fastaReader.py

'''
Author: David L. Bernick
Edited by: Jairo Navarro

The MIT License (MIT)

Copyright (c) 2015 David L. Bernick, Jairo Navarro
'''

import sys
class FastAreader :
    '''
    Class to provide reading of a file containing one or more FASTA
    formatted sequences:
    object instantiation:
    FastAreader(<file name>):
 
    object attributes:
    fname: the initial file name
 
    methods:
    readFasta() : returns header and sequence as strings.
    Author: David Bernick
    Date: April 19, 2013
    '''
    
    def __init__ (self, fname=''):
        '''contructor: saves attribute fname '''
        
        self.fname = fname
            
    def doOpen (self):
        if self.fname is '':
            return sys.stdin
        else:
            return open(self.fname)
 
    def readFasta (self):
        '''
        using filename given in init, returns each included FastA record
        as 2 strings - header and sequence. If filename was not provided,
        stdin is used. Whitespace is removed, and sequence is upcased.
        The initial '>' is removed from the header.
        '''
        header = ''
        sequence = ''
        
        with self.doOpen() as fileH:
            # initialize return containers
            header = ''
            sequence = ''
 
            # skip to first fasta header
            line = fileH.readline()
            while not line.startswith('>') :
                line = fileH.readline()
            header = line[1:].rstrip()
 
            # header is saved, get the rest of the sequence
            # up until the next header is found
            # then yield the results and wait for the next call.
            # next call will resume at the yield point
            # which is where we have the next header
            for line in fileH:
                if line.startswith ('>'):
                    yield header,sequence
                    header = line[1:].rstrip()
                    sequence = ''
                else :
                    sequence += ''.join(line.rstrip().split()).upper()
        # final header and sequence will be seen with an end of file
        # with clause will terminate, so we do the final yield of the data
        yield header,sequence