Export DNA sequences of selected scaffolds

Writes the DNA sequences of a given set of scaffolds from the assembly to a FASTA file.

mmexport(
  scaffolds,
  assembly = get("assembly", envir = .GlobalEnv),
  file = "exported_assembly.fa"
)

Arguments

scaffolds	(required) Either a vector of scaffold names or a dataframe loaded with mmload containing the scaffolds to extract from the assembly.
assembly	(required) The assembly to subset and export. Must be an object of class "DNAStringSet" as loaded with readDNAStringSet. By default any object named "assembly" in the global environment will be used.
file	The file path and file name of the file to write the sequences to. (Default: "exported_assembly.fa")

Author

Kasper Skytte Andersen ksa@bio.aau.dk

Soren M. Karst smk@bio.aau.dk

Mads Albertsen MadsAlbertsen85@gmail.com

Examples

library(mmgenome2)
data(mmgenome2)
mmgenome2
#> # A tibble: 97,285 x 13
#>    scaffold length    gc cov_C13.11.14 cov_C13.11.25 cov_C13.12.03 cov_C14.01.09
#>    <chr>     <dbl> <dbl>         <dbl>         <dbl>         <dbl>         <dbl>
#>  1 1          8264  57.8       1.44             53.6         0             0.066
#>  2 2          1027  57.0       0.625            24.2         0             0    
#>  3 3          1665  55.9      13.5             434.          0.166         0.177
#>  4 4          9056  35.9       0.01             23.4         0             0    
#>  5 5          3343  64.0       3.20             16.4         0             0    
#>  6 6         98207  39.1       0.00966          24.5         3.29          9.85 
#>  7 7          6480  63.0       2.61             19.2         1.46         12.3  
#>  8 8         15790  61.7       2.78             21.2         1.62         10.3  
#>  9 9          1403  70.4      85.1             192.          0             0    
#> 10 10         2018  70.2      50.3             101.          0             0    
#> # … with 97,275 more rows, and 6 more variables: PC1 <dbl>, PC2 <dbl>,
#> #   PC3 <dbl>, geneID <chr>, taxonomy <fct>, rRNA16S <fct>
selection <- data.frame(
  cov_C13.11.25 = c(7.2, 16.2, 25.2, 23.3, 10.1),
  cov_C14.01.09 = c(47, 77, 52.8, 29.5, 22.1)
)
mmgenome2_extraction <- mmextract(mmgenome2,
  min_length = 3000,
  selection = selection,
  inverse = FALSE
)
#> 47 scaffolds (or 1.33% of the scaffolds in mm, weighted by length) remain after 97238 of 97285 scaffolds have been filtered.
mmgenome2_extraction
#> # A tibble: 47 x 13
#>    scaffold length    gc cov_C13.11.14 cov_C13.11.25 cov_C13.12.03 cov_C14.01.09
#>    <chr>     <dbl> <dbl>         <dbl>         <dbl>         <dbl>         <dbl>
#>  1 180       22093  74.0         0.298          12.0          7.34          37.9
#>  2 227      190826  65.4         0.348          13.0          6.91          38.5
#>  3 253      296715  70.2         1.06           15.2          7.00          41.1
#>  4 315      218862  71.7         0.366          12.6          7.17          38.8
#>  5 343       27203  57.6         0.235          10.7          5.07          32.0
#>  6 381        6128  67.2         8.11           22.6          5.89          48.7
#>  7 386      164942  68.2         0.359          12.3          6.73          37.2
#>  8 396        7448  72.6         0.329          13.0          7.59          41.0
#>  9 423      100199  68.7         1.40           15.3          6.71          40.0
#> 10 431      446220  72.4         0.409          12.6          6.80          37.9
#> # … with 37 more rows, and 6 more variables: PC1 <dbl>, PC2 <dbl>, PC3 <dbl>,
#> #   geneID <chr>, taxonomy <fct>, rRNA16S <fct>
if (FALSE) {
mmexport(mmgenome2_extraction,
  assembly = assembly,
  file = "bins/exported_assