Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/seq/FastaUtils.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 # Copyright INRA (Institut National de la Recherche Agronomique) |
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2 # http://www.inra.fr |
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3 # http://urgi.versailles.inra.fr |
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4 # |
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5 # This software is governed by the CeCILL license under French law and |
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6 # abiding by the rules of distribution of free software. You can use, |
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7 # modify and/ or redistribute the software under the terms of the CeCILL |
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8 # license as circulated by CEA, CNRS and INRIA at the following URL |
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9 # "http://www.cecill.info". |
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10 # |
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11 # As a counterpart to the access to the source code and rights to copy, |
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12 # modify and redistribute granted by the license, users are provided only |
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13 # with a limited warranty and the software's author, the holder of the |
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14 # economic rights, and the successive licensors have only limited |
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15 # liability. |
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16 # |
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17 # In this respect, the user's attention is drawn to the risks associated |
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18 # with loading, using, modifying and/or developing or reproducing the |
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19 # software by the user in light of its specific status of free software, |
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20 # that may mean that it is complicated to manipulate, and that also |
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21 # therefore means that it is reserved for developers and experienced |
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22 # professionals having in-depth computer knowledge. Users are therefore |
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23 # encouraged to load and test the software's suitability as regards their |
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24 # requirements in conditions enabling the security of their systems and/or |
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25 # data to be ensured and, more generally, to use and operate it in the |
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26 # same conditions as regards security. |
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27 # |
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28 # The fact that you are presently reading this means that you have had |
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29 # knowledge of the CeCILL license and that you accept its terms. |
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30 |
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31 |
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32 import os |
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33 import sys |
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34 import string |
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35 import math |
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36 import shutil |
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37 import re |
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38 import glob |
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39 from commons.core.seq.BioseqDB import BioseqDB |
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40 from commons.core.seq.Bioseq import Bioseq |
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41 from commons.core.coord.MapUtils import MapUtils |
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42 from commons.core.coord.Range import Range |
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43 from commons.core.checker.CheckerUtils import CheckerUtils |
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44 from commons.core.launcher.LauncherUtils import LauncherUtils |
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45 from commons.core.coord.ConvCoord import ConvCoord |
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46 from commons.core.parsing.FastaParser import FastaParser |
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47 |
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48 |
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49 ## Static methods for fasta file manipulation |
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50 # |
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51 class FastaUtils( object ): |
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52 |
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53 ## Count the number of sequences in the input fasta file |
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54 # |
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55 # @param inFile name of the input fasta file |
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56 # |
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57 # @return integer number of sequences in the input fasta file |
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58 # |
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59 @staticmethod |
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60 def dbSize( inFile ): |
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61 nbSeq = 0 |
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62 inFileHandler = open( inFile, "r" ) |
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63 line = inFileHandler.readline() |
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64 while line: |
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65 if line[0] == ">": |
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66 nbSeq = nbSeq + 1 |
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67 line = inFileHandler.readline() |
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68 inFileHandler.close() |
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69 |
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70 return nbSeq |
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71 |
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72 |
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73 ## Compute the cumulative sequence length in the input fasta file |
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74 # |
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75 # @param inFile handler of the input fasta file |
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76 # |
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77 @staticmethod |
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78 def dbCumLength( inFile ): |
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79 cumLength = 0 |
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80 line = inFile.readline() |
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81 while line: |
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82 if line[0] != ">": |
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83 cumLength += len(string.rstrip(line)) |
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84 line = inFile.readline() |
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85 |
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86 return cumLength |
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87 |
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88 |
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89 ## Return a list with the length of each sequence in the input fasta file |
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90 # |
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91 # @param inFile string name of the input fasta file |
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92 # |
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93 @staticmethod |
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94 def dbLengths( inFile ): |
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95 lLengths = [] |
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96 inFileHandler = open( inFile, "r" ) |
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97 currentLength = 0 |
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98 line = inFileHandler.readline() |
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99 while line: |
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100 if line[0] == ">": |
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101 if currentLength != 0: |
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102 lLengths.append( currentLength ) |
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103 currentLength = 0 |
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104 else: |
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105 currentLength += len(line[:-1]) |
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106 line = inFileHandler.readline() |
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107 lLengths.append( currentLength ) |
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108 inFileHandler.close() |
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109 return lLengths |
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110 |
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111 |
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112 ## Retrieve the sequence headers present in the input fasta file |
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113 # |
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114 # @param inFile string name of the input fasta file |
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115 # @param verbose integer level of verbosity |
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116 # |
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117 # @return list of sequence headers |
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118 # |
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119 @staticmethod |
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120 def dbHeaders( inFile, verbose=0 ): |
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121 lHeaders = [] |
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122 |
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123 inFileHandler = open( inFile, "r" ) |
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124 line = inFileHandler.readline() |
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125 while line: |
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126 if line[0] == ">": |
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127 lHeaders.append( string.rstrip(line[1:]) ) |
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128 if verbose > 0: |
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129 print string.rstrip(line[1:]) |
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130 line = inFileHandler.readline() |
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131 inFileHandler.close() |
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132 |
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133 return lHeaders |
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134 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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135 |
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136 ## Cut a data bank into chunks according to the input parameters |
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137 # If a sequence is shorter than the threshold, it is only renamed (not cut) |
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138 # |
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139 # @param inFileName string name of the input fasta file |
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140 # @param chkLgth string chunk length (in bp, default=200000) |
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141 # @param chkOver string chunk overlap (in bp, default=10000) |
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142 # @param wordN string N stretch word length (default=11, 0 for no detection) |
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143 # @param outFilePrefix string prefix of the output files (default=inFileName + '_chunks.fa' and '_chunks.map') |
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144 # @param clean boolean remove 'cut' and 'Nstretch' files |
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145 # @param verbose integer (default = 0) |
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146 # |
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147 @staticmethod |
