ERROR message "can't read /var/mail/Bio" running the Cleanup the genome sequences step from the Tutorial IV: Identifying UCE Loci and Designing Baits To Target Them

[Ruben9161]

Dear Brant,

I'm starting to run "Tutorial IV: Identifying UCE Loci and Designing Baits To Target Them", but I got stuck in the very first steps. Specifically in step of "Cleanup the genome sequences", right after downloading and unziping the genomes.

I used the function:

from Bio import SeqIO with open("Name_of_Genome_File.fna", "rU") as infile: with open("outfileName.fasta", "w") as outf: for seq in SeqIO.parse(infile, 'fasta'): seq.name = "" seq.description = "" outf.write(seq.format('fasta'))

But it didn't work. So, I am wondering if I have to load any dependecies so the BIO - SeqIO can work. I don´t have much experience about programming and functions, so I don't know how to procede.

The error message is as follows (with the actual names of the files): (phyluce-1.7.1) Alejandros-iMac:uce-coleoptera alejandro$ from Bio import SeqIO from: can't read /var/mail/Bio (phyluce-1.7.1) Alejandros-iMac:uce-coleoptera alejandro$ (phyluce-1.7.1) Alejandros-iMac:uce-coleoptera alejandro$ with open("GCA_000390285.1_Agla_1.0_genomic.fna", "rU") as infile: -bash: syntax error near unexpected token (phyluce-1.7.1) Alejandros-iMac:uce-coleoptera alejandro$ with open("anoGla1.fasta", "w") as outf: -bash: syntax error near unexpected token (phyluce-1.7.1) Alejandros-iMac:uce-coleoptera alejandro$ for seq in SeqIO.parse(infile, 'fasta'): -bash: syntax error near unexpected token (phyluce-1.7.1) Alejandros-iMac:uce-coleoptera alejandro$ seq.name = "" -bash: seq.name: command not found (phyluce-1.7.1) Alejandros-iMac:uce-coleoptera alejandro$ seq.description = "" -bash: seq.description: command not found (phyluce-1.7.1) Alejandros-iMac:uce-coleoptera alejandro$ outf.write(seq.format('fasta')) -bash: syntax error near unexpected token `seq.format'

As you can see in the message above, each line of the function is treated as a separate command line. As I said before, I don't have much of experience so I don't know how to proceed, nor what I am doing wrong, or what should I do next.

The phyluce version is 1.7.1, does the tutorial works properly with this version, or it is better if I upgrade to the lattest version?

Thanks for your help, Rubén.

[brantfaircloth]

It looks like you are trying to run this without starting the Python interpreter, first (e.g. type "python" at the command line, and the python interpreter will start).

[Ruben9161]

Thanks, that was the problem!!!!