startswith TypeError in function

Question

Here is the code:

    def readFasta(filename):         """ Reads a sequence in Fasta format """         fp = open(filename, 'rb')         header = ""         seq = ""         while True:             line = fp.readline()             if (line == ""):                 break             if (line.startswith('>')):                 header = line[1:].strip()             else:                 seq = fp.read().replace('\n','')                 seq = seq.replace('\r','')          # for windows                 break         fp.close()         return (header, seq)      FASTAsequence = readFasta("MusChr01.fa") 

The error I'm getting is:

TypeError: startswith first arg must be bytes or a tuple of bytes, not str 

But the first argument to startswith is supposed to be a string according to the docs... so what is going on?

I'm assuming I'm using at least Python 3 since I'm using the latest version of LiClipse.

Answer 1

It's because you're opening the file in bytes mode, and so you're calling bytes.startswith() and not str.startswith().

You need to do line.startswith(b'>'), which will make '>' a bytes literal.