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148 def dbChunks( inFileName, chkLgth="200000", chkOver="10000", wordN="11", outFilePrefix="", clean=False, verbose=0 ): |
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149 nbSeq = FastaUtils.dbSize( inFileName ) |
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150 if verbose > 0: |
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151 print "cut the %i input sequences with cutterDB..." % ( nbSeq ) |
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152 sys.stdout.flush() |
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153 |
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154 prg = "cutterDB" |
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155 cmd = prg |
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156 cmd += " -l %s" % ( chkLgth ) |
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157 cmd += " -o %s" %( chkOver ) |
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158 cmd += " -w %s" % ( wordN ) |
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159 cmd += " %s" % ( inFileName ) |
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160 returnStatus = os.system( cmd ) |
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161 if returnStatus != 0: |
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162 msg = "ERROR: '%s' returned '%i'" % ( prg, returnStatus ) |
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163 sys.stderr.write( "%s\n" % ( msg ) ) |
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164 sys.exit(1) |
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165 |
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166 nbChunks = FastaUtils.dbSize( "%s_cut" % ( inFileName ) ) |
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167 if verbose > 0: |
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168 print "done (%i chunks)" % ( nbChunks ) |
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169 sys.stdout.flush() |
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170 |
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171 if verbose > 0: |
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172 print "rename the headers..." |
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173 sys.stdout.flush() |
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174 |
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175 if outFilePrefix == "": |
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176 outFastaName = inFileName + "_chunks.fa" |
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177 outMapName = inFileName + "_chunks.map" |
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178 else: |
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179 outFastaName = outFilePrefix + ".fa" |
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180 outMapName = outFilePrefix + ".map" |
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181 |
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182 inFile = open( "%s_cut" % ( inFileName ), "r" ) |
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183 line = inFile.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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184 |
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185 outFasta = open( outFastaName, "w" ) |
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186 outMap = open( outMapName, "w" ) |
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187 |
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188 # read line after line (no need for big RAM) and change the sequence headers |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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189 while line: |
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190 |
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191 if line[0] == ">": |
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192 if verbose > 1: |
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193 print "rename '%s'" % ( line[:-1] ); sys.stdout.flush() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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194 data = line[:-1].split(" ") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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195 seqID = data[0].split(">")[1] |
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196 newHeader = "chunk%s" % ( str(seqID).zfill( len(str(nbChunks)) ) ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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197 oldHeader = data[2] |
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198 seqStart = data[4].split("..")[0] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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199 seqEnd = data[4].split("..")[1] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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200 outMap.write( "%s\t%s\t%s\t%s\n" % ( newHeader, oldHeader, seqStart, seqEnd ) ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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201 outFasta.write( ">%s\n" % ( newHeader ) ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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202 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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203 else: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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204 outFasta.write( line.upper() ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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205 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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206 line = inFile.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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207 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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208 inFile.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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209 outFasta.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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210 outMap.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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211 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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212 if clean == True: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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213 os.remove(inFileName + "_cut") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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214 os.remove(inFileName + ".Nstretch.map") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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215 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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216 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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217 ## Split the input fasta file in several output files |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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218 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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219 # @param inFile string name of the input fasta file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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220 # @param nbSeqPerBatch integer number of sequences per output file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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221 # @param newDir boolean put the sequences in a new directory called 'batches' |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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222 # @param useSeqHeader boolean use sequence header (only if 'nbSeqPerBatch=1') |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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223 # @param prefix prefix in output file name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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224 # @param verbose integer verbosity level (default = 0) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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225 # |
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226 @staticmethod |
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227 def dbSplit( inFile, nbSeqPerBatch, newDir, useSeqHeader=False, prefix="batch", verbose=0 ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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228 if not os.path.exists( inFile ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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229 msg = "ERROR: file '%s' doesn't exist" % ( inFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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230 sys.stderr.write( "%s\n" % ( msg ) ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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231 sys.exit(1) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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232 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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233 nbSeq = FastaUtils.dbSize( inFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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234 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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235 nbBatches = int( math.ceil( nbSeq / float(nbSeqPerBatch) ) ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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236 if verbose > 0: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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237 print "save the %i input sequences into %i batches" % ( nbSeq, nbBatches ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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238 sys.stdout.flush() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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239 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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240 if nbSeqPerBatch > 1 and useSeqHeader: |
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241 useSeqHeader = False |
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242 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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243 if newDir == True: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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244 if os.path.exists( "batches" ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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245 shutil.rmtree( "batches" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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246 os.mkdir( "batches" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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247 os.chdir( "batches" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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248 os.system( "ln -s ../%s ." % ( inFile ) ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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249 |
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250 inFileHandler = open( inFile, "r" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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251 inFileHandler.seek( 0, 0 ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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252 countBatch = 0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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253 countSeq = 0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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254 line = inFileHandler.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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255 while line: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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256 if line == "": |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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257 break |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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258 if line[0] == ">": |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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259 countSeq += 1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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260 if nbSeqPerBatch == 1 or countSeq % nbSeqPerBatch == 1: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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261 if "outFile" in locals(): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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262 outFile.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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263 countBatch += 1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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264 if nbSeqPerBatch == 1 and useSeqHeader: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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265 outFileName = "%s.fa" % ( line[1:-1].replace(" ","_") ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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266 else: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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267 outFileName = "%s_%s.fa" % ( prefix, str(countBatch).zfill( len(str(nbBatches)) ) ) |
