Entering edit mode
2.5 years ago
Nelo
▴
20
AF131201
AF326487
AF326488
AF326489
AF326490
This are the some the accession number of protein. Firstly i dont know what kind of accession number is this. beacuse usually protein accession number start with XP_/NP_. Problem arise when i try the following command using the accession number given above:
- esearch -db protein -query "AF131201" | efetch -format fasta > output.fasta
- esearch -db nuccore -query "AF131201" | elink -target protein | efetch -db protein -format fasta
- Or directly submitting a bunch of accession number file to Entrez batch.
But i got nothing. Reason for the error is very sure due to the accession number i used. Can somebody help a way to solve this.
Thanks
Thank you so much for the help.
But some times the following text are also displayed on the terminal whenever i used the said command.
1) Can't locate Time/HiRes.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .). BEGIN failed--compilation aborted.
Is it necessary to download this Time-hiRes module ?
2) Unable to locate transmute executable. Please execute the following:
nquire -dwn ftp.ncbi.nlm.nih.gov entrez/entrezdirect transmute.Linux.gz gunzip -f transmute.Linux.gz chmod +x transmute.Linux
3) <PhraseNotFound>ABK60194[ACCN]</PhraseNotFound>
I am new to this kind of work. Don't know what I am asking exactly.
Not sure how you installed Entrezdirect but it does not seem to be installed properly.
It may be simplest to use
conda
to install. Seeconda
part of this tutorial: Creating workflows with snakemake and condaconda create -n edirect entrez-direct
.okie! I will try this
Do i have to sign in to NCBI API key ? If so why, is it necessary?
Tnq so much
If you are planning to do number of queries then you should. See this: https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
Okay
Thank you for responding