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listGenomes() and biomart()listGenomes() filter error #107Some cool new generalization, and check out function biomartr:::supported_biotypes(db = "refseq"). This function will simplify a lot of stuff downstream. (#104)
Tests are now much quicker to run, because biomartr::is.genome.available (which is used basically everywhere) now reads files with data.table instead of reader. (#104)
is.genome.available() where the skip_bacteria argument was not passed on internally to is.genome.available.refseq.genbank() (#105)Over 5000 lines have been edited, most of them removed (#100), to generalize the package to make it more safe for future development. This progress is still ongoing.
UniProt database is now updated to the new API/FTP path system. Now users can retrieve proteomes using the functions getProteome(db = "uniprot", ...) and getProteomeSet(db = "uniprot", ...) (see #82)getBioSet: Generic Bio data set extractorgetBio: A wrapper to all bio getters, selected with ‘type’ argumentgetUniProtSTATS(): Retrieve UniProt Database Information File (STATS)The package now supports caching of back end files which used to be saved to /tmp folder (i.e. lost on computer restart). This make it easy for power users who want higher speed. For more info, see the function ?cachedir_set
getSummaryFile() all columns of the assembly_summary.txt are now specified with names and correct data types (#92)get*() functions, the getKingdomAssemblySummary(), and is.genome.available.refseq.genbank() all receive a new argument skip_bacteria which is set to TRUE by default. This ensures that the huge dataset file for bacteria is not downloaded by default when retrieving summary files from GenBank. Users who wish to retrieved data from particular bacteria can actively set skip_bacteria = TRUE in all get*() functions.getKingdomAssemblySummary() was called by all get*() functions, due to an error in the assembly_summary.txt file for viruses where the total gene count was stored as character and not as integer (as is the case for all other assembly_summary.txt files), an error occurred stating that dplyr::bind_rows() cannot join column $X35 due to differences in data types. This has now been resolved by parsing the correct data types with readr. Many thanks to … for pointing this out to me. (#92)get*() functionshttp to https curl requests (Many thanks to @Roleren)New function check_annotation_biomartr() helps to check whether downloaded GFF or GTF files are corrupt. Find more details here
new function getCollectionSet() allows users to retrieve a Collection: Genome, Proteome, CDS, RNA, GFF, Repeat Masker, AssemblyStats of multiple species
Example:
# define scientific names of species for which
# collections shall be retrieved
organism_list <- c("Arabidopsis thaliana",
"Arabidopsis lyrata",
"Capsella rubella")
# download the collection of Arabidopsis thaliana from refseq
# and store the corresponding genome file in '_ncbi_downloads/collection'
getCollectionSet( db = "refseq",
organism = organism_list,
path = "set_collections")getGFF() function receives a new argument remove_annotation_outliers to enable users to remove corrupt lines from a GFF file Example:the getGFFSet() function receives a new argument remove_annotation_outliers to enable users to remove corrupt lines from a GFF file
the getGTF() function receives a new argument remove_annotation_outliers to enable users to remove corrupt lines from a GTF file
adding a new message system to biomartr::organismBM(), biomartr::organismAttributes(), and biomartr::organismFilters() so that large API queries don’t seem so unresponsive
getCollection() receives new arguments release, remove_annotation_outliers, and gunzip that will now be passed on to downstream retrieval functions
the getGTF(), getGenome() and getGenomeSet() functions receives a new argument assembly_type = "toplevel" to enable users to choose between toplevel and primary assembly when using ensembl database. Setting assembly_type = "primary_assembly" will save a lot a space on hard drives for people using large ensembl genomes.
all get*() functions with release argument now check if the ENSEMBL release is >45 (Many thanks to @Roleren #31 #61)
in all get*() functions, the readr::write_tsv(path = ) was exchanged to readr::write_tsv(file = ), since the readr package version > 1.4.0 is depreciating the path argument.
