Tag: SQLite

I am looking into what is required to support nanotime objects in RSQLite queries. They are just integer64 wrappers. Here is an example: con <- DBI::dbConnect(RSQLite::SQLite(), “:memory:”) ts <- nanotime::as.nanotime(Sys.time()) str(ts) # integer64 2023-06-04 17:30:21.669581000 DBI::dbGetQuery(con, ‘SELECT :ts AS x’, list(‘ts’ = ts)) # returns 5.757609e-196 tsi <- bit64::as.integer64(ts) DBI::dbGetQuery(con,…

Project Introduction: This project is going to utlize techniques our team has learned from our cloud computing class, Social Media Data Analytics Class, & EDA clasess. We are going to utilizes a corpus of text from multiple data sources and apply different topic modeling algorithms. The Data Analytical method: Simple…

A compilation of metadata from NCBI GEO Bioconductor version: 2.6 The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and…

The Genomics Research Center (GRC) is a center of excellence for genetics and genomics that supports both Discovery and Development. The GRC plays an integral role towards our goal of developing extraordinary genetics and genomics research, focusing on finding the right targets and helping us better understand not only human…

chat version: 2.0.0 hub error log [W 2023-05-11 08:27:49.529 JupyterHub app:2860] init_spawners did not complete within 10 seconds. Allowing to complete in the background. [I 2023-05-11 08:27:49.529 JupyterHub app:3057] Not starting proxy [I 2023-05-11 08:27:49.553 JupyterHub app:3093] Hub API listening on http://:8081/hub/ [I 2023-05-11 08:27:49.553 JupyterHub app:3095] Private Hub API…

Hello, I am working on the pathfinding step of the PHG pipeline and am currently trying to resolve a related issue regarding the correct parameters, described here . However when I try to rerun only the pathfinding step I run into the same error repeatedly. I have had the same…

Hi, I am getting some conflicts when I am trying to install some older version of pytorch. Using the command “conda install pytorch==1.8.0 torchvision==0.9.0 torchaudio==0.8.0 cudatoolkit=10.2 -c pytorch”. Also in the end pytorch is not getting installed. Below is what is printed on the terminal after running the above command….

minrk April 20, 2023, 12:21pm 1 JupyterHub 4.0 is out! 4.0 is a major release, but a small one. There are three major changes that should be invisible to most users: Groups can now have ‘properties’, editable via the admin page, which can be used by Spawners for their operations.This…

DOI: 10.18129/B9.bioc.AHLRBaseDbs   This is the development version of AHLRBaseDbs; for the stable release version, see AHLRBaseDbs. LRBaseDbs for AnnotationHub Bioconductor version: Development (3.17) Supplies AnnotationHub with `LRbaseDb` Ligand-Receptor annotation databases for many species. All the SQLite files are generated by our Snakemake workflow [lrbase-workflow](https://github.com/rikenbit/lrbase-workflow). For the details, see the…

Despite its recent gain in popularity, big data is still relatively uncertain compared to other established tech fields. As a result, most beginners find practicing and studying theories and concepts difficult because of a lack of data and resources. However, by using Kaggle for data science, you can overcome this…

The Genomics Research Center (GRC) is a center of excellence for genetics and genomics that supports both Discovery and Development. The GRC plays an integral role towards our goal of developing extraordinary genetics and genomics research, focusing on finding the right targets and helping us better understand not only human…

System Information Strapi Version: 4.9.0 Operating System: Windows 11 Database: sqlite Node Version: 18.15.0 NPM Version: 9.5.0 Yarn Version: 1.22.19 OpenApi generator version: typescript-fetch 6.5.0 Hiya strapi-community, I’ve added the documentation plugin to Strapi to generate OpenApi-compliant documentation. The documentation is generated and can be viewed on the Swagger documentation…

AbbVie’s Genomics Research Center Computational Genomics is looking for a highly motivated computational biologist (Senior Scientist I/II, Bioinformatics) to join a team of bioinformatics scientists investigating aging and age-related diseases. AbbVie’s GRC is a center of excellence for bioinformatics, functional genomics, and human genetics. The GRC works across all R&D…

The Center for Quantitative Genetics and Genomics (QGG) at Aarhus University invites applications for a position as Postdoc in the field of bioinformatics and sequence analysis as per 1 August 2023 or as soon as possible thereafter. Expected start date and duration of employmentThe position is a fixed-term full-time position…

I’m trying to set up a jupyterhub on my server and access it via an external network. I’m new on it so I’m using this repo as a starting point. I changed jupyterhub_config.py to use a Dummy authenticator. The complete file looks like this: import os c = get_config()  #…

