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Old 02-24-2016, 05:13 PM   #1
bfp7
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Location: NH

Join Date: Nov 2015
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Default how to edit header in a fast file with python

I am looking to edit the header of a fast file using python. I am converting the DNA sequence to an amino acid sequence and I need to add "-aa" where the first space in the header is located.

The header looks like this:
>ANIS1000.x1 ET TIME...

It needs to look like this:
>ANIS1000.x1-aa ET TIME...

I can locate the index of the space using this:
locate = dnaHeader.find(' ')

But then I cannot insert the '-aa' using the insert function:
dnaHeader = dnaHeader.insert(locate, ' ')

The error says 'str' object does not support item assignment.

Thanks!
Brian
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Old 02-25-2016, 02:49 AM   #2
dariober
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Default

You could use:

Code:
newHeader= dnaHeader[0:locate] + '-aa' + dnaHeader[locate:]
Maybe it's not the most efficient strategy since you need to create a new string but unless your file is massive it should be good enough.

.insert() is a method for lists not for strings, which are immutable.
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