I have a fasta file formatted as follows:
>UPF0471 protein C1orf63 homolog
some sequence
>WD repeat-containing protein 43
some sequence
>transmembrane protein 41A
some sequence
When I print out record.id or make dictionaries, biopython cannot handle the spaces in the sequence names. What should I do to let biopython recognize the name as whole rather than just taking the first word of the name?
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3 answers
You can get the whole header by using record.description
Answering your second question, how to make a dictionary using SeqIO.to_dict with the full descriptions with spaces as keys - you would need to use the key_function as help(to_dict) tries to explain, e.g.
my_dict = to_dict(sequences, key_function=lambda rec: rec.description)
Then how do I make dictionaries with SeqIO.to_dict?
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Replace the spaces with "_" or "-"?
You'll find most tools will take the same attitude to spaces and FASTA identifiers, so good idea!