# Tag Info

15

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: tabix "https://storage.googleapis.com/gnomad-public/release-170228/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz" "22:17265182-17265182" 22 17265182 . A T 762.04 PASS AC=1;AF=4.78057e-06;AN=209180;BaseQRankSum=-... 11 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 a programming exercise. Whereas developing a quick proof-of-concept read mapper is usually easy, turning it into a real competitor of existing and well-tuned ... 9 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 basic documentation. Paired-end mapping is doable, but not well exposed. Several teams, including GATK and MS genomics, have been using bwa-mem as a library. 7 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 then proceed to "checkout" to download the files of interest. 6 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 we are actively working on developing an API for ExAC/gnomAD. If you would like to learn about GraphQL, which we will use to work with the API, an overview can ... 5 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: https://github.com/ENCODE-DCC/submission_sample_scripts 5 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 associated genomic position. You can subtract the transcript’s start position from that position to find out the residue (of the translated sequence, and be careful ... 5 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 <ERROR>UID=1440: cannot get document summary</ERROR>. List of example uids using the term "ncbi+blast": https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=books&term=ncbi+blast Summary ... 4 Further inspecting the source code of the downloaded page, I found the following: <li id="nav-sequences" class="module-load transcript" wname="sequences" href="/rest/widget/transcript/K06C4.12/sequences"> <span class="ui-icon ui-icon-close module-close" wname="sequences" </span> Sequences </li> This suggested me ... 4 You can browse gnomAD variants with ClinGen Allele Registry (there is API spec available). 4 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 FMIndex specialisation instead of — as in the example — the IndexQGram. 4 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. 3 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 id:Q9UJL9. You will want to follow a redirect, and there are some rare cases where that might still lead to more than one entry if the id was made secondary and attached to multiple ... 3 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 association of gene/variation with the disease ( Piñero et al., 2016, Piñero et al., 2015): Gene Disease Associations from UniProt, PsyGeNET, ClinVar, ... 3 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: all_cpds = meta.get_class_all_instances('|Compounds|') for each compound, you can also get its common name, or all its synonyms: cpd_names = {} for cpd_frame_id in all_cpds: cpd_names[cpd_frame_id] ... 3 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 L-valine. I expect that they use similar naming for other amino acids. If you cannot find something, you can use their compound search through the website. 3 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): import pypdb all_info = pypdb.get_all_info('1kf6') print(all_info) the output is as follows: {'polymer': [{'@entityNr': '1', '@length': '602', '@type': 'protein', '@weight': '66057.6', 'chain': [{'@id': 'A'}, {'@id': 'M'}], '... 3 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 allows you to simply pipe esearch output to efetch: esearch -db books -query NBK1440 | efetch -format docsum or esearch -db books -query NBK1440 | esummary 2 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: #This is the main function which uses Ensembl REST API to access the Enesembl Compara database #And retrive the alignment blocks which correspond to the MM10 standard.... 2 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 residue level. curl --silent "ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/1kf6.xml.gz" | gunzip | python parse_sifts.py 1kf6 A M 0 ...

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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 here for the docs: https://graphql.org/learn/queries/ gnomAD Python Api https://github.com/furkanmtorun/gnomad_python_api

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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 given experiment, e.g. https://www.encodeproject.org/search/?type=File&dataset=/experiments/ENCSR000CKC/ Then further select file properties (status, format, etc.) using the facets on the left. ...

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Staff from rcsb kindly reminds me the solution - add the following lines in the json query. "request_options": { "return_all_hits": true }

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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 off 1-2 per second, I think you'll be ok. For example, for rs1490381980, you could try something like: curl -X GET 'https://api.ncbi.nlm.nih.gov/variation/v0/...

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REST API overlap region endpoint. For example.

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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/download_subsequences

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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 uploaded via ftp or sftp rather than via the http(s) interface.

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If you're looking for a python API, nanopore have created one (although I am not sure how "maintained" it is) https://github.com/nanoporetech/bwapy

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