From GeneSetEnrichmentAnalysisWiki GSEA Home | Downloads | Molecular Signatures Database | Documentation | Contact Introduction With the release of MSigDB 2023.1 we have created a new SQLite database for the fully annotated gene sets in both the Human (2023.1.Hs) and the Mouse (2023.1.Ms) resources. Each ships as a single-file database…

We are looking to hire a motivated Postdoc in bioinformatics and sequence analysis to join our stellar team at Aarhus Universitet in Århus C.Growing your career as a Full Time Postdoc in bioinformatics and sequence analysis is a great opportunity to develop useful skills.If you are strong in cooperation, people…

If you are a developer familiar with RESTful APIs, you might have heard of OpenAPI. It is a specification for describing RESTful APIs in a format readable for humans and machines. Building a public-facing OpenAPI includes three tasks: Authoring an OpenAPI specification which serves as the contract between the API…

I am trying to annotate a list of SNPs using the hg38 genome (knownGene) and locateVariants(). The program is able to successfully run and provide “GeneIDs” for several of the loci. However, some GeneIDs are applied to SNPs in completely different regions and on completely different chromosomes. When I cross…

Hello! I am trying to do the last few steps of the Practical Haplotype Graph pipeline as described here . I am running PHG v1.2, have loaded the Haplotypes to the database, created the pangenome fasta and am now trying to impute the best paths for different samples using WGS…

What are some alternatives? When comparing bwa-mem2 and htslib you can also consider the following projects: minimap2 – A versatile pairwise aligner for genomic and spliced nucleotide sequences bowtie2 – A fast and sensitive gapped read aligner genozip – A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF,…

I have an error in my pathing step in the PHG (version 1.3) pipeline. I have 19 taxa each with ~71,000 reference ranges, anchorwave haplotypes from assemblies, and I have been able to map short-read samples to the indexed pangenome. However, when I try to run the -imputePipeline plugin to…

Embeds the SQLite database engine in R, providing a DBI-compliant interface. SQLite is a public-domain, single-user, very light-weight database engine that implements a decent subset of the SQL 92 standard, including the core table creation, updating, insertion, and selection operations, plus transaction management. You can install the latest released version…

Video Timeline 00:00 Video Bumper00:06 Introduction00:17 Description of pre-requisites: Homebrew videoVisit http:/00:45 Go to the Spotlight search in top right00:50 Type Terminal in spotlight search to open Terminal00:59 Install the homebrew package for unixodbc01:30 Install the homebrew package for sqliteodbc02:20 View driver configuration required for the SQLite Driver on the…

Clarification on the usage of pangenomeHaplotypeMethod/pathHaplotypeMethod 0 Hello! I am currently trying to impute paths through a built Practical Haplotype Graph, i.e. use the -ImputePipelinePlugin -imputeTarget command. The PHG version I use is 1.2. I populated the database using assemblies and the built-in anchorwave plugin. I have fastq files as…

Changing Ownership Many of the files and directories mentioned in this chapter are, by default, owned by the rstudio-pm user. If you change the RunAs user for the RStudio Package Manager service, you will need to change ownership of these files and directories. See C for details on changing the…

sam123 February 8, 2023, 5:01pm 1 Hi, there, I rebuild Hub docker image based on amazon linux2. When I tried to run it locally, I got error:For the sqlite version error: sqlalchemy.exc.NotSupportedError: (sqlite3.NotSupportedError) deterministic=True requires SQLite 3.8.3 or higher The default SQLite coming with amazon linux2 is 3.7.17. However, I…

Hi there, a bit mystified with how to pass this parameter. It’s there in my config file, and seems to be read, but then eventually i get the warning that localGVCFFolder doesn’t have a parameter in the config file WARN net.maizegenetics.pangenome.pipeline.MakeInitialPHGDBPipelinePlugin – No localGVCFFolder parameter in config file – will…

Gene trans map for Trinotate input using non-Trinity assembled transcriptome? 2 I am following the Trinotate pipeline to functionally annotate an IsoSeq transcriptome for a non-model organism. I’ve performed all of the necessary TransDecoder steps and am at the stage of the Trinotate pipeline where I am loading data into…

issues with amber_minimize.py failing to use CUDA within alphafold 0 When I try and run alphafold from ubuntu command line with amber enabled, it’s throwing these errors. I0125 17:33:14.174568 47215575258112 amber_minimize.py:407] Minimizing protein, attempt 1 of 100. I0125 17:33:14.555528 47215575258112 amber_minimize.py:68] Restraining 685 / 1336 particles. I0125 17:33:14.747518 47215575258112 amber_minimize.py:417]…