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268 outFile = open( outFileName, "w" ) |
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269 if verbose > 1: |
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270 print "saving seq '%s' in file '%s'..." % ( line[1:40][:-1], outFileName ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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271 sys.stdout.flush() |
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272 outFile.write( line ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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273 line = inFileHandler.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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274 inFileHandler.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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275 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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276 if newDir == True: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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277 os.remove( os.path.basename( inFile ) ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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278 os.chdir( ".." ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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279 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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280 |
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281 ## Split the input fasta file in several output files |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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282 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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283 # @param inFileName string name of the input fasta file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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284 # @param maxSize integer max cumulative length for each output file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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285 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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286 @staticmethod |
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287 def splitFastaFileInBatches(inFileName, maxSize = 200000): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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288 iBioseqDB = BioseqDB(inFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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289 lHeadersSizeTuples = [] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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290 for iBioseq in iBioseqDB.db: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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291 lHeadersSizeTuples.append((iBioseq.getHeader(), iBioseq.getLength())) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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292 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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293 lHeadersList = LauncherUtils.createHomogeneousSizeList(lHeadersSizeTuples, maxSize) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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294 os.mkdir("batches") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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295 os.chdir("batches") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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296 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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297 iterator = 0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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298 for lHeader in lHeadersList : |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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299 iterator += 1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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300 with open("batch_%s.fa" % iterator, 'w') as f : |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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301 for header in lHeader : |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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302 iBioseq = iBioseqDB.fetch(header) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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303 iBioseq.write(f) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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304 os.chdir("..") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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305 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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306 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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307 ## Split the input fasta file in several output files according to their cluster identifier |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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308 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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309 # @param inFileName string name of the input fasta file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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310 # @param clusteringMethod string name of the clustering method (Grouper, Recon, Piler, Blastclust) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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311 # @param simplifyHeader boolean simplify the headers |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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312 # @param createDir boolean put the sequences in different directories |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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313 # @param outPrefix string prefix of the output files (default='seqCluster') |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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314 # @param verbose integer (default = 0) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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315 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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316 @staticmethod |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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317 def splitSeqPerCluster( inFileName, clusteringMethod, simplifyHeader, createDir, outPrefix="seqCluster", verbose=0 ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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318 if not os.path.exists( inFileName ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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319 print "ERROR: %s doesn't exist" % ( inFileName ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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320 sys.exit(1) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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321 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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322 inFile = open( inFileName, "r" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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323 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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324 line = inFile.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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325 if line: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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326 name = line.split(" ")[0] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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327 if "Cluster" in name: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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328 clusterID = name.split("Cluster")[1].split("Mb")[0] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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329 seqID = name.split("Mb")[1] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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330 else: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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331 clusterID = name.split("Cl")[0].split("Gr")[1] # the notion of 'group' in Grouper corresponds to 'cluster' in Piler, Recon and Blastclust |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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332 if "Q" in name.split("Gr")[0]: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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|
333 seqID = name.split("Gr")[0].split("MbQ")[1] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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334 elif "S" in name: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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335 seqID = name.split("Gr")[0].split("MbS")[1] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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336 sClusterIDs = set( [ clusterID ] ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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337 if simplifyHeader == True: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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338 header = "%s_Cluster%s_Seq%s" % ( clusteringMethod, clusterID, seqID ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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339 else: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
340 header = line[1:-1] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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341 if createDir == True: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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342 if not os.path.exists( "%s_cluster_%s" % ( inFileName, clusterID ) ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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|
343 os.mkdir( "%s_cluster_%s" % ( inFileName, clusterID ) ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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344 os.chdir( "%s_cluster_%s" % ( inFileName, clusterID ) ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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345 outFileName = "%s%s.fa" % ( outPrefix, clusterID ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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346 outFile = open( outFileName, "w" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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347 outFile.write( ">%s\n" % ( header ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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348 prevClusterID = clusterID |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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|
349 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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|
350 line = inFile.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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changeset
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351 while line: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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352 if line[0] == ">": |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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353 name = line.split(" ")[0] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
354 if "Cluster" in name: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
355 clusterID = name.split("Cluster")[1].split("Mb")[0] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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changeset
|
356 seqID = name.split("Mb")[1] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
357 else: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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358 clusterID = name.split("Cl")[0].split("Gr")[1] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
359 if "Q" in name.split("Gr")[0]: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
360 seqID = name.split("Gr")[0].split("MbQ")[1] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
361 elif "S" in name: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