tbl_df() was deprecated in dplyr 1.0.0. Please use tibble::as_tibble() instead. -> adjusted organismBM() accordingly
custom_download(), getGENOMEREPORT(), and other download functions now have specified withr::local_options(timeout = max(30000000, getOption("timeout"))) which extends the default 60sec timeout to 30000000sec
Fixing bug where genome availability check in getCollection() was only performed in NCBI RefSeq and not in other databases due to a constant used in is.genome.available() rather than a variable (Many thanks to Takahiro Yamada for catching the bug) #53
fixing an issue that caused the read_cds() function to fail in data.table mode (Many thanks to Clement Kent) #57
fixing an SSL bug that was found on Ubuntu 20.04 systems #66 (Many thanks to Håkon Tjeldnes)
fixing global variable issue that caused clean.retrieval() to fail when no documentation file was in a meta.retrieval() folder
The NCBI recently started adding NA values as FTP file paths in their species summary files for species without reference genomes. As a result meta.retrieval() stopped working, because no FTP paths were found for some species. This issue was now fixed by adding the filter rule !is.na(ftp_path) into all get*() functions (Many thanks for making me aware of this issue Ashok Kumar Sharma #34 and Dominik Merges #72)
Fixing an issue in custom_download() where the method argument was causing issues when downloading from https directed ftp sites (Many thanks to @cmatKhan) #76
Fixing issue when trying to combine multiple summary-stats files where NA’s were present in the list item that was passed along for combination in meta.retrieval() #73 (Many thanks to Dominik Merges)
Fixing a bug in download.database.all() where the lack of removing listed file *-metadata.json caused corruption of the download process (Many thanks to Jaruwatana Lotharukpong)
biomartr 0.9.2 - minor changes to comply with CRAN policy regarding Internet access failure -> Instead of using warnings or error messages, only gentle messages are allowed to be used
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.
clean.retrieval() enables formatting and automatic unzipping of meta.retrieval output (find out more here: https://docs.ropensci.org/biomartr/articles/MetaGenome_Retrieval.html#un-zipping-downloaded-files)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.getProteomeSet() allows users to easily retrieve proteomes of multiple specified speciesgetCDSSet() allows users to easily retrieve coding sequences of multiple specified speciesgetGFFSet() allows users to easily retrieve GFF annotation files of multiple specified speciesgetRNASet() allows users to easily retrieve RNA sequences of multiple specified speciessummary_genome() allows users to retrieve summary statistics for a genome assembly file to assess the influence of genome assembly qualities when performing comparative genomics taskssummary_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.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 testgetGTF(): users can now specify the NCBI Taxonomy ID or Accession ID in addition to the scientific name in argument ‘organism’ to retrieve genome assembliesgetGFF(): 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 assembliesgetMarts() 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 qualityreference is now set from reference = TRUE to reference = FALSE (= new default)get*() functions now received a new argument release which allows users to retrieve specific release versions of genomes, proteomes, etc from ENSEMBL and ENSEMBLGENOMESget*() 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 analysesgetCollection() for retrieval of a collection: the genome sequence, protein sequences, gff files, etc for a particular speciesgetProteome() can now retrieve proteomes from the UniProt database by specifying getProteome(db = "uniprot").
