genomejs / dna2json Goto Github PK

I had to manually install JSONStream, to complete the conversion instructions in the README. should move the dependency declaration outside of only development.

From what I can see in the demo genomes, all vendors provide as chromosomal location, is there any reason why this isn't included a a property in the SNP-JSON.

Is there a demo genome out there that can be used to test with the library? I think this would be super helpful to people trying to get test out this project.

Preferably a demo genome from each of the services listed in the readme (23andMe, ancestryDNA, FamilyTree).

Hi genomejs, hi @contra

I am one of the dudes of BioJS.
Basically we try to write reusable JavaScript for life sciences with a special focus on visualization - so I do think that some of our goals overlap and that both of us could profit beneficial from each other. Here is a raw list of ideas that come to mind just after discovering your project:

• Use existing visualizations <-> or share yours with the community
• List your parsers on the BioJS registry (we have built a registry where people can share and discover bio* related components)
• Work on an easy-to-embed genome browser
• Or maybe you have even an amazing idea for a GSoC project.

I do believe there are more even ways to work together - so we are very open for your ideas :)

Cheers,
Seb

Other BioJS dudes that are interested and would be happy to help include at least @daviddao, @manuelcorpas, @selewis, @nathundunn, @ljgarcia, @saketc.

I tried to parse my genome from the text file downloaded from 23andMe. It appears to get stuck while parsing the SNPs. I let the script run for 3 hours and it appeared to be stuck on "Parsed 960613 SNPs".

Is there an error log or debug feature that I can use to find out what is happening? The example listed in the readme says "This will take awhile..." What is the average time it takes to parse a genome?

Some other information that may be useful:
genome file downloaded from 23andMe is 24 MB
After stopping the data2json process after 3 hours, the json file was 34 MB.

Thanks for any help you can provide

Please excuse my ignorance, if this question is ill-informed.

I have a sample TXT file from AncestryDNA. Unlike the other two vendors, it looks like they list the two alleles for each rs# in separate columns. As a result, my JSON file only contains one allele per rs#. The result looks like this:

"rs4477212": { "chromosome": 1, "genotype": "T" }, "rs3131972": { "chromosome": 1, "genotype": "A" }, "rs12562034": { "chromosome": 1, "genotype": "G" }

Is this an error on my part, or a limitation with AncestryDNA's TXT file formatting?

Thanks!

Specs are at http://samtools.sourceforge.net/

Hey, do you have any interest in adding a parser for Genes for Good? It's a group at University of Michigan that offers free genotyping.

They provide users with text files formatted in the same manner as 23andMe. Because of that, it should be pretty straightforward to create a new parser based on the one already written for 23andMe. If you are interested, I could test it out with some Genes for Good TXT files I have from a friend.

Where I can find a guide/tutorial/reference to write useful GQLs queries for genosets?

I'm still learning and re-learning all this sequencing stuff, so this may or may not be an issue. Has orientation been considered for the three vendors listed in the readme? I've read that 23andMe reports genotype information based on the plus strand of GRCh37, while some other companies use the minus strand (I'm not sure what FamilyTree and AncestryDNA use). If that's the case, this would need to be accounted for, since use of the opposite strand would require that all A/T, and all G/C nucleobases be 'flipped' for queries to be accurate. (This is discussed more on SNPedia.)

Is this already known and accounted for? Thanks!

Thanks for the incredible work on this library. Also, thanks for the great usage documentation. I'm new to coding, and was able to quickly get this working in both CLI and a node app.

Quick question. I saw one example on a blog where someone had implemented dna2json with JSONStream, like so:

var dna = require('dna2json');
var JSONStream = require('JSONStream');
var fs = require('fs');

fs.createReadStream("./data/23andme-male.txt")
.pipe(dna.createParser())
.pipe(JSONStream.stringify())
.pipe(fs.createWriteStream("./data/23andme-male.json"));

Is this necessary? What are the pros/cons?

does this library support the fastq format:

https://en.wikipedia.org/wiki/FASTQ_format

23andMe indicates deletions with D. Other groups use other standards.

genomejs/gql#4 (comment)
genomejs/gql#4 (comment)