API Reference
Ortholog discovery
Infer orthologs and summarize comparative-genetics results.
- Orthologs.Blast.BaseComparativeGenetics
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Base class in the Blast module.
- Orthologs.Blast.ComparativeGenetics
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Main Comparative Genetics class.
- Orthologs.Blast.BaseBlastN
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Base BlastN class.
- Orthologs.Blast.OrthoBlastN
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OrthoBlastN provides a preconfigured and orthology optimized version
Sequence retrieval
Retrieve and organize GenBank records and NCBI datasets.
- Orthologs.GenBank.GenBank
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This class will handle GenBank files in various ways.
- Tools.ftp.BaseFTPClient
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Provide shared connection management for FTP clients.
- Tools.ftp.NcbiFTPClient
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Access NCBI directories over FTP and download data over HTTPS.
- Tools.mygene.MyGene
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Import a csv of refseq accessions & get gene information from mygene.
Alignment and phylogenetics
Prepare alignments and run supported phylogenetic programs.
- Orthologs.Align.ClustalO
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Align genes using Clustal Omega.
- Orthologs.Align.Guidance2Commandline
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Command line wrapper for GUIDANCE2.
- Orthologs.Align.Pal2NalCommandline
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Command line wrapper for PAL2NAL.
- Orthologs.Align.MultipleSequenceAlignment
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The MultipleSequenceAlignment (MSA) class uses the standard configuration
- Orthologs.Phylogenetics.RelaxPhylip
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Convert a multiple sequence alignment file to relaxed-phylip format.
- Orthologs.Phylogenetics.ETE3PAML
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Integration of ETE3 for using PAML’s codeml.
- Orthologs.Phylogenetics.PhyML
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PhyML tools.
- Orthologs.Phylogenetics.Phylip
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Phylip tools.
- Orthologs.Phylogenetics.IQTreeCommandline
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Command line wrapper for GUIDANCE2.
- Orthologs.Phylogenetics.FilteredTree
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Run IQTree to generate a “filtered” tree or best tree.
- Orthologs.Phylogenetics.TreeViz
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Tree Vizualization tools.
- Orthologs.Phylogenetics.PAML.CodemlRun
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Run PAML’s codeml program using Biopython’s codeml wrapper.
Project and data management
Create project layouts and coordinate data and database workflows.
- Manager.management.Management
- Manager.management.RepoManagement
- Manager.management.UserManagement
- Manager.management.WebsiteManagement
- Manager.management.ProjectManagement
- Manager.data_management.DataMana
- Manager.database_management.BaseDatabaseManagement
- Manager.database_management.DatabaseManagement
- Manager.database_dispatcher.DatabaseDispatcher
- Manager.biosql.biosql.BaseBioSQL
- Manager.biosql.biosql.SQLiteBioSQL
- Manager.biosql.biosql.MySQLBioSQL
Execution and supporting tools
Run local, PBS, Slurm, logging, and transfer helpers.
- Tools.pbs.BaseQsub
- Tools.pbs.Qsub
- Tools.pbs.BaseQstat
- Tools.pbs.Qstat
- Tools.pbs.MultiQstat
- Tools.pbs.TargetJobKeyError
- Tools.slurm.SlurmClient
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Run one-shot Slurm submission and inspection commands.
- Tools.slurm.SlurmJob
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Normalized job information shared by active and historical queries.
- Tools.slurm.SlurmCommandNotFoundError
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Report that a required Slurm executable is unavailable.
- Tools.parallel.Multiprocess
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Use multiple processes with a function.
- Tools.logit.LogIt
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LogIt makes logging easier by creating easy loggers.
- Tools.pybasher.PyBasher
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Common bash commands.
- Tools.send2server.S2S
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S2S (Send 2 Server) is designed for use with a public ssh key.
- Tools.slackify.Slackify
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Send messages or milestones to a slack channel.
Templates and utilities
Create project templates and use shared package utilities.
- Cookies.Oven
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Class that deploys cookiecutter templates.
- Cookies.CookBook
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Class of cookiecutter related functions.
- resources.package_resource_path()
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Return a filesystem path for a resource in an installed package.
- utilities.DuplicateAnalysis
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Duplicate groups and the counts consumed by post-BLAST reporting.
- utilities.BlastUtils
- utilities.GenbankUtils
- utilities.OrthologUtils
- utilities.ManagerUtils
- utilities.CookieUtils
- utilities.PackageVersion
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Get the version of an installed python package.
- utilities.FunctionRepeater
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Repeats a function every interval. Ref: https://tinyurl.com/yckgv8m2
- utilities.FullUtilities
- OrthoEvolWarning
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This is the OrthoEvol main warning class.
- OrthoEvolDevelopmentWarning
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This is the OrthoEvol developmental code warning subclass.
- OrthoEvolDeprecationWarning
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This is the Deprecation Warning subclass.