/sci/ - Science & Math

[Anonymous No.11337240]

>Like using InterProScan
>Decide to include it in an automated pipeline
>Download the program
>~10GB
>mfw

Is there a way to use a webpage from the command line?
That would make things a lot easier.

[Anonymous No.11337264]

>>11337240
Maybe, usually yes.

>How
Depends on the site

[Anonymous No.11337428]

>>11337240
These bioinformatics sites often have web APIs so that you can access them programmatically. Been a long time since I used them in a pipeline and I haven't used interproscan like that but maybe these will help? (https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/Job+Dispatcher+Sequence+Analysis+Tools+Home, https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/InterProScan+5+Help+and+Documentation)) The second link is accessible through one of the links in the first one if you scroll down, and they have instruction videos on how to integrate the programs.

But the web services of such sites have a queue system and limit how much you can use. You will have to send sequence batches in a file instead of single sequences, and even then you're gonna have to wait until the batch is done before you send another. If you're looking to do heavy duty analysis (i.e. whole proteome) then you should probably use the downloaded version.

[Anonymous No.11337433]

>>11337240
nigga 10 gigs in 2020 is nothing

you can get a fucking 100 gig usb stick for 20 bucks ffs

[Anonymous No.11337586]

Ah, thank you so much!