Mercurial > repos > yufei-luo > s_mart

comparison commons/pyRepetUnit/fastaTranslation/allFrames/TranslateInAllFramesAndReplaceStopByX.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 from commons.core.utils.FileUtils import FileUtils
2 from commons.core.seq.BioseqUtils import BioseqUtils
3
4 class TranslateInAllFramesAndReplaceStopByX(object):
5
6 def __init__(self):
7 self._inputFile = ""
8 self._outputFile = ""
9
10 def setInputFile(self, input):
11 self._inputFile = input
12
13 def setOutputFile(self, output):
14 self._outputFile = output
15
16 def run(self):
17 """
18 read a fasta file with nucleotide sequences and translate all sequences in all frames, write the result in a file
19 """
20 if not FileUtils.isRessourceExists(self._inputFile):
21 raise Exception("Warning your input file %s does not exist!\n" % self._inputFile)
22 bioseqList = BioseqUtils.extractBioseqListFromFastaFile(self._inputFile)
23 bioseqListInAllFrames = BioseqUtils.translateBioseqListInAllFrames(bioseqList)
24 bioseqListTranslatedAndStopsReplace = BioseqUtils.replaceStopCodonsByXInBioseqList(bioseqListInAllFrames)
25 BioseqUtils.writeBioseqListIntoFastaFile(bioseqListTranslatedAndStopsReplace, self._outputFile)
26