Hi, I ( a biologist and a newcomer to informatics) need help. Really trying hard to learn biopython, but that's another story.
In my folder I have a downloaded java script and a lot of fasta-to-text converted files.
Fasta had to be manually converted to text files individually , but no complaint there.
I run java script in a way;
java -jar ABC.local.jar xaa.txt Out.txt
"java -jar ABC.local.jar" is the command I am supposed to write(copy$paste) in the terminal.
xaa.txt is the input text file converted from fasta.
Out.txt (I name it) is the result file of xaa.txt that was processed through java -jar ABC.local.jar.
It runs beautifully, and I check every 10 minutes and surely get the results I want.
There is a quite number of input file (xaa.txt, xab.txt, xac.txt......), all generating corresponding xaa.txt Out.txt, xab.txt Out.txt, xac.txt Out.txt...result files by the afore-mentioned script.
I assume there would be a way for this process (javascript run) to repeat by itself until all the input files are processed, but it is beyond me.
Or is there? May I ask someone to suggest one?
I know critiques, such as "why haven't you tried at all? etc". I am just not at that stage. Thanks
Fasta format files are plain text. So what is
fasta-to-text
? Multi-fasta (multiple seq in one file) to one sequence per file fasta?On a bit of a tangent: take the plunge into BioPython sooner rather than later would be my advice ;)
Java is not the most widely used language in bioinformatics really.
There's a lot of boilerplate BioPython code out there these days that should require very little tweaking but just enough for you to learn.
Thanks for the tip !
java != java "script"