map_3\t242\t123\n") + f.write("ORF|1|464\tMivi_sl_Blaster_Grouper_2_Map_3\t304\t768\n") + f.write("ORF|3|305\tMivi_sl_Blaster_Grouper_2_Map_3\t669\t974\n") + f.write("ORF|-3|251\tMivi_sl_Blaster_Grouper_2_Map_3\t1094\t843\n") + f.write("ORF|-2|245\tMivi_sl_Blaster_Grouper_2_Map_3\t531\t286\n") + f.write("ORF|-3|224\tMivi_sl_Blaster_Grouper_2_Map_3\t791\t567\n") + f.write("ORF|-2|215\tMivi_sl_Blaster_Grouper_2_Map_3\t1098\t883\n") + f.write("ORF|2|197\tMivi_sl_Blaster_Grouper_2_Map_3\t353\t550\n") + f.write("ORF|3|173\tMivi_sl_Blaster_Grouper_2_Map_3\t288\t461\n") + f.write("ORF|-1|173\tMivi_sl_Blaster_Grouper_2_Map_3\t1087\t914\n") + f.write("ORF|-1|143\tMivi_sl_Blaster_Grouper_2_Map_3\t310\t167\n") + f.write("ORF|3|626\tMivi_sl_Blaster_Grouper_3_Map_3\t141\t767\n") + f.write("ORF|2|434\tMivi_sl_Blaster_Grouper_3_Map_3\t164\t598\n") + f.write("ORF|3|365\tMivi_sl_Blaster_Grouper_3_Map_3\t768\t1133\n") + f.write("ORF|-3|359\tMivi_sl_Blaster_Grouper_3_Map_3\t1514\t1155\n") + f.write("ORF|-1|320\tMivi_sl_Blaster_Grouper_3_Map_3\t1879\t1559\n") + f.write("ORF|3|272\tMivi_sl_Blaster_Grouper_3_Map_3\t1299\t1571\n") + f.write("ORF|-2|248\tMivi_sl_Blaster_Grouper_3_Map_3\t1503\t1255\n") + f.write("ORF|1|236\tMivi_sl_Blaster_Grouper_3_Map_3\t1576\t1812\n") + f.write("ORF|-1|227\tMivi_sl_Blaster_Grouper_3_Map_3\t1423\t1196\n") + f.write("ORF|-3|227\tMivi_sl_Blaster_Grouper_3_Map_3\t368\t141\n") + f.close() + + _createFastaFile_three_sequences_with_ORFs_expected = staticmethod ( _createFastaFile_three_sequences_with_ORFs_expected ) + + + def _createLinkFile_four_sequences_with_new_headers(fileName): + f = open(fileName, 'w') + f.write("seq 1\tReconCluster1Mb155 chunk183 {Fragment} 1..5506\t1\t127\n") + f.write("seq 2\tMbQ3Gr2Cl0 chunk440 {Fragment} 2678..3645\t1\t307\n") + f.write("seq 3\tMbS2Gr2Cl0 chunk622 {Fragment} 104..1078\t1\t427\n") + f.write("seq 4\tPilerCluster3.574Mb796 chunk0117 {Fragment} 51582..50819\t1\t307\n") + + _createLinkFile_four_sequences_with_new_headers = staticmethod ( _createLinkFile_four_sequences_with_new_headers ) + + + def _createLinkFile_four_sequences_same_headers(fileName): + f = open(fileName, 'w') + f.write("seq 1\tseq 1\t1\t127\n") + f.write("seq 2\tseq 2\t1\t307\n") + f.write("seq 3\tseq 3\t1\t427\n") + f.write("seq 4\tseq 4\t1\t307\n") + + _createLinkFile_four_sequences_same_headers = staticmethod ( _createLinkFile_four_sequences_same_headers )