Get fasta sequence protein with idfecth, ERROR: Output
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?
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Pierre Lindenbaum
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Buffo
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$ echo -e "P50395\nP15924\nQ86YZ3\nP60842" | while read F; do curl "http://www.uniprot.org/uniprot/${F}.fasta" ; done
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works for me! Probably you have some hidden non-printable characters in the my_list.txt file. Try with other manually created list
This is manually created :(, and still not working.
try different version of idfetch then!
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.
Happy that it got resolved :)