Mercurial > repos > yufei-luo > s_mart
view commons/core/seq/test/Utils_for_T_FastaUtils.py @ 11:2da30502c2f1
Updated CompareOverlappingSmallQuery.xml
author | m-zytnicki |
---|---|
date | Thu, 14 Mar 2013 05:37:08 -0400 |
parents | 769e306b7933 |
children |
line wrap: on
line source
# 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 )