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pythonfasta

Issue with invalid syntax error in python 2.7.3

I am trying to run a script (see below) to read in a fasta file and output a taxonomy file (printing only the sequence header without the '>' character) but I keep getting a syntax error which I have not been able to resolve. As a result the script creates the cleanseqs.tax file but the file is blank. Could anyone help?

Thank you!

>>> Fasta = open("testseqs.fasta", "r")
>>> Tax = open("cleanseqs.tax", "w")
>>> while 1:
...     SequenceHeader= Fasta.readline()
...     Sequence= Fasta.readline()
...     if SequenceHeader == '':
...             break
...     Tax.write(SequenceHeader.replace('>', ''))
... Fasta.close()
  File "<stdin>", line 7
    Fasta.close()
        ^
SyntaxError: invalid syntax
>>> Tax.close()
Solution

  • A file object is a context manager, so you can use the with statement to automatically close the files:

    with open("testseqs.fasta", "r") as fasta, open("cleanseqs.tax", "w") as tax:
    while True:
        ...