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15 votes
Accepted

Is there public RESTful api for Gnomad?

As far as I know, no but the vcf.gz files are behind a http server that supports Byte-Range, so you can use tabix or any related API: ...
Pierre's user avatar
  • 1,511
11 votes
Accepted

Library for computing BWT-based alignments

First, let us remark that there exist several hundred read mappers, most of which have been even published (see, e.g., pages 25-29 of this thesis). Developing a new mapper probably makes sense only as ...
Karel Břinda's user avatar
9 votes

Library for computing BWT-based alignments

BWA-MEM can be used as a library. File bwa/example.c shows the basic functionality for single-end mapping. It should give identical mapping to the bwa-mem command line. Header bwa/bwamem.h contains ...
user172818's user avatar
  • 6,525
7 votes

How do you query and explore ENCODE data?

I don't know whether there is an API, but ENCODE's website does provide an interactive data matrix where you can filter data based on assay and sample type, place data sets in a "shopping cart", and ...
Daniel Standage's user avatar
6 votes

Is there public RESTful api for Gnomad?

The new gnomAD site (as of August 2019) says no, no API yet: How do I query a batch of variants? Do you have an API? We currently do not have a way to submit batch queries on the browser, but ...
Jesse's user avatar
  • 947
5 votes

How do you query and explore ENCODE data?

You can just add /?format=json to any page to get the JSON output. ENCODE REST API documentation: https://www.encodeproject.org/help/rest-api/ Example scripts: ...
burger's user avatar
  • 2,169
5 votes
Accepted

Retrieve abstract/summary for NCBI bookshelf via Entrez

Entrez requires the unique identifiers(UID) for fetching related info. The id you are using in the query is RID. I guess that why you are getting ...
arup's user avatar
  • 604
5 votes

How can I find mutations associated with disease in human histone residues?

Ensembl contains this information: When you go to the “phenotype” menu item of a given gene, you will see a list of variants (potentially after clicking on “ALL associated variants”) with their ...
Konrad Rudolph's user avatar
4 votes

Is there public RESTful api for Gnomad?

You can browse gnomAD variants with ClinGen Allele Registry (there is API spec available).
user1690's user avatar
4 votes

Library for computing BWT-based alignments

SeqAn supports BWT tables for use with their parametrisable alignment algorithms. To use it, follow the general outline for building a SeqAn short-read aligner, and use the ...
Konrad Rudolph's user avatar
4 votes
Accepted

Getting species from ensembl sequence id

The lookup/id endpoint will get it for you. Of you can just look up the three letter species code, in this case MOD, on the list in the documentation.
Emily_Ensembl's user avatar
4 votes

Automating sequence download from Wormbase

Further inspecting the source code of the downloaded page, I found the following: ...
bli's user avatar
  • 3,130
3 votes
Accepted

Why is the UniProt REST API returning multiple results, when I am only providing one ID to be checked?

it is because you do a text search and the "word" Q9UJL9 appears in multiple entries. If you want an id search, specifically say so and for that the query syntax is ...
Jerven's user avatar
  • 166
3 votes

Retrieve abstract/summary for NCBI bookshelf via Entrez

As arupgsh says, you need to use esearch to get a list of unique identifiers before using efetch to retrieve info about each result. I think the easiest way to do this is to use Entrez Direct, which ...
heathobrien's user avatar
  • 1,816
3 votes

How can I find mutations associated with disease in human histone residues?

I found DisGeNET useful for my purpose, a database that associates genes with diseases and, if known, gene variants with diseases. It integrates several sources of information for computing a score of ...
plat's user avatar
  • 1,032
3 votes

What methods should I use from PythonCyc API to query metabolites in BioCyc database?

Pathway-tools has a unique identifier (called a Frame-ID) for each metabolite in its database. You can get the list of all compounds with this api call: ...
Djinnome's user avatar
3 votes

What methods should I use from PythonCyc API to query metabolites in BioCyc database?

UPD: As suggested by Llopis, maybe the correct identifier is VAL? I think there is no metabolite with such name in the database. I tried their search, the correct name seems to be ...
Iakov Davydov's user avatar
3 votes
Accepted

How to map PDB chains to Uniprot IDs using API services

I found the answer and I thought it may be useful for others. we can use pypdb package for that purpose (it works in unix systems): ...
Sara's user avatar
  • 777
2 votes

Is there public RESTful api for Gnomad?

I found Jesse's code quite usefull ! For those who try to reproduce it, you should now add the reference genome ID, such as : ...
BretSnoop's user avatar
2 votes

Is there public RESTful api for Gnomad?

I faced same issue recently, I found those link and python script: gnomAD GraphQL api https://gnomad.broadinstitute.org/api It works great but it is a kind of different query language. Please check ...
John t_eckerd's user avatar
2 votes

How to map PDB chains to Uniprot IDs using API services

An alternative solution involves the use of the SIFTS resource from the EBI. I wrote a python parser for their xml format, which will give you a mapping between a pdb and a uniprot entry at the single ...
mgalardini's user avatar
2 votes

How to map PDB chains to Uniprot IDs using API services

While not as nice as using SIFT. You can use the uniprot sparql endpoint as well to get mappings. ...
Jerven's user avatar
  • 166
2 votes

Error while performing "lift-over" of genomic coordinates between two species using Ensembl Compara API

While I wouldn't consider this as the best answer or solution - I decided to use Ensembl REST api to extract the coordinates of alignment blocks. The quick fix - in python looks like this: ...
Siddharth's user avatar
  • 345
2 votes

How do you query and explore ENCODE data?

So let's say I want to get the bed file of this experiment using curl encodeproject.org/experiments/ENCSR000CKC You can also search for files that belong to a ...
ksgraham's user avatar
2 votes
Accepted

RCSB API: limited returned result

Staff from rcsb kindly reminds me the solution - add the following lines in the json query. "request_options": { "return_all_hits": true }
Simon's user avatar
  • 195
2 votes

e-utils api: get chromosome position for each snp on a gene

If your dataset is limited to human SNPs, and you know the list of SNPs, I would advise taking a look at the dedicated NCBI Variation Services. This would be one request for each SNP, but if you fire ...
Brad Holmes's user avatar
2 votes

How to run python request for list of url's with multiple page numbers?

@Megha The requestIt(link) function returns a list of dictionary objects. So your "data" variable is a list of dictionary objects. Every item on this list (a dict) has a key named "...
punxx's user avatar
  • 21
2 votes
Accepted

Remote NCBI's Blast Perl API: maximising hits returned via command line

While I haven't used your exact method above, using the BLAST command line tools return the desired number of target sequences ...
Scot's user avatar
  • 782
1 vote

How to extract all peptide sequences for a UniProt protein entry with an API?

If downloading the complete database is not an option, you may able to use the instructions from this help page (based on the gff format for any given query): https://www.uniprot.org/help/...
Elisabeth.Gasteiger's user avatar
1 vote

How to upload and process a data set to Galaxy instance and retrieve results programmatically?

You best bet is bioblend, since it's a more convenient wrapper around the Galaxy API, but if you really want to you could use that directly. I should note that large files should probably still be ...
Devon Ryan's user avatar
  • 19.6k

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