Python Fasta.gen_header_sequence_pairs 예제들

예제 #1

파일: 20120405a.py 프로젝트: BIGtigr/xgcode

def make_xml(start_pos, stop_pos, nsamples):
    """
    @return: location of xml file, location of log file
    """
    out = StringIO()
    print >> out, g_xml_pre_alignment
    print >> out, """
        <!-- The sequence alignment (each sequence refers to a taxon above). -->
        <alignment id="alignment" dataType="nucleotide">
    """
    lines = g_fasta_string.splitlines()
    for header, seq in Fasta.gen_header_sequence_pairs(lines):
        print >> out, '<sequence>'
        print >> out, '<taxon idref="%s"/>' % header
        print >> out, seq
        print >> out, '</sequence>'
    print >> out, '</alignment>'
    print >> out, """
        <patterns id="firsthalf.patterns" from="%d" to="%d">
            <alignment idref="alignment"/>
        </patterns>
    """ % (start_pos, stop_pos)
    print >> out, get_xml_post_alignment(nsamples)
    log_loc = Util.get_tmp_filename(prefix='beast', suffix='.log')
    print >> out, get_log_xml(log_loc)
    xml_loc = Util.create_tmp_file(out.getvalue(),
                                   prefix='beast',
                                   suffix='.xml')
    return xml_loc, log_loc

예제 #2

파일: 20120405a.py 프로젝트: argriffing/xgcode

def make_xml(start_pos, stop_pos, nsamples):
    """
    @return: location of xml file, location of log file
    """
    out = StringIO()
    print >> out, g_xml_pre_alignment
    print >> out, """
        <!-- The sequence alignment (each sequence refers to a taxon above). -->
        <alignment id="alignment" dataType="nucleotide">
    """
    lines = g_fasta_string.splitlines()
    for header, seq in Fasta.gen_header_sequence_pairs(lines):
        print >> out, '<sequence>'
        print >> out, '<taxon idref="%s"/>' % header
        print >> out, seq
        print >> out, '</sequence>'
    print >> out, '</alignment>'
    print >> out, """
        <patterns id="firsthalf.patterns" from="%d" to="%d">
            <alignment idref="alignment"/>
        </patterns>
    """ % (start_pos, stop_pos)
    print >> out, get_xml_post_alignment(nsamples)
    log_loc = Util.get_tmp_filename(prefix='beast', suffix='.log')
    print >> out, get_log_xml(log_loc)
    xml_loc = Util.create_tmp_file(
            out.getvalue(), prefix='beast', suffix='.xml')
    return xml_loc, log_loc

예제 #3

파일: 20080119b.py 프로젝트: argriffing/xgcode

def get_response_content(fs):
    out = StringIO()
    try:
        alignment = Fasta.Alignment(fs.fasta.splitlines())
        print >> out, 'This is a valid alignment.'
    except Fasta.AlignmentError as e:
        alignment = None
        print >> out, 'This is not a valid alignment:', e
    if alignment:
        try:
            old_column_count = len(alignment.columns)
            alignment.force_nucleotide()
            removed_column_count = old_column_count - len(alignment.columns)
            if removed_column_count:
                print >> out, ('After removing %d' % removed_column_count),
                print >> out, 'columns this is a valid nucleotide alignment.'
            else:
                print >> out, 'This is a valid nucleotide alignment.'
        except Fasta.AlignmentError as e:
            print >> out, 'This is not a valid nucleotide alignment:', e
    for header, seq in Fasta.gen_header_sequence_pairs(StringIO(fs.fasta)):
        print >> out, '%s: %d' % (header, len(seq))
    return out.getvalue()

예제 #4

파일: 20080119b.py 프로젝트: BIGtigr/xgcode

def get_response_content(fs):
    out = StringIO()
    try:
        alignment = Fasta.Alignment(fs.fasta.splitlines())
        print >> out, 'This is a valid alignment.'
    except Fasta.AlignmentError as e:
        alignment = None
        print >> out, 'This is not a valid alignment:', e
    if alignment:
        try:
            old_column_count = len(alignment.columns)
            alignment.force_nucleotide()
            removed_column_count = old_column_count - len(alignment.columns)
            if removed_column_count:
                print >> out, ('After removing %d' % removed_column_count),
                print >> out, 'columns this is a valid nucleotide alignment.'
            else:
                print >> out, 'This is a valid nucleotide alignment.'
        except Fasta.AlignmentError as e:
            print >> out, 'This is not a valid nucleotide alignment:', e
    for header, seq in Fasta.gen_header_sequence_pairs(StringIO(fs.fasta)):
        print >> out, '%s: %d' % (header, len(seq))
    return out.getvalue()

예제 #5

def get_header_seq_pairs():
    lines = g_fasta_string.splitlines()
    return list(Fasta.gen_header_sequence_pairs(lines))

예제 #6

파일: beasttut.py 프로젝트: argriffing/xgcode

def get_header_seq_pairs():
    lines = g_fasta_string.splitlines()
    return list(Fasta.gen_header_sequence_pairs(lines))