362 seqID = name.split("Gr")[0].split("MbS")[1] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
363 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
364 if clusterID != prevClusterID: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
365 outFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
366 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
367 if simplifyHeader == True: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
368 header = "%s_Cluster%s_Seq%s" % ( clusteringMethod, clusterID, seqID ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
369 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
370 header = line[1:-1] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
371 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
372 if createDir == True: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
373 os.chdir( ".." ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
374 if not os.path.exists( "%s_cluster_%s" % ( inFileName, clusterID ) ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
375 os.mkdir( "%s_cluster_%s" % ( inFileName, clusterID ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
376 os.chdir( "%s_cluster_%s" % ( inFileName, clusterID ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
377 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
378 outFileName = "%s%s.fa" % ( outPrefix, clusterID ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
379 if not os.path.exists( outFileName ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
380 outFile = open( outFileName, "w" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
381 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
382 if clusterID != prevClusterID: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
383 outFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
384 outFile = open( outFileName, "a" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
385 outFile.write( ">%s\n" % ( header ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
386 prevClusterID = clusterID |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
387 sClusterIDs.add( clusterID ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
388 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
389 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
390 outFile.write( line ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
391 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
392 line = inFile.readline() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
393 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
394 outFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
395 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
396 print "number of clusters: %i" % ( len(sClusterIDs) ); sys.stdout.flush() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
397 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
398 if createDir == True: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
399 os.chdir("..") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
400 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
401 print "WARNING: empty input file - no cluster found"; sys.stdout.flush() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
402 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
403 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
404 ## Filter a fasta file in two fasta files using the length of each sequence as a criteron |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
405 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
406 # @param len_min integer length sequence criterion to filter |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
407 # @param inFileName string name of the input fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
408 # @param verbose integer (default = 0) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
409 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
410 @staticmethod |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
411 def dbLengthFilter( len_min, inFileName, verbose=0 ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
412 file_db = open( inFileName, "r" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
413 file_dbInf = open( inFileName+".Inf"+str(len_min), "w" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
414 file_dbSup = open( inFileName+".Sup"+str(len_min), "w" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
415 seq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
416 numseq = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
417 nbsave = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
418 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
419 seq.read( file_db ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
420 while seq.sequence: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
421 l = seq.getLength() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
422 numseq = numseq + 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
423 if l >= len_min: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
424 seq.write( file_dbSup ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
425 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
426 print 'sequence #',numseq,'=',l,'[',seq.header[0:40],'...] Sup !!' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
427 nbsave=nbsave+1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
428 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
429 seq.write( file_dbInf ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
430 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
431 print 'sequence #',numseq,'=',l,'[',seq.header[0:40],'...] Inf !!' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
432 nbsave=nbsave+1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
433 seq.read( file_db ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
434 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
435 file_db.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
436 file_dbInf.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
437 file_dbSup.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
438 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
439 print nbsave,'saved sequences in ',inFileName+".Inf"+str(len_min)," and ", inFileName+".Sup"+str(len_min) |
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 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
442 ## Extract the longest sequences from a fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
443 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
444 # @param num integer maximum number of sequences in the output file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
445 # @param inFileName string name of the input fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
446 # @param outFileName string name of the output fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
447 # @param minThresh integer minimum length threshold (default=0) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
448 # @param verbose integer (default = 0) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
449 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
450 @staticmethod |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
451 def dbLongestSequences( num, inFileName, outFileName="", verbose=0, minThresh=0 ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
452 bsDB = BioseqDB( inFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
453 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
454 print "nb of input sequences: %i" % ( bsDB.getSize() ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
455 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
456 if outFileName == "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
457 outFileName = inFileName + ".best" + str(num) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
458 outFile = open( outFileName, "w" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
459 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
460 if bsDB.getSize()==0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
461 return 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
462 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
463 num = int(num) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
464 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
465 print "keep the %i longest sequences" % ( num ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
466 if minThresh > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
467 print "with length > %i bp" % ( minThresh ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
468 sys.stdout.flush() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
469 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
470 # retrieve the length of each input sequence |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
471 tmpLSeqLgth = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
472 seqNum = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
473 for bs in bsDB.db: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
474 seqNum += 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
475 tmpLSeqLgth.append( bs.getLength() ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
476 if verbose > 1: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
477 print "%d seq %s : %d bp" % ( seqNum, bs.header[0:40], bs.getLength() ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
478 sys.stdout.flush() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
479 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
480 # sort the lengths |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
481 tmpLSeqLgth.sort() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
482 tmpLSeqLgth.reverse() |
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 # select the longest |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
485 lSeqLgth = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
486 for i in xrange( 0, min(num,len(tmpLSeqLgth)) ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
487 if tmpLSeqLgth[i] >= minThresh: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
488 lSeqLgth.append( tmpLSeqLgth[i] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
489 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
490 print "selected max length: %i" % ( max(lSeqLgth) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
491 print "selected min length: %i" % ( min(lSeqLgth) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
492 sys.stdout.flush() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
493 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
494 # save the longest |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
495 inFile = open( inFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
496 seqNum = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
497 nbSave = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
498 for bs in bsDB.db: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
499 seqNum += 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
500 if bs.getLength() >= min(lSeqLgth) and bs.getLength() >= minThresh: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
501 bs.write( outFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
502 if verbose > 1: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
503 print "%d seq %s : saved !" % ( seqNum, bs.header[0:40] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
504 sys.stdout.flush() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
505 nbSave += 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
506 if nbSave == num: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
507 break |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
508 inFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
509 outFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
510 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
511 print nbSave, "saved sequences in ", outFileName |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
512 sys.stdout.flush() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
513 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
514 return 0 |
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 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
517 ## Extract all the sequence headers from a fasta file and write them in a new fasta file |
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 # @param inFileName string name of the input fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
520 # @param outFileName string name of the output file recording the headers (default = inFileName + '.headers') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
521 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
522 @staticmethod |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
523 def dbExtractSeqHeaders( inFileName, outFileName="" ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
524 lHeaders = FastaUtils.dbHeaders( inFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
525 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
526 if outFileName == "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
527 outFileName = inFileName + ".headers" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
