How to get RID from blast rest api url using php

Question

[muraliniceguy97]

Iam working on blast api. I created program to get RID I don't know how to get that RID. Here another problem in NCBI blast common url documentation Format_type available for CMD=Put also but url not return the xml format. Here is the code.

https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Put&QUERY=SSWWAHVEMGPPDPILGVTEAYKRDTNSKK&PROGRAM=blastp&FILTER=L&DATABASE=nr&FORMAT_TYPE=XML";
$nblast = new BlastAPI();
$nblast->blastdata($url);

Answer 1

[Pierre Lindenbaum]

I don't know how to get that RID

you have to "grep" the RID in the BLAST output:

curl -sL "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Put&QUERY=SSWWAHVEMGPPDPILGVTEAYKRDTNSKK&PROGRAM=blastp&FILTER=L&DATABASE=nr&FORMAT_TYPE=XML" | grep "RID = "
    RID = AGRY2BNM015

and reuse it to ping the blast server until you get the final XML.

[muraliniceguy97]

your solutions is worked in command line php environment but i need web environment solution. I used file_get_content method for retrive url content it gives output like this. http://prnt.sc/eac1cf

[Pierre Lindenbaum]

so , you are able to retrieve the RID. What's you're problem ?

[muraliniceguy97]

I want to display rid. Here my problem is FORMAT_TYPE=XML not working it only showing default html. I have checked in this url: "https://ncbi.github.io/blast-cloud/dev/api.html" we can use format_type xml in cmd=put. I need xml out put.

[Freek]

I have the same issue, did you solve it? The response is always one long line of html. I want json which should be a valid FORMAT_TYPE yet I always get the same type of response back.

[cmdcolin]

From what I can tell, NCBI ignores FORMAT_TYPE for the initial query to BLAST. it only respects it in the second stage of returning the results