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1 from commons.core.utils.FileUtils import FileUtils
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2 from commons.core.seq.BioseqUtils import BioseqUtils
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3
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4 class TranslateInAllFramesAndReplaceStopByX(object):
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5
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6 def __init__(self):
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7 self._inputFile = ""
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8 self._outputFile = ""
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9
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10 def setInputFile(self, input):
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11 self._inputFile = input
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12
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13 def setOutputFile(self, output):
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14 self._outputFile = output
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15
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16 def run(self):
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17 """
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18 read a fasta file with nucleotide sequences and translate all sequences in all frames, write the result in a file
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19 """
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20 if not FileUtils.isRessourceExists(self._inputFile):
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21 raise Exception("Warning your input file %s does not exist!\n" % self._inputFile)
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22 bioseqList = BioseqUtils.extractBioseqListFromFastaFile(self._inputFile)
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23 bioseqListInAllFrames = BioseqUtils.translateBioseqListInAllFrames(bioseqList)
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24 bioseqListTranslatedAndStopsReplace = BioseqUtils.replaceStopCodonsByXInBioseqList(bioseqListInAllFrames)
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25 BioseqUtils.writeBioseqListIntoFastaFile(bioseqListTranslatedAndStopsReplace, self._outputFile)
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26 |