528 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
529 outFile = open( outFileName, "w" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
530 for i in lHeaders: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
531 outFile.write( i + "\n" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
532 outFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
533 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
534 return 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
535 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
536 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
537 ## Extract sequences and their headers selected by a given pattern from a fasta file and write them in a new fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
538 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
539 # @param pattern regular expression to search in headers |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
540 # @param inFileName string name of the input fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
541 # @param outFileName string name of the output file recording the selected bioseq (default = inFileName + '.extracted') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
542 # @param verbose integer verbosity level (default = 0) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
543 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
544 @staticmethod |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
545 def dbExtractByPattern( pattern, inFileName, outFileName="", verbose=0 ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
546 if pattern == "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
547 return |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
548 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
549 if outFileName == "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
550 outFileName = inFileName + '.extracted' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
551 outFile = open( outFileName, 'w' ) |
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 patternTosearch = re.compile( pattern ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
554 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
555 bioseqNb = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
556 savedBioseqNb = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
557 inFile = open( inFileName, "r" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
558 bioseq.read( inFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
559 while bioseq.sequence: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
560 bioseqNb = bioseqNb + 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
561 m = patternTosearch.search( bioseq.header ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
562 if m: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
563 bioseq.write( outFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
564 if verbose > 1: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
565 print 'sequence num',bioseqNb,'matched on',m.group(),'[',bioseq.header[0:40],'...] saved !!' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
566 savedBioseqNb = savedBioseqNb + 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
567 bioseq.read( inFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
568 inFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
569 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
570 outFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
571 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
572 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
573 print "%i sequences saved in file '%s'" % ( savedBioseqNb, outFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
574 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
575 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
576 ## Extract sequences and their headers selected by patterns contained in a file, from a fasta file and write them in a new fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
577 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
578 # @param patternFileName string file containing regular expression to search in headers |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
579 # @param inFileName string name of the input fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
580 # @param outFileName string name of the output file recording the selected bioseq (default = inFileName + '.extracted') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
581 # @param verbose integer verbosity level (default = 0) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
582 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
583 @staticmethod |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
584 def dbExtractByFilePattern( patternFileName, inFileName, outFileName="", verbose=0 ): |
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 if patternFileName == "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
587 print "ERROR: no file of pattern" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
588 sys.exit(1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
589 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
590 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
591 bioseqNb = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
592 savedBioseqNb = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
593 lHeaders = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
594 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
595 inFile = open( inFileName, "r" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
596 bioseq.read( inFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
597 while bioseq.sequence != None: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
598 lHeaders.append( bioseq.header ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
599 bioseq.read( inFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
600 inFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
601 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
602 lHeadersToKeep = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
603 patternFile = open( patternFileName, "r" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
604 for pattern in patternFile: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
605 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
606 print "pattern: ",pattern[:-1]; sys.stdout.flush() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
607 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
608 patternToSearch = re.compile(pattern[:-1]) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
609 for h in lHeaders: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
610 if patternToSearch.search(h): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
611 lHeadersToKeep.append(h) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
612 patternFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
613 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
614 if outFileName == "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
615 outFileName = inFileName + ".extracted" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
616 outFile=open( outFileName, "w" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
617 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
618 inFile = open( inFileName, "r" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
619 bioseq.read(inFile) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
620 while bioseq.sequence: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
621 bioseqNb += 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
622 if bioseq.header in lHeadersToKeep: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
623 bioseq.write(outFile) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
624 if verbose > 1: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
625 print 'sequence num',bioseqNb,'[',bioseq.header[0:40],'...] saved !!'; sys.stdout.flush() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
626 savedBioseqNb += 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
627 bioseq.read(inFile) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
628 inFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
629 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
630 outFile.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 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
633 print "%i sequences saved in file '%s'" % ( savedBioseqNb, outFileName ) |
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 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
636 ## Extract sequences and their headers not selected by a given pattern from a fasta file and write them in a new fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
637 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
638 # @param pattern regular expression to search in headers |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
639 # @param inFileName string name of the input fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
640 # @param outFileName string name of the output file recording the selected bioseq (default = inFileName + '.extracted') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
641 # @param verbose integer verbosity level (default = 0) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
642 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
643 @staticmethod |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
644 def dbCleanByPattern( pattern, inFileName, outFileName="", verbose=0 ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
645 if pattern == "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
646 return |
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 patternToSearch = re.compile(pattern) |
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 if outFileName == "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
651 outFileName = inFileName + '.cleaned' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
652 outFile = open(outFileName,'w') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
653 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
654 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
655 bioseqNb = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
656 savedBioseqNb = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
657 inFile = open(inFileName) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
658 bioseq.read(inFile) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
659 while bioseq.sequence != None: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
660 bioseqNb += 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
661 if not patternToSearch.search(bioseq.header): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
662 bioseq.write(outFile) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
663 if verbose > 1: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
664 print 'sequence num',bioseqNb,'[',bioseq.header[0:40],'...] saved !!' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
665 savedBioseqNb += 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
666 bioseq.read(inFile) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
667 inFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
668 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
669 outFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
670 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
671 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
672 print "%i sequences saved in file '%s'" % ( savedBioseqNb, outFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
673 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
674 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
675 ## Extract sequences and their headers not selected by patterns contained in a file, from a fasta file and write them in a new fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
676 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
677 # @param patternFileName string file containing regular expression to search in headers |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
678 # @param inFileName string name of the input fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
679 # @param outFileName string name of the output file recording the selected bioseq (default = inFileName + '.extracted') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
680 # @param verbose integer verbosity level (default = 0) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
681 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
682 @staticmethod |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
683 def dbCleanByFilePattern( patternFileName, inFileName, outFileName="", verbose=0 ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
684 if patternFileName == "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
685 print "ERROR: no file of pattern" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
686 sys.exit(1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
687 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
688 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
689 bioseqNb = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
690 savedBioseqNb = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