is.genome.available() now prints out more useful interactive messages when searching for available organisms
is.genome.available() can now handle taxids and assembly_accession ids in addition to the scientific name when specifying argument organism
is.genome.available() can now check for organism availability in the UniProt database
getGenome(): users can now specify the NCBI Taxonomy ID or Accession ID in addition to the scientific name in argument ‘organism’ to retrieve genome assemblies
getProteome(): users can now specify the NCBI Taxonomy ID or Accession ID in addition to the scientific name in argument ‘organism’ to retrieve proteomes
getCDS(): users can now specify the NCBI Taxonomy ID or Accession ID in addition to the scientific name in argument ‘organism’ to retrieve CDS
getRNA(): users can now specify the NCBI Taxonomy ID or Accession ID in addition to the scientific name in argument ‘organism’ to retrieve RNAs
is.genome.available(): argument order was changed from is.genome.available(organism, details, db) to is.genome.available(db, organism, details) to be logically more consistent with all get*() functionsmeta.retrieval receives a new argument restart_at_last to indicate whether or not the download process when re-running the meta.retrieval function shall pick up at the last species or whether it should crawl through all existing files to check the md5checksummeta.retrieval now generates an csv overview file in the doc folder which stores genome version, date, origin, etc information for all downloaded organisms and can be directly used as Supplementary Data file in publications to increase computational and biological reproducibility of the genomics studydownload.database.all() can now skip already downloaded files and internally removes corrupted files with non-matching md5checksum. Re-downloading of currupted files and be performed by simply re-running the download.database.all() command
the function meta.retrieval() will now pick up the download at the organism where it left off and will report which species have already been retrieved
all get*() functions and the meta.retrieval() function receive a new argument reference which allows users to retrieve not-reference or not-representative genome versions when downloading from NCBI RefSeq or NCBI Genbank
the argument order in meta.retrieval() changed from meta.retrieval(kingdom, group, db, ...) to meta.retrieval(db,kingdom, group, ...) to make the argument order more consistent with the get*() functions
the argument order in getGroups() changed from getGroups(kingdom, db) to getGroups(db, kingdom) to make the argument order more consistent with the get*() and meta.retrieval() functions
existingOrganisms() and existingOrganisms_ensembl() which check the organisms that have already been downloadedfixing a bug in exists.ftp.file() and getENSEMBLGENOMES.Seq() that caused bacterial genome, proteome, etc retrieval to fail due to the wrong construction of a query ftp request https://github.com/ropensci/biomartr/issues/7 (Many thanks to @dbsseven)
fix a major bug in which organisms having no representative genome would generate NULL paths that subsequently crashed the meta.retrieval() function when it tried to print out the result paths.
new function getRepeatMasker() for retrieval of Repeat Masker output files
new function getGTF() for genome annotation retrieval from ensembl and ensemblgenomes in gtf format (Thanks for suggesting it Ge Tan)
new function getRNA() to perform RNA Sequence Retrieval from NCBI and ENSEMBL databases (Thanks for suggesting it @carlo-berg)
new function read_rna() for importing Repeat Masker output files downloaded with getRepeatMasker()
new function read_rm() for importing RNA downloaded with getRNA() as Biostrings or data.table object
new helper function custom_download() that aims to make the download process more robust and stable -> In detail, the download process is now adapting to the operating system, e.g. using either curl (macOS), wget (Linux), or wininet (Windows)
function name listDatabases() has been renamed listNCBIDatabases(). In biomartr version 0.6.0 the function name listDatabases() will be depreciated
meta.retieval() and meta.retieval.all() now allow the bulk retrieval of GTF files for type = 'ensembl' and type = 'esnemblgenomes' via type = "gtf". See getGTF() for more details.
meta.retieval() and meta.retieval.all() now allow the bulk retrieval of RNA files via type = "rna". See getRNA() for more details.
meta.retieval() and meta.retieval.all() now allow the bulk retrieval of Repeat Masker output files via type = "rm". See getRepeatMasker() for more details.
all get*() retrieval functions now skip the download of a particular file if it already exists in the specified file path
download.database() and download.database.all() now internally perform md5 check sum checks to make sure that the file download was successful
download.database() and download.database.all() now return the file paths of the downloaded file so that it is easier to use these functions when constructing pipelines, e.g. download.database() %>% ... or download.database.all() %>% ....
meta.retrieval() and meta.retrieval.all() now return the file paths of the downloaded file so that it is easier to use these functions when constructing pipelines, e.g. meta.retrieval() %>% ... or meta.retrieval() %>% ....
getGenome(), getProteome(), getCDS(), getRNA(), getGFF(), and getAssemblyStats() now internally perform md5 checksum tests to make sure that files are retrieved intact.
