view smart_toolShed/commons/core/parsing/test/Test_FastaParser.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

from commons.core.parsing.FastaParser import FastaParser
from SMART.Java.Python.structure.Sequence import Sequence
import unittest

class Test_FastaParser(unittest.TestCase):

    def test_getSubsequence(self):
        fastaFile = "myFastaInput.fasta"
        self._writeInputFastaFile(fastaFile)
        parser = FastaParser(fastaFile)
        chromosome = "1"
        expSeq = Sequence("1:1-20 (1)", "CCTAAGCCATTGCTTGGTGA")
        obsSeq = parser.getSubSequence(chromosome, 1, 20, 1)
        self.assertEquals(expSeq, obsSeq)

    def test_getSubsequence_long_sequence(self):
        fastaFile = "myFastaInput.fasta"
        self._writeInputFastaFile(fastaFile)
        parser = FastaParser(fastaFile)
        chromosome = "2"
        expSeq = Sequence("subsequence", "TGAAGA")
        obsSeq = parser.getSubSequence(chromosome, 55, 60, 1, "subsequence")
        self.assertEquals(expSeq, obsSeq)

    def test_getSubsequence_long_sequence_inside_and_outside(self):
        fastaFile = "myFastaInput.fasta"
        self._writeInputFastaFile(fastaFile)
        parser = FastaParser(fastaFile)
        chromosome = "2"
        expSeq = Sequence("subsequence", "TTA")
        obsSeq = parser.getSubSequence(chromosome, 137, 151, 1, "subsequence")
        self.assertEquals(expSeq, obsSeq)

    def test_getSubsequence_long_sequence_last_letter(self):
        fastaFile = "myFastaInput.fasta"
        self._writeInputFastaFile(fastaFile)
        parser = FastaParser(fastaFile)
        chromosome = "2"
        expSeq = Sequence("subsequence", "A")
        obsSeq = parser.getSubSequence(chromosome, 139, 151, 1, "subsequence")
        self.assertEquals(expSeq, obsSeq)

    def test_getSubsequence_long_sequence_totally_outside(self):
        fastaFile = "myFastaInput.fasta"
        self._writeInputFastaFile(fastaFile)
        parser = FastaParser(fastaFile)
        chromosome = "2"
        isSysExit = False
        try:
            parser.getSubSequence(chromosome, 140, 151, 1, "subsequence")
        except:
            isSysExit = True
        self.assertTrue(isSysExit)
        
    def test_setTags(self):
        fastaFile = "myFastaInput.fasta"
        self._writeInputFastaFile(fastaFile)
        parser = FastaParser(fastaFile)
        parser.setTags()
        expTags = {"1" : 0,
                   "2" : 54}
        obsTags = parser.getTags()
        self.assertEquals(expTags, obsTags)
        
    def _writeInputFastaFile(self, fastaFile):
        myHandler = open(fastaFile, 'w')
        myHandler.write(">1\n")
        myHandler.write("CCTAAGCCATTGCTTGGTGATTATGAAGGCAGTAGTCAAACCTCCACAAT\n")
        myHandler.write(">2\n")
        myHandler.write("TATGAGATCAACAGGGGCTTTGCTAGCCTGAGGGCGATTGGTCAAGGCCG\n")
        myHandler.write("GACCTGAAGAAATTCCTGATTGTACGTTCTGGTTACTCTTCAATTTGGGC\n")
        myHandler.write("TGCTTAATTATCTCCTCAATTTCAATTTGGCCATGCTTA\n")

if __name__ == "__main__":
    unittest.main()