691 lHeaders = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
692 inFile = open( inFileName, "r" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
693 bioseq.read( inFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
694 while bioseq.sequence != None: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
695 bioseqNb += 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
696 lHeaders.append( bioseq.header ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
697 bioseq.read( inFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
698 inFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
699 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
700 patternFile = open( patternFileName, "r") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
701 lHeadersToRemove = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
702 for pattern in patternFile: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
703 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
704 print "pattern: ",pattern[:-1]; sys.stdout.flush() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
705 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
706 patternToSearch = re.compile( pattern[:-1] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
707 for h in lHeaders: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
708 if patternToSearch.search(h): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
709 lHeadersToRemove.append(h) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
710 patternFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
711 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
712 if outFileName == "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
713 outFileName = inFileName + '.cleaned' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
714 outFile = open( outFileName, 'w' ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
715 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
716 bioseqNum = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
717 inFile=open( inFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
718 bioseq.read( inFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
719 while bioseq.sequence != None: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
720 bioseqNum += 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
721 if bioseq.header not in lHeadersToRemove: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
722 bioseq.write( outFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
723 if verbose > 1: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
724 print 'sequence num',bioseqNum,'/',bioseqNb,'[',bioseq.header[0:40],'...] saved !!'; sys.stdout.flush() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
725 savedBioseqNb += 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
726 bioseq.read( inFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
727 inFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
728 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
729 outFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
730 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
731 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
732 print "%i sequences saved in file '%s'" % ( savedBioseqNb, outFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
733 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
734 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
735 ## Find sequence's ORFs from a fasta file and write them in a tab file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
736 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
737 # @param inFileName string name of the input fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
738 # @param orfMaxNb integer Select orfMaxNb best ORFs |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
739 # @param orfMinLength integer Keep ORFs with length > orfMinLength |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
740 # @param outFileName string name of the output fasta file (default = inFileName + '.orf.map') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
741 # @param verbose integer verbosity level (default = 0) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
742 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
743 @staticmethod |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
744 def dbORF( inFileName, orfMaxNb = 0, orfMinLength = 0, outFileName = "", verbose=0 ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
745 if outFileName == "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
746 outFileName = inFileName + ".ORF.map" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
747 outFile = open( outFileName, "w" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
748 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
749 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
750 bioseqNb = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
751 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
752 inFile = open( inFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
753 bioseq.read( inFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
754 while bioseq.sequence != None: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
755 bioseq.upCase() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
756 bioseqNb += 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
757 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
758 print 'sequence num',bioseqNb,'=',bioseq.getLength(),'[',bioseq.header[0:40],'...]' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
759 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
760 orf = bioseq.findORF() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
761 bestOrf = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
762 for i in orf.keys(): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
763 orfLen = len(orf[i]) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
764 for j in xrange(1, orfLen): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
765 start = orf[i][j-1] + 4 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
766 end = orf[i][j] + 3 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
767 if end - start >= orfMinLength: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
768 bestOrf.append( ( end-start, i+1, start, end ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
769 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
770 bioseq.reverseComplement() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
771 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
772 orf = bioseq.findORF() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
773 seqLen = bioseq.getLength() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
774 for i in orf.keys(): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
775 orfLen = len(orf[i]) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
776 for j in xrange(1, orfLen): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
777 start = seqLen - orf[i][j-1] - 3 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
778 end = seqLen - orf[i][j] - 2 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
779 if start - end >= orfMinLength: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
780 bestOrf.append( ( start-end, (i+1)*-1, start, end ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
781 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
782 bestOrf.sort() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
783 bestOrf.reverse() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
784 bestOrfNb = len(bestOrf) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
785 if orfMaxNb != 0 and orfMaxNb < bestOrfNb: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
786 bestOrfNb = orfMaxNb |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
787 for i in xrange(0, bestOrfNb): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
788 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
789 print bestOrf[i] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
790 outFile.write("%s\t%s\t%d\t%d\n"%("ORF|"+str(bestOrf[i][1])+\ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
791 "|"+str(bestOrf[i][0]),bioseq.header, |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
792 bestOrf[i][2],bestOrf[i][3])) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
793 bioseq.read( inFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
794 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
795 inFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
796 outFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
797 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
798 return 0 |
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 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
801 ## Sort sequences by increasing length (write a new file) |
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 # @param inFileName string name of the input fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
804 # @param outFileName string name of the output fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
805 # @param verbose integer verbosity level |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
806 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
807 @staticmethod |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
808 def sortSequencesByIncreasingLength(inFileName, outFileName, verbose=0): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
809 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
810 print "sort sequences by increasing length" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
811 sys.stdout.flush() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
812 if not os.path.exists( inFileName ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
813 print "ERROR: file '%s' doesn't exist" % ( inFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
814 sys.exit(1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
815 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
816 # read each seq one by one |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
817 # save them in distinct temporary files |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
818 # with their length in the name |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
819 inFileHandler = open( inFileName, "r" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
820 countSeq = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
821 bs = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
822 bs.read( inFileHandler ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
823 while bs.header: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
824 countSeq += 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
825 tmpFile = "%ibp_%inb" % ( bs.getLength(), countSeq ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
826 bs.appendBioseqInFile( tmpFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
827 if verbose > 1: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
828 print "%s (%i bp) saved in '%s'" % ( bs.header, bs.getLength(), tmpFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
829 bs.header = "" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
830 bs.sequence = "" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
831 bs.read( inFileHandler ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
832 inFileHandler.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
833 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
834 # sort temporary file names |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
835 # concatenate them into the output file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
836 if os.path.exists( outFileName ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
837 os.remove( outFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
838 lFiles = glob.glob( "*bp_*nb" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
839 lFiles.sort( key=lambda s:int(s.split("bp_")[0]) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
840 for fileName in lFiles: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
841 cmd = "cat %s >> %s" % ( fileName, outFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
842 returnValue = os.system( cmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
843 if returnValue != 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
844 print "ERROR while concatenating '%s' with '%s'" % ( fileName, outFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
845 sys.exit(1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
846 os.remove( fileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
847 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
848 return 0 |
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 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
851 ## Sort sequences by header |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
852 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
853 # @param inFileName string name of the input fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
854 # @param outFileName string name of the output fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
855 # @param verbose integer verbosity level |
