Can Biopython Properly Import Fasta Headers With Spaces In Them?
When I use BioPython to create a sequence iterator, I find that any characters after the first space (" ") in the header are ignored. For instance:
If file.fasta is:
>A Header With Spaces
ATCGATCGATGC
The following code:
for sequence in SeqIO.parse(open("file.fasta"), "fasta"):
print sequence.id
Will print:
A
Is there a way to get the full sequence id while still taking advantage of BioPython's utility?
1 answer
sequence.description should give you the entire header
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Damian Kao
A good way of seeing what methods/properties are in a python object without looking up the API is to just use the dir() function. Try printing dir(sequence) and it should list all it's props/methods.
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The ID in FASTA is defined as everything that comes before the first space, so this behaviour is exactly right.