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@HajkD HajkD released this 19 May 21:57
· 383 commits to master since this release
v0.9.0
12fb224

Please be aware that as of April 2019, ENSEMBLGENOMES
was retired (see details here). Hence, all biomartr functions were updated
and won't support data retrieval from ENSEMBLGENOMES servers anymore.

New Functions

  • New function clean.retrieval() enables formatting and automatic unzipping of meta.retrieval output (find out more here: https://ropensci.github.io/biomartr/articles/MetaGenome_Retrieval.html#un-zipping-downloaded-files)
  • New function getGenomeSet() allows users to easily retrieve genomes of multiple specified species.
    In addition, the genome summary statistics for all retrieved species will be stored as well to provide
    users with insights regarding the genome assembly quality of each species. This file can be used as Supplementary Information file
    in publications to facilitate reproducible research.
  • New function getProteomeSet() allows users to easily retrieve proteomes of multiple specified species
  • New function getCDSSet() allows users to easily retrieve coding sequences of multiple specified species
  • New function getGFFSet() allows users to easily retrieve GFF annotation files of multiple specified species
  • New function getRNASet() allows users to easily retrieve RNA sequences of multiple specified species
  • New function summary_genome() allows users to retrieve summary statistics for a genome assembly file to assess
    the influence of genome assembly qualities when performing comparative genomics tasks
  • New function summary_cds() allows users to retrieve summary statistics for a coding sequence (CDS) file.
    We noticed, that many CDS files stored in NCBI or ENSEMBL databases contain sequences that aren't divisible by 3 (division into codons).
    This makes it difficult to divide CDS into codons for e.g. codon alignments or translation into protein sequences. In
    addition, some CDS files contain a significant amount of sequences that do not start with AUG (start codon).
    This function enables users to quantify how many of these sequences exist in a downloaded CDS file to process
    these files according to the analyses at hand.

New Features of Existing Functions

  • the default value of argument reference in meta.retrieval() changed from reference = TRUE to reference = FALSE.
    This way all genomes (reference AND non-reference) genomes will be downloaded by default. This is what users seem to prefer.
  • getCollection() now also retrieves GTF files when db = 'ensembl'
  • getAssemblyStats() now also performs md5 checksum test
  • all md5 checksum tests now retrieve the new md5checkfile format from NCBI RefSeq and Genbank
  • getGTF(): users can now specify the NCBI Taxonomy ID or Accession ID in addition to the scientific name in argument 'organism' to retrieve genome assemblies
  • getGFF(): users can now specify the NCBI Taxonomy ID or Accession ID for ENSEMBL in addition to the scientific name in argument 'organism' to retrieve genome assemblies
  • getMarts() will now throw an error when BioMart servers cannot be reached (#36)
  • getGenome() now also stores the genome summary statistics (see ?summary_genome()) for the retrieved species in the documentation folder to provide
    users with insights regarding the genome assembly quality
  • In all get*() functions the default for argument reference is now set from reference = TRUE to reference = FALSE (= new default)
  • all get*() functions now received a new argument release which allows users to retrieve
    specific release versions of genomes, proteomes, etc from ENSEMBL and ENSEMBLGENOMES
  • all get*() functions received two new arguments clean_retrieval and gunzip which
    allows users to upzip the downloaded files directly in the get*() function call and rename
    the file for more convenient downstream analyses
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