Here, presented my PHG scripts, config, wgs_keyfile. 1. Create valid intervals docker run –name test_assemblies –rm -v /DATA/jysong/PHG/ver1.0_phg/:/phg/ -t maizegenetics/phg:1.0 /tassel-5-standalone/run_pipeline.pl -Xmx100G -debug -configParameters /phg/Masterconfig.txt -CreateValidIntervalsFilePlugin -intervalsFile /phg/inputDir/reference/glyma.Wm82.gnm4.ann1.T8TQ.gene_models_main.bed -referenceFasta /phg/inputDir/reference/glyma.Wm82.gnm4.4PTR.genome_main.fixed.fna.gz -mergeOverlaps true -generatedFile /phg/validBedFile.bed -endPlugin &> Log/1.Create_validinterval.txt & 2. Create initial DB docker run –name create_initial_db –rm -v /DATA/jysong/PHG/ver1.0_phg/:/phg/ -t…

Recently, in the development process, binary files need to be saved in the database, so I learned about the data type of sqlite3 and found that blob can store binary data. But what about blobs? What sentence do you use? In fact, it needs to operate some underlying APIs of…

DOI: 10.18129/B9.bioc.AHEnsDbs     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see AHEnsDbs. EnsDbs for AnnotationHub Bioconductor version: 3.10 Supplies AnnotationHub with EnsDb Ensembl-based annotation databases for all species. EnsDb SQLite databases are generated separately from Ensembl MySQL databases using functions from the…

python – OperationalError: database is locked I have made some repetitive operations in my application(testing it), and suddenly I’m getting a weird error: OperationalError: database is locked I’ve restarted the server, but the error persists.… how to close resultset in RMySQL? I…

DOI: 10.18129/B9.bioc.AHLRBaseDbs     LRBaseDbs for AnnotationHub Bioconductor version: Release (3.14) Supplies AnnotationHub with `LRbaseDb` Ligand-Receptor annotation databases for many species. All the SQLite files are generated by our Snakemake workflow [lrbase-workflow](https://github.com/rikenbit/lrbase-workflow). For the details, see the README.md of lrbase-workflow. Author: Koki Tsuyuzaki [aut, cre], Manabu Ishii [aut], Itoshi Nikaido…

I now think that the default mode should be to return an error here. That ship has sailed now. SQLite is fairly unique in its flexibility to store arbitrary data in the columns. For your use case I’d recommend segmenting by data type: library(RSQLite) con <- dbConnect(SQLite(), “:memory:”) dbGetQuery(con, “SELECT…

A simple SQLite clone in Rust. This is basically a translation of the C code present on this brilliant tutorial into Rust(not fully idiomatic). This code contains implementation only upto Part 5 in the tutorial. This a very simple database and is a small project I took up to gain…

SQLite is a file level database, hence to reference it requires a full directory path. No where do you specify the working directory or a full path in the file name. By default, R will use the current working directory contained in getwd(). If database is not contained in this…

Hi, I’m trying to learn how to use RSQLite but I’m already having a problem, wondered if anyone knows how to fix it. I have a pre-existing database (.data) file which does not have attribute names and I am trying to create a SQLite database with a table defined with…

Description Copies a database connection to a file or to another database connection. It can be used to save an in-memory database (created using dbname = “:memory:” or dbname = “file::memory:”) to a file or to create an in-memory database a copy of another database. Usage sqliteCopyDatabase(from, to) Arguments from…

You’re not using the pattern suggested by the RSQLite documentation. That documentation uses dbWriteTable to copy a data frame into a SQLite table: dbWriteTable(con, “mtcars”, mtcars) According to this documentation, your full code would look something like this: con <- dbConnect(RSQLite::SQLite(), “./mtcars.db”) data(mtcars) dbWriteTable(con, “mtcars”, mtcars) dbListTables(con) # Fetch all…

I am trying to scrape some pitchf/x data and store it in an SQLite database. However, I am receiving the following error when I run the following code: library(RSQLite) library(dplyr) db <- src_sqlite(“pitchfx.sqlite3”, create = T) This is the error: Error in h(simpleError(msg, call)) : error in evaluating the argument…

This may be a very basic question for guys who handle daily with programming issues! And until today I was not able to find the right words to ask and now I hope I can explain clearly what I want! It is technically not a coding question! It is not…

I’ve tried using the standard alphafold2 setup via docker (converted to a singularity container) via the setup described at github.com/kalininalab/alphafold_non_docker, and both result in the following error: […] E1210 12:01:01.009660 22603932526400 hhblits.py:141] – 11:49:18.512 INFO: Iteration 1 E1210 12:01:01.009703 22603932526400 hhblits.py:141] – 11:49:19.070 INFO: Prefiltering database E1210 12:01:01.009746 22603932526400 hhblits.py:141]…

Platform Design Information Package Builder Bioconductor version: 2.5 Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg….

tabix for ID column 4 Hello, I’m looking for something similar to tabix. But instead of looking for informations within a given region, I would like to use the values in the ID column for quickly lookup. So for example I would like to take the compressed dbSNP file, index…