Can Biopython Properly Import Fasta Headers With Spaces In Them?

Question

[David M]

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?

[Michael Schubert]

The ID in FASTA is defined as everything that comes before the first space, so this behaviour is exactly right.

Answer 1

[Damian Kao]

sequence.description should give you the entire header

[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.

[David M]

That did it. I can't tell you how long I've been working around this quirk when there's such a simple solution. Thanks!