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 @staticmethod |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
858 def sortSequencesByHeader(inFileName, outFileName = "", verbose = 0): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
859 if outFileName == "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
860 outFileName = "%s_sortByHeaders.fa" % os.path.splitext(inFileName)[0] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
861 iBioseqDB = BioseqDB(inFileName) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
862 f = open(outFileName, "w") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
863 lHeaders = sorted(iBioseqDB.getHeaderList()) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
864 for header in lHeaders: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
865 iBioseq = iBioseqDB.fetch(header) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
866 iBioseq.write(f) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
867 f.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
868 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
869 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
870 ## Return a dictionary which keys are the headers and values the length of the sequences |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
871 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
872 # @param inFile string name of the input fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
873 # @param verbose integer verbosity level |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
874 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
875 @staticmethod |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
876 def getLengthPerHeader( inFile, verbose=0 ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
877 dHeader2Length = {} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
878 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
879 inFileHandler = open( inFile, "r" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
880 currentSeqHeader = "" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
881 currentSeqLength = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
882 line = inFileHandler.readline() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
883 while line: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
884 if line[0] == ">": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
885 if currentSeqHeader != "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
886 dHeader2Length[ currentSeqHeader ] = currentSeqLength |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
887 currentSeqLength = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
888 currentSeqHeader = line[1:-1] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
889 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
890 print "current header: %s" % ( currentSeqHeader ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
891 sys.stdout.flush() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
892 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
893 currentSeqLength += len( line.replace("\n","") ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
894 line = inFileHandler.readline() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
895 dHeader2Length[ currentSeqHeader ] = currentSeqLength |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
896 inFileHandler.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
897 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
898 return dHeader2Length |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
899 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
900 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
901 ## Convert headers from a fasta file having chunk coordinates |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
902 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
903 # @param inFile string name of the input fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
904 # @param mapFile string name of the map file with the coordinates of the chunks on the chromosomes |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
905 # @param outFile string name of the output file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
906 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
907 @staticmethod |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
908 def convertFastaHeadersFromChkToChr(inFile, mapFile, outFile): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
909 inFileHandler = open(inFile, "r") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
910 outFileHandler = open(outFile, "w") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
911 dChunk2Map = MapUtils.getDictPerNameFromMapFile(mapFile) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
912 iConvCoord = ConvCoord() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
913 line = inFileHandler.readline() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
914 while line: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
915 if line[0] == ">": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
916 if "{Fragment}" in line: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
917 chkName = line.split(" ")[1] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
918 chrName = dChunk2Map[chkName].seqname |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
919 lCoordPairs = line.split(" ")[3].split(",") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
920 lRangesOnChk = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
921 for i in lCoordPairs: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
922 iRange = Range(chkName, int(i.split("..")[0]), int(i.split("..")[1])) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
923 lRangesOnChk.append(iRange) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
924 lRangesOnChr = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
925 for iRange in lRangesOnChk: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
926 lRangesOnChr.append(iConvCoord.getRangeOnChromosome(iRange, dChunk2Map)) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
927 newHeader = line[1:-1].split(" ")[0] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
928 newHeader += " %s" % chrName |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
929 newHeader += " {Fragment}" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
930 newHeader += " %i..%i" % (lRangesOnChr[0].start, lRangesOnChr[0].end) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
931 for iRange in lRangesOnChr[1:]: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
932 newHeader += ",%i..%i" % (iRange.start, iRange.end) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
933 outFileHandler.write(">%s\n" % newHeader) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
934 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
935 chkName = line.split("_")[1].split(" ")[0] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
936 chrName = dChunk2Map[chkName].seqname |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
937 coords = line[line.find("[")+1 : line.find("]")] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
938 start = int(coords.split(",")[0]) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
939 end = int(coords.split(",")[1]) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
940 iRangeOnChk = Range(chkName, start, end) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
941 iRangeOnChr = iConvCoord.getRangeOnChromosome(iRangeOnChk, dChunk2Map) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
942 newHeader = line[1:-1].split("_")[0] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
943 newHeader += " %s" % chrName |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
944 newHeader += " %s" % line[line.find("(") : line.find(")")+1] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
945 newHeader += " %i..%i" % (iRangeOnChr.getStart(), iRangeOnChr.getEnd()) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
946 outFileHandler.write(">%s\n" % newHeader) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
947 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
948 outFileHandler.write(line) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
949 line = inFileHandler.readline() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
950 inFileHandler.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
951 outFileHandler.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
952 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
953 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
954 ## Convert a fasta file to a length file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
955 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
956 # @param inFile string name of the input fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
957 # @param outFile string name of the output file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
958 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
959 @staticmethod |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
960 def convertFastaToLength(inFile, outFile = ""): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
961 if outFile == "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
962 outFile = "%s.length" % inFile |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
963 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
964 if inFile != "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
965 with open(inFile, "r") as inFH: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
966 with open(outFile, "w") as outFH: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
967 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
968 bioseq.read(inFH) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
969 while bioseq.sequence != None: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
970 seqLen = bioseq.getLength() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
971 outFH.write("%s\t%d\n" % (bioseq.header.split()[0], seqLen)) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
972 bioseq.read(inFH) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
973 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
974 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
975 ## Convert a fasta file to a seq file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
976 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
977 # @param inFile string name of the input fasta file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
978 # @param outFile string name of the output file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
979 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
980 @staticmethod |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
981 def convertFastaToSeq(inFile, outFile = ""): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
982 if outFile == "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
983 outFile = "%s.seq" % inFile |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
984 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
985 if inFile != "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
986 with open(inFile, "r") as inFH: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
987 with open(outFile, "w") as outFH: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
988 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
989 bioseq.read(inFH) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
990 while bioseq.sequence != None: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
991 seqLen = bioseq.getLength() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
992 outFH.write("%s\t%s\t%s\t%d\n" % (bioseq.header.split()[0], \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
993 bioseq.sequence, bioseq.header, seqLen)) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
994 bioseq.read(inFH) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
995 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
996 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
997 ## Splice an input fasta file using coordinates in a Map file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
998 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
