fasta-parser is a "Buffer Stream parser from FASTA to JSON.", which means it's just a Node.JS Stream that takes an input Streamed Buffer containing data in fasta format and Streams out Buffer containing JSON. There should be no major speed issue since it doesn't not serialise anything to object. You can think of fasta-parser as just the parsing algorithm (and maybe we can even improve it for speed).
bionode-fasta is a bionode module that uses fasta-parser as a dependency and does a lot more, to follow the bionode standards and be more user friendly (i.e. read fasta files, provide a command line interface, etc)
bionode-fasta only serialises the data to JSON if you use it in Object mode (i.e., fasta.obj(), please see https://github.com/bionode/bionode-fasta#usage)
If you find any issue or have more questions, please let us know here or on GitHub :)
Do you happen to know about how big
fasta-parser is off the top of your head?
Hi Hitesh, the most documented modules of bionode are https://github.com/bionode/bionode-fasta, https://github.com/bionode/bionode-seq, https://github.com/bionode/bionode-ncbi
Nowadays our main focus of development is focused in bionode-watermill (https://github.com/bionode/bionode-watermill). We are starting to have more documentation but since it is something that me and @thejmazz are working on a daily basis some things might get difficult to understand. We are currently working on the somewhat stable
dev branch. However, bionode-watermill might be hard for beginners, but if you want to give it a try... we are here to help.
Then, there are a lot of other modules still in draft or under-documented (https://github.com/bionode) that are simple and you can also have a look at. For instance, bionode-fastq (https://github.com/bionode/bionode-fastq), I have made a branch for it but I would like that someone else gives it a look and it still needs a CLI (https://github.com/bionode/bionode-fastq/tree/Refactoring).
You can have a look at the issues of each bionode module and see if you can start with some of those issues. Otherwise, you may test some of the documented modules and start playing around to see if something can be improved.
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1770-1 NGS pipelines made with Nextflow
cli- command line interface or anything else
Otherwise it can return a function with callback, promise, or node stream (though I think the code that checks for this is WIP - and probably we should add an option to
task for user to declare what their operationCreator returns)
So basically anything you can run from terminal
One cool thing to do would be to use ES6 template literals to do something like
const { task, python } = require('bionode-watermill')
const mytask = task({
input: '*.txt',
output: '*.foo',
name: 'My task'
}, ({ input }) => python`
with open('output.foo') as output:
with open('${input}') as input:
for line in input:
output.write(line.upper())
`)
// where `python` returns something like
// { language: 'python', executer: '/usr/bin/env python3', code }
// watermill writes the script, marks it executable, stores it in task dirthen it would be frictionless to experiment with quick scripts in a bunch of languages, write small simple scripts for visualization with R, etc. using ${variable in source code for a script is kinda sketchy but maybe OK for quick experimentaion. Nextflow has something similar for scripts in any language (you just put #!/usr/bin/env python3 at top)
OR maybe that program should go under a prop of the task, so it is called as a CLI like usual
(excuse my python im not sure if its correct)
the
operationCreator is the second paramater passed to task, the first is the object props
and I'm thinking I will give a small presentation on bionode-ncbi telling other guys how to use it
My professors are loving this library
Thanks for using it! Would love to see those slides and know more about how you are using bionode-ncbi in your work
Does anyone have data flow diagram of bionode-ncbi because I have to show how this library actually works
But
bionode-ncbi download sra PRJNA183192 repeats the first SRA file, SRR629557.sra until infinity
also,
bionode-ncbi download is very verbose by default (to pipe into other tools)
you can try
bionode-ncbi download sra --pretty PRJNA183192 to display a progress bar instead
or if you don't have
jq installed: bionode-ncbi urls sra PRJNA183192 | sed 's|.*url":"\(.*\)","uid.*|\1|' | xargs wget
bionode-watermill