Example #1
0
def _write_fasta( seq, linelength, hea ):

    output = ['>', seq.name]

    if hea and seq.hea:
        output.append( ' ' + seq.hea)

    output.append('\n')
    if linelength:
        output.append( wrap(seq.seq, linelength) )
    else:
        output.append( seq.seq + '\n')

    return ''.join(output)
Example #2
0
def _writeEMBLLine(key, val, linelength ):

    lmar = 5
    fstr = '%-' + `lmar` + 's%s'

    strList = []
    strLen =  linelength-lmar
    if not val.strip():
        strList.append( fstr %(key, ' ') )
    else:
        # word wrap val
        valLines = wrap(val, strLen, output='list')
        for line in valLines:
            strList.append( fstr %(key, line) )

    return os.linesep.join(strList)
Example #3
0
def print_align(q_al_str, t_al_str, width):

    for q,t in zip(wrap(q_al_str,width,'list'), wrap(t_al_str,width,'list')):
        print q
        print t
        print ''
Example #4
0
    def __repr__(self):
        """Special method to return string representation of the
        whole sequence object when `obj` or repr(obj) is called"""

        return """>%s%s\n%s""" % (self.name, self.hea, wrap(self.seq, 60))