999 # @note the coordinates should be merged beforehand! |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1000 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1001 @staticmethod |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1002 def spliceFromCoords( genomeFile, coordFile, obsFile ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1003 genomeFileHandler = open( genomeFile, "r" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1004 obsFileHandler = open( obsFile, "w" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1005 dChr2Maps = MapUtils.getDictPerSeqNameFromMapFile( coordFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1006 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1007 bs = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1008 bs.read( genomeFileHandler ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1009 while bs.sequence: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1010 if dChr2Maps.has_key( bs.header ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1011 lCoords = MapUtils.getMapListSortedByIncreasingMinThenMax( dChr2Maps[ bs.header ] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1012 splicedSeq = "" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1013 currentSite = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1014 for iMap in lCoords: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1015 minSplice = iMap.getMin() - 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1016 if minSplice > currentSite: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1017 splicedSeq += bs.sequence[ currentSite : minSplice ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1018 currentSite = iMap.getMax() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1019 splicedSeq += bs.sequence[ currentSite : ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1020 bs.sequence = splicedSeq |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1021 bs.write( obsFileHandler ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1022 bs.read( genomeFileHandler ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1023 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1024 genomeFileHandler.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1025 obsFileHandler.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1026 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1027 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1028 ## Shuffle input sequences (single file or files in a directory) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1029 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1030 @staticmethod |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1031 def dbShuffle( inData, outData, verbose=0 ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1032 if CheckerUtils.isExecutableInUserPath("esl-shuffle"): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1033 prg = "esl-shuffle" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1034 else : prg = "shuffle" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1035 genericCmd = prg + " -d INPUT > OUTPUT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1036 if os.path.isfile( inData ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1037 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1038 print "shuffle input file '%s'" % inData |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1039 cmd = genericCmd.replace("INPUT",inData).replace("OUTPUT",outData) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1040 print cmd |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1041 returnStatus = os.system( cmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1042 if returnStatus != 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1043 sys.stderr.write( "ERROR: 'shuffle' returned '%i'\n" % returnStatus ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1044 sys.exit(1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1045 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1046 elif os.path.isdir( inData ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1047 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1048 print "shuffle files in input directory '%s'" % inData |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1049 if os.path.exists( outData ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1050 shutil.rmtree( outData ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1051 os.mkdir( outData ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1052 lInputFiles = glob.glob( "%s/*.fa" %( inData ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1053 nbFastaFiles = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1054 for inputFile in lInputFiles: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1055 nbFastaFiles += 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1056 if verbose > 1: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1057 print "%3i / %3i" % ( nbFastaFiles, len(lInputFiles) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1058 fastaBaseName = os.path.basename( inputFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1059 prefix, extension = os.path.splitext( fastaBaseName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1060 cmd = genericCmd.replace("INPUT",inputFile).replace("OUTPUT","%s/%s_shuffle.fa"%(outData,prefix)) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1061 returnStatus = os.system( cmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1062 if returnStatus != 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1063 sys.stderr.write( "ERROR: 'shuffle' returned '%i'\n" % returnStatus ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1064 sys.exit(1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1065 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1066 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1067 ## Convert a cluster file (one line = one cluster = one headers list) into a fasta file with cluster info in headers |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1068 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1069 # @param inClusterFileName string input cluster file name |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1070 # @param inFastaFileName string input fasta file name |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1071 # @param outFileName string output file name |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1072 # @param verbosity integer verbosity |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1073 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1074 @staticmethod |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1075 def convertClusterFileToFastaFile(inClusterFileName, inFastaFileName, outFileName, clusteringTool = "", verbosity = 0): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1076 dHeader2ClusterClusterMember, clusterIdForSingletonCluster = FastaUtils._createHeader2ClusterMemberDict(inClusterFileName, verbosity) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1077 iFastaParser = FastaParser(inFastaFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1078 with open(outFileName, "w") as f: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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1079 for iSequence in iFastaParser.getIterator(): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1080 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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1081 header = iSequence.getName() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1082 if dHeader2ClusterClusterMember.get(header): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1083 cluster = dHeader2ClusterClusterMember[header][0] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1084 member = dHeader2ClusterClusterMember[header][1] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1085 else: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1086 clusterIdForSingletonCluster += 1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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1087 cluster = clusterIdForSingletonCluster |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1088 member = 1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1089 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1090 newHeader = "%sCluster%sMb%s_%s" % (clusteringTool, cluster, member, header) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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1091 iSequence.setName(newHeader) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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1092 f.write(iSequence.printFasta()) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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|
1093 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1094 @staticmethod |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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1095 def _createHeader2ClusterMemberDict(inClusterFileName, verbosity = 0): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1096 dHeader2ClusterClusterMember = {} |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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1097 clusterId = 0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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1098 with open(inClusterFileName) as f: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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|
1099 line = f.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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1100 while line: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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1101 lineWithoutLastChar = line.rstrip() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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1102 lHeaders = lineWithoutLastChar.split("\t") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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|
1103 clusterId += 1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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|
1104 if verbosity > 0: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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1105 print "%i sequences in cluster %i" % (len(lHeaders), clusterId) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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|
1106 memberId = 0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
1107 for header in lHeaders: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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|
1108 memberId += 1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
1109 dHeader2ClusterClusterMember[header] = (clusterId, memberId) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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|
1110 line = f.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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|
1111 if verbosity > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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|
1112 print "%i clusters" % clusterId |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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|
1113 return dHeader2ClusterClusterMember, clusterId |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
1114 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
1115 @staticmethod |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1116 def convertClusteredFastaFileToMapFile(fastaFileNameFromClustering, outMapFileName = ""): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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1117 """ |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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1118 Write a map file from fasta output of clustering tool. |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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1119 Warning: only works if input fasta headers are formated like LTRharvest fasta output. |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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1120 """ |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1121 if not outMapFileName: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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1122 outMapFileName = "%s.map" % (os.path.splitext(fastaFileNameFromClustering)[0]) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1123 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
1124 fileDb = open(fastaFileNameFromClustering , "r") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1125 fileMap = open(outMapFileName, "w") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1126 seq = Bioseq() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1127 numseq = 0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1128 while 1: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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1129 seq.read(fileDb) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1130 if seq.sequence == None: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
1131 break |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1132 numseq = numseq + 1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1133 ID = seq.header.split(' ')[0].split('_')[0] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1134 chunk = seq.header.split(' ')[0].split('_')[1] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1135 start = seq.header.split(' ')[-1].split(',')[0][1:] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1136 end = seq.header.split(' ')[-1].split(',')[1][:-1] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1137 line = '%s\t%s\t%s\t%s' % (ID, chunk, start, end) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
1138 fileMap.write(line + "\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
1139 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
1140 fileDb.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
1141 fileMap.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
1142 print "saved in %s" % outMapFileName |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
1143 |