nuin / beginning-python-for-bioinformatics

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beginning-python-for-bioinformatics / scripts / motifs / fasta.py
100644 48 lines (40 sloc) 1.077 kb
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#! /usr/bin/env python
 
class Fasta:
    def __init__(self, name, sequence):
        self.name = name
        self.sequence = sequence
 
def read_fasta(file):
    items = []
    index = 0
    for line in file:
        if line.startswith(">"):
           if index >= 1:
               items.append(aninstance)
           index+=1
           name = line.strip()
           seq = ''
           aninstance = Fasta(name, seq)
        else:
           seq += line.strip()
           aninstance = Fasta(name, seq)
 
    items.append(aninstance)
    return items
 
def read_seqs(file):
    items = []
    seq = ''
    index = 0
    for line in file:
        if line.startswith(">"):
            if index >= 1:
                items.append(seq)
                seq = ''
            index += 1
        else:
            seq += line[:-1]
 
    items.append(seq)
    return items
 
def format_output(sequence, length):
    temp = []
    for j in range(0,len(sequence),length):
        temp.append(sequence[j:j+length])
    return '\n'.join(temp)