Package: geneutils
geneutilsThis tool was originally inspired by thework herefor dealing with nucleotide sequences and more tools will be added as needed. This toolbox requires python 3 and can be installed.Table of contentsInstallationgeneutils cli toolsinitblasthitInstallationThis assumes that you have native python 3 & pip installed in your system, you can test this by going to the terminal (or windows command prompt) and tryingpythonand thenpip listIf you get no errors and you have python 3 or higher you should be good to go. To installgeneutilsyou can install using two methodspip install geneutilsor you can also trypip install geneutils --userTo upgrade to a new version from old you can trypip install geneutils --upgradeorpip install geneutils --user --upgradeor you can also trygit clone https://github.com/samapriya/geneutils.git
cd geneutils
python setup.py installThough there is a conda installer for linux/mac for geneutilsconda install -c samapriya geneutilsThe recommended way would be to use the conda environment/terminal and then do apip install geneutilsInstallation is an optional step; the application can be also run directly by executing geneutils.py script. The advantage of having it installed is being able to execute porg as any command line tool. I recommend installation within virtual environment. If you don't want to install, browse into the geneutils folder and trypython geneutils.py -hto get to the same result.geneutils cli toolsThis is a command line tool and it is designed to simply call the tools you need.initTurns out there are benefits of registering for a NCBI account and to use your email address and your API key. Apart from NCBI having a way of contacting you, the API key raises the rate limit imposed on your queries. This is a recommended step and a user should not skip thought it is possible to use the blashit tool without the API key.From the NCBI account page you can find this informationE-utils users are allowed 3 requests/second without an API key. Create an API key to increase your e-utils limit to 10 requests/second......Only one API Key per user. Replacing or deleting will inactivate the current key. Use this key by passing it with api_key=API_KEY parameter.Generate your API KeyThe init tool saves your email address and API key to be saved in your local machine which can be used instead of typing out your email over and over again. The API key is a clear entry meaning you cannot see when you type in or paste your API key for safety.blasthitThis script is intended for taxonomic annotation ofblastresults (blastn, tblastn, blastp or blastx) saved inHit Table CSVformat where GenBank accession numbers are in the 4th column. It usesefetchfunction fromBio.Entrezpackage to get information about accessions fromGenBank Nucleotide (Nuccore)orProteindatabases.
The output is an annotated CSV file "*_annotated.csv" with the following columns added:Record nameSpecies nameFull taxonomyReferenceDate of updateargumentsdescriptionpathPathway to csv-formatted Hit Table file with blastn results. Positional argumentdbFor the output ofnucleotide blastortblastn, usen. For the output ofprotein blastorblastx, usep. Positional argumentemailYour NCBI email. Optional argument-h, --helpShow help message and exit. Optional argumentChangelog0.0.6Dedupes accession ids & remove empty rowsSubset handling is cleaner and better error handling with try except blocksgeneral code improvements to run style and functionalityperformance improvements to overall runtime0.0.5Fixed issue with empty rowsIncludes version checkgeneral code cleanup0.0.4Fixed issue with path basename0.0.3Fixed issue with repeating email id for accession blocksUpdated ReadMe to includegeneutils initas first step.Fixed CSV write issue outside loop0.0.2Added credential tool to save NCBI email and API KeyMinor fixes to overall functionality.