Get fasta sequence protein with idfecth, ERROR: Output

Question

[Buffo]

I have a list of accession numbers in txt file, like this:

P50395 
P15924 
Q86YZ3 
P60842

And I want to get a fasta file with all fasta sequences, I have done it before with idfecth but this time something goes wrong, and I can´t find a solution, my line:

idfetch -G my_list.txt -t 5

Result:

Invalid value(s) [13] in VisibleString [P50395# ...]
[idfetch] ERROR: Output

Any suggestions?

[Santosh Anand]

works for me! Probably you have some hidden non-printable characters in the my_list.txt file. Try with other manually created list

[Buffo]

This is manually created :(, and still not working.

[Santosh Anand]

try different version of idfetch then!

[Buffo]

Even when it was a manually created text list (with a python parser script), indeed it had a non-printable characters that idfetch cannot translate. That was the error.

[Santosh Anand]

Happy that it got resolved :)

Answer 1

[Pierre Lindenbaum]

$ echo -e "P50395\nP15924\nQ86YZ3\nP60842" | while read F; do curl "http://www.uniprot.org/uniprot/${F}.fasta" ; done

[Buffo]

Thanks pierre, but my list have more than 300 access numbers.