get*() (genome, proteome, gff, etc.) and meta.retrieval*() functions the meta retrieval process errored and terminated whenever NCBI or ENSEMBL didn’t store all types of sequences for a particular organism: genome, proteome, cds, etc. This has been fixed now and function calls such as meta.retrieval(kingdom = "bacteria", db = "genbank", type = "proteome") should work properly now (Thanks to @ARamesh123 for making me aware if this bug). Hence, this bug affected all attempts to download all proteome sequences e.g. for bacteria and viruses, because NCBI does not store genome AND proteome information for all bacterial or viral species.new function getAssemblyStats() allows users to retrieve the genome assembly stats file from NCBI RefSeq or Genbank, e.g. ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.36_GRCh38.p10/GCF_000001405.36_GRCh38.p10_assembly_stats.txt
new function read_assemblystats() allows to import the genome assembly stats file from NCBI RefSeq or Genbank that was retrieved using the getAssemblyStats() function
meta.retrieval() and meta.retrieval.all() can now also download genome assembly stats for all selected species
meta.retrieval() receives a new argument group that allows users to retrieve species belonging to a subgroup instead of the entire kingdom. Available groups can be retrieved with getGroups().
functions getSubgroups() and listSubgroups() have been removed and their initial functionality has been merged and integrated into getGroups() and listGroups()
listGroups() receives a new argument details that allows users to retrieve the organism names that belong to the corresponding subgroups
getGroups() is now based on listGroups()
internal function getGENOMESREPORT() is now exported and available to the user
all organism*() functions now also support Ensembl Plants, Ensembl Metazoa, Ensembl Protist, and Ensembl Fungi (Thanks for pointing out Alex Gabel)
getMarts() and getDatasets() now also support Ensembl Plants, Ensembl Metazoa, Ensembl Protist, and Ensembl Fungi (Thanks for pointing out Alex Gabel)
Meta-Genome Retrieval has more examples how to download genomes of species that belong to the same subgroupgetSummaryFile(), getKingdomAssemblySummary(), getMetaGenomeSummary(), getENSEMBL.Seq() and getENSEMBLGENOMES.Seq() functions causing quoted lines in the assembly_summary.txt to be omitted when reading these files. This artefact caused that e.g. instead of information of 80,000 Bacteria genomes only 40,000 (which non-quotations) were read (Thanks to Xin Wu).In this version of biomartr the organism*() functions were adapted to the new ENSEMBL 87 release in which organism name specification in the Biomart description column was changed from a scientific name convention to a mix of common name and scientific name convention.
all organism*() functions have been adapted to the new ENSEMBL 87 release organism name notation that is used in the Biomart description
fixing error handling bug that caused commands such as download.database(db = "nr.27.tar.gz") to not execute properly
In this version, biomartr was extended to now retrieve genome, proteome, CDS, GFF and meta-genome data also from ENSEMBL and ENSEMLGENOMES. Furthermore, all NCBI retrieval functions were updated to the new server folder structure standards of NCBI.
new meta-retrieval function meta.retrieval.all() allows users to download all individual genomes of all kingdoms of life with one command
new metagenome retrieval function getMetaGenomes() allows users to retrieve metagenome projects from NCBI Genbank
new metagenome retrieval function getMetaGenomeAnnotations() allows users to retrieve annotation files for genomes belonging to a metagenome project stored at NCBI Genbank
new retrieval function getGFF() allows users to retrieve annotation (*.gff) files for specific genomes from NCBI and ENSEMBL databases
new import function read_gff() allowing users to import GFF files downloaded with getGFF()
new internal functions to check for availability of ENSEMBL or ENSEMBLGENOMES databases
new database retrieval function download.database.all() allows users to download entire NCBI databases with one command
new function listMetaGenomes() allowing users to list available metagenomes on NCBI Genbank
new external helper function getSummaryFile() to retrieve the assembly_summary.txt file from NCBI
new external helper function getKingdomAssemblySummary() to retrieve the assembly_summary.txt files from NCBI for all kingdoms and combine them into one big data.frame
new function listKingdoms() allows users to list the number of available species per kingdom of life
new function listGroups() allows users to list the number of available species per group
new function listSubgroups() allows users to list the number of available species per subgroup
new function getGroups() allows users to retrieve available groups for a kingdom of life
new function getSubgroups() allows users to retrieve available subgroups for a kingdom of life
new external helper function getMetaGenomeSummary() to retrieve the assembly_summary.txt files from NCBI genbank metagenomes
new internal helper function getENSEMBL.Seq() acting as main interface function to communicate with the ENSEMBL database API for sequence retrieval
new internal helper function getENSEMBLGENOMES.Seq() acting as main interface function to communicate with the ENSEMBL database API for sequence retrieval
new internal helper function getENSEMBL.Annotation() acting as main interface function to communicate with the ENSEMBL database API for GFF retrieval
new internal helper function getENSEMBLGENOMES.Annotation() acting as main interface function to communicate with the ENSEMBL database API for GFF retrieval
new internal helper function get.ensemblgenome.info() to retrieve general organism information from ENSEMBLGENOMES
new internal helper function get.ensembl.info() to retrieve general organism information from ENSEMBL
new internal helper function getGENOMEREPORT() to retrieve the genome reports file from ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/overview.txt
new internal helper function connected.to.internet() enabling internet connection check
functions getGenome(), getProteome(), and getCDS() now can also in addition to NCBI retrieve genomes, proteomes or CDS from ENSEMBL and ENSEMLGENOMES
the functions getGenome(), getProteome(), and getCDS() were completely re-written and now use the assembly_summary.txt files provided by NCBI to retrieve the download path to the corresponding genome. Furthermore, these functions now lost the kingdom argument. Users now only need to specify the organism name and not the kingdom anymore. Furthermore, all get* functions now return the path to the downloaded genome so that this path can be used as input to all read_* functions.
download_databases() has been renamed to download.databases() to be more consistent with other function notation
the argument db_format was removed from listDatabases() and download.database() because it was misleading
the command listDatabases("all") now returns all available NCBI databases that can be retrieved with download.database()
download.database() now internally checks if input database specified by the user is actually available on NCBI servers
the documentary file generated by getGenome(), getProteome(), and getCDS() is now extended to store more details about the downloaded genome
argument database in is.genome.available() and listGenomes() has been renamed to db to be consistent with all other sequence retrieval functions
is.genome.available() now also checks availability of organisms in ENSEMBL. See db = "ensembl"
the argument db_name in listDatabases() has been renamed db to be more consistent with the notation in other functions
the argument name in download.database() has been renamed db to be more consistent with the notation in other functions
getKingdoms() now retrieves also kingdom information for ENSEMBL and ENSEMBLGENOMES
getKingdoms() received new argument db to specify from which database (e.g. refseq, genbank, ensembl or ensemblgenomes) kingdom information shall be retrieved
getKingdoms(db = "refseq") received one more member: "viral", allowing the genome retrieval of all viruses
argument out.folder in meta.retrieval() has been renamed to path to be more consistent with other retrieval functions
all read_* functions now received a new argument obj.type allowing users to choose between storing input genomes as Biostrings object or data.table object
all read_* functions now have format = "fasta" as default
the kingdom argument in the listGenomes() function was renamed to type, now allowing users to specify not only specify kingdoms, but also groups and subgroups. Use: listGenomes(type = "kingdom") or listGenomes(type = "group") or listGenomes(type = "subgroup")
the listGenomes() function receives a new argument subset to specify a subset of the selected type argument. E.g. subset = "Eukaryota" when specifying type = "kingdom"
Meta-Genome RetrievalIntroduction VignetteDatabase Retrieval VignetteSequence Retrieval VignetteFunctional Annotation Vignettefixing a parsing error of the file ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/assembly_summary.txt The problem was that comment lines were introduced and columns couldn’t be parsed correctly anymore. This caused that genomes, proteomes, and CDS files could not be downloaded properly. This has been fixed now.
genomes, proteome, and CDS as well as meta-genomes can now be retrieved from RefSeq and Genbank (not only RefSeq); only getCDS() does not have genebank access, becasue genbank does not provide CDS sequences
adding new function meta.retrieval() to mass retrieve genomes for entire kingdoms of life
fixed a major bug in organismBM() causing the function to fail. The failure of this function affected all downstream organism*() functions. Bug is now fixed and everything works properly
updated Vignettes
updating unit tests for new API
fixing API problems that caused all BioMart related functions to fail
fixing retrieval problems in getCDS(), getProteome(), and getGenome()
the listDatabases() function now has a new option db_name = "all" allowing users to list all available databases stored on NCBI
Release Version
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.