These are chat archives for bio4j/bio4j

29th
Nov 2015
Fadel
@FadelBerakdar
Nov 29 2015 04:08
Is there any python API for Bio4j ? if not how much java should I know before i start a simple bio4j project ?
Fadel
@FadelBerakdar
Nov 29 2015 04:23
btw Im undergraduate student and I chose a topic related to Bio4j to do my final year project :D
sounds crazy but yeah I will do it :D
Alexey Alekhin
@laughedelic
Nov 29 2015 13:30

@FadelBerakdar hi!
There is no Python API for Bio4j. But I believe, that you don't really need any Java knowledge to start with Bio4j :wink:
The current version uses TitanDB v0.5.4 as a backend (see bio4j-titan repo). So you can interact with the database in a number of ways:

  • through the Bio4j Java API :sparkles:
  • through the raw TitanDB Java API
  • through the Tinkerpop/Gremlin API, for which, I think, there are various implementations including Python (probably this?).

Anyway, it may be good for starting with it, but if you are really going to do something serious with Bio4j, it's worth using the Bio4j Java API (we are also working on a Scala version), because it let's you to take advantage of the quite complex schema of the database :+1:

Fadel
@FadelBerakdar
Nov 29 2015 14:39
thanks @laughedelic,
I still have some simple questions if u don't mind :)
Fadel
@FadelBerakdar
Nov 29 2015 14:55
like
I couldn't find RefSeq module in bio4j-lite nor bio4j-full !
500 GB is the size of bio4j-lite.tar or Bio4j-lite ? sorry if u found my questions quite naive, I'm just trying to figure out how much exactly the AWS will cost me :'(
Alexey Alekhin
@laughedelic
Nov 29 2015 21:45
@FadelBerakdar, I think about AWS is better to ask @eparejatobes