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src/b/i/biopython-1.63/Bio/SeqIO/_convert.py   biopython(Download)
    """
    #Map unexpected chars to null
    from Bio.SeqIO.QualityIO import phred_quality_from_solexa
    mapping = "".join([chr(0) for ascii in range(0, 59)]
                      + [chr(33 + int(round(phred_quality_from_solexa(q))))
    """
    #Map unexpected chars to null
    from Bio.SeqIO.QualityIO import phred_quality_from_solexa
    mapping = "".join([chr(0) for ascii in range(0, 59)]
                      + [chr(64 + int(round(phred_quality_from_solexa(q))))
def _fastq_solexa_convert_qual(in_handle, out_handle, alphabet=None):
    """Fast Solexa FASTQ to QUAL conversion (PRIVATE)."""
    from Bio.SeqIO.QualityIO import phred_quality_from_solexa
    mapping = dict((chr(q + 64), str(int(round(phred_quality_from_solexa(q)))))
                   for q in range(-5, 62 + 1))

src/b/i/biopython-HEAD/Bio/SeqIO/_convert.py   biopython(Download)
    """
    #Map unexpected chars to null
    from Bio.SeqIO.QualityIO import phred_quality_from_solexa
    mapping = "".join([chr(0) for ascii in range(0, 59)]
                      + [chr(33 + int(round(phred_quality_from_solexa(q))))
    """
    #Map unexpected chars to null
    from Bio.SeqIO.QualityIO import phred_quality_from_solexa
    mapping = "".join([chr(0) for ascii in range(0, 59)]
                      + [chr(64 + int(round(phred_quality_from_solexa(q))))
def _fastq_solexa_convert_qual(in_handle, out_handle, alphabet=None):
    """Fast Solexa FASTQ to QUAL conversion (PRIVATE)."""
    from Bio.SeqIO.QualityIO import phred_quality_from_solexa
    mapping = dict((chr(q + 64), str(int(round(phred_quality_from_solexa(q)))))
                   for q in range(-5, 62 + 1))

src/b/i/biopython-1.63/Tests/test_SeqIO_QualityIO.py   biopython(Download)
        #Mapping from Solexa to PHRED is lossy, but so is PHRED to Solexa.
        #Assume "old" is the original, and "new" has been converted.
        converted = [round(QualityIO.phred_quality_from_solexa(q))
                     for q in old.letter_annotations["solexa_quality"]]
        if truncate:
        seq = "N"*68
        qual = "".join(chr(64+q) for q in range(-5, 63))
        expected_phred = [round(QualityIO.phred_quality_from_solexa(q))
                          for q in range(-5, 63)]
        in_handle = StringIO("@Test\n%s\n+\n%s" % (seq, qual))

src/b/i/biopython-HEAD/Tests/test_SeqIO_QualityIO.py   biopython(Download)
        #Mapping from Solexa to PHRED is lossy, but so is PHRED to Solexa.
        #Assume "old" is the original, and "new" has been converted.
        converted = [round(QualityIO.phred_quality_from_solexa(q))
                     for q in old.letter_annotations["solexa_quality"]]
        if truncate:
        seq = "N"*68
        qual = "".join(chr(64+q) for q in range(-5, 63))
        expected_phred = [round(QualityIO.phred_quality_from_solexa(q))
                          for q in range(-5, 63)]
        in_handle = StringIO("@Test\n%s\n+\n%s" % (seq, qual))

src/b/i/biopython-HEAD/Tests/test_SeqIO_convert.py   biopython(Download)
        #Mapping from Solexa to PHRED is lossy, but so is PHRED to Solexa.
        #Assume "old" is the original, and "new" has been converted.
        converted = [round(QualityIO.phred_quality_from_solexa(q))
                     for q in old.letter_annotations["solexa_quality"]]
        if truncate:

src/b/i/biopython-1.63/Tests/test_SeqIO_convert.py   biopython(Download)
        #Mapping from Solexa to PHRED is lossy, but so is PHRED to Solexa.
        #Assume "old" is the original, and "new" has been converted.
        converted = [round(QualityIO.phred_quality_from_solexa(q))
                     for q in old.letter_annotations["solexa_quality"]]
        if truncate: