README.md

In vaulot/dvutils: A set of utilities

dvutils, a R package

A set of R utilities developped by Daniel Vaulot ([e-mail])

• Graphics
• Databases
• Bioinfo
  • interface with Phyloseq
  • interface with dada2 (taxonomy assignation with the Wang assigner)
  • fasta file read and write
  • Genbank parsing
  • reformating and analysis of BLAST output
• Interface and management to pecific databases
  • PR2 (18S rRNA sequences)
  • MetaPR2 (metabarcodes)
  • RCC (Roscoff Culture Collection)

Installation

You need to install a few packages from Bioconductor and also the pr2database package (used for analysis of BLAST files)

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("dada2")
BiocManager::install("genbankr")
BiocManager::install("phyloseq")

install.packages(devtools)
devtools::install_github("pr2database/pr2database")
devtools::install_github("vaulot/dvutils")

Functions

Function | Aim --- | ---- blast_18S_reformat|Process a tabular output from blastn (BLAST+) blast_summary|Write a summary for a tabular output from blastn (BLAST+) dada2_assign|Assign sequences using dada2 wang assigner db_append_records|Write new records to a table. db_connect|Establish a connection database db_connect_sqlite|Establish a connection to a SQLite database db_disconnect|Disconnect an existing connection db_execute_query_vector|Execute a vector of query. db_get_query|Read a query into a dataframe. db_info|Get the connection info for a specific database db_sql_escape|Put a string between single quotes db_update_field_string|Build a string to update a field in a database fasta_filter|Filter a fasta file fasta_read|Read a fasta file into a data frame fasta_write|Write a fasta file with the taxonomy fastq_subsample|Subsample fastq files filename_append|Append a string at the end of a file name before the exension filename_change_ext|Change the extension of the file name file_unix2dos|Convert between Unix and Dos text format genbank_search|Search sequences in GenBank genbank_download|Download sequences from GenBank genbank_download_parse|Download and parse sequences from GenBank genbank_features|Read features of sequences from GenBank genbank_field|Read a single field from a set of existing GenBank files genbank_locus|Read locus from a set of existing GenBank files genbank_taxonomy|Read NCBI taxo get_primer_position|Get primer position on sequence set gg_bar_discrete|Do a simple barplot gg_boxplot|Plot a box plot gg_density|Plot simple density plot to compare factors gg_hist|Plot simple histogram gg_violin|Plot a violin and a box plot kmer|Get all kmers in a sequence kmer_set|Get all kmers in a set of sequence latex_fix_bibfile|Fix bib library file created by Mendeley lat_long_dec|Convert lat and long to decimal map_distribution|Draw distribution map from data frame map_get_world|Get the world map for the rworldmap package map_leaflet|Map with leaflet package (OpenStreetMap) map_US|Background US map using the maps package to extract a specific country map_world|Background map using the maps package map_world_google|Background map using the ggmap package map_zoom_europe|Zoom a map on Europe metapr2_export_asv|Exports the metapr2 database pcr_sequences|In silico amplification phyloseq_filter_abundant_taxa|Filter a phyloseq table keeping only abundant taxa phyloseq_filter_autotrophic_taxa|Filter a phyloseq table keeping only autotrophic taxa phyloseq_import_mothur|Create a phyloseq file from mothur database file pr2_buid_taxons|Build taxon table (long format) pr2_build_taxonomy|Buikd taxonomy table (wide format) from taxon table (long format) pr2_export|Export the PR2 database (one file) pr2_export_all|Export the PR2 database (all files) pr2_export_sqlite|Export the PR2 database to a SQLite file pr2_extract_one_taxo_level|Extract one level of taxonomy pr2_read|Reads the whole PR2 database into a data frame pr2_sequence_label|Create a simple label for a sequence pr2_sequence_reassign|Reassign pr2 sequences pr2_taxo_check|Check taxonomy pr2_taxo_list|Build a list of taxa pr2_taxo_read|Reads the PR2 taxonomic database into a data frame pr2_taxo_update|Update pr2 taxonomy pr2_taxo_X|Add _X for taxon that are repeated on same line pr2_treemap|Draw a simple treemap from pr2. rcc_customers|Format "customers.csv" for import into rcc database rcc_export|Export tables from MySQL database rcc_genbank|Prepare list of GenBank entries to include in rcc database rcc_orders|Format "orders.csv" for import into rcc database rcc_order_details|Format "order_details.csv" for import into rcc database theme_dviz_grid|Theme - grid lines along major axis ticks, no axes theme_dviz_hgrid|Theme - horizontal grid lines only theme_dviz_vgrid|Theme - vertical grid lines only treemap_dv|Do a simple treemap XStringSet_to_df|Transforms a DNA or AA String set into a data frame

Examples

Searching GenBank, downloading and parsing

Functions built around the rentrez package: https://cran.r-project.org/web/packages/rentrez/vignettes/rentrez_tutorial.html https://github.com/ropensci/rentrez

seq_search <- dvutils::genbank_search(query = "28S[TITL] AND rRNA[TITL] AND Chlorophyta[ORGN]", 
                                      seq_max = 500)

seq_parsed <- dvutils::genbank_download_parse(accession = seq_search$genbank_accession, 
                                              directory = "genbank/", sequence_keep=TRUE)

vaulot/dvutils documentation built on Nov. 20, 2021, 11:01 a.m.