[Biopython] Issues parsing sequences

Markus Piotrowski Markus.Piotrowski at ruhr-uni-bochum.de
Sat Jan 13 19:22:37 UTC 2018

Dear Fernanda,

 From you description it seems that you run Python from a command line 
and then insert the code.
The '...' indicate an indented block. Your second line is a for loop 
that ends with a ':', so the following lines will be indented (they are 
the body of the for loop). You just have to hit 'ENTER' two times to 
make Python clear that you are ready to execute the code block.
The execution will probably fail, if you don't have the file 
"ls_orchid.fasta" in the same directory where you have started your 
Python session.

Best, Markus

Am 13.01.2018 um 18:55 schrieb Fernanda Trancoso:
> Hello guys,
> I'm trying to do the biopython tutorial and cookbook but i got stuck 
> on the "2.4.1 Simple FASTA parsing example". It says
> Now try this in Python:
> from Bio import SeqIO
> for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"):
>      print(seq_record.id <http://seq_record.id>)
>      print(repr(seq_record.seq))
>      print(len(seq_record))
> But from the second line forward the ">>>" turns into "..." and I have 
> no idea of what input is missing, since I did copy/paste to be sure 
> that i wasn't writing something wrong.
> Does anyone knows what might be going wrong?
> Thanks
> -- 
> Fernanda Fontes Trancoso
> Aluna de Graduação em Ciências Biológicas na UFMG
> Iniciação Científica no Laboratório de Sistemática de Insetos 
> <http://abelhasufmg.wix.com/lsea>
> +55 (31) 9156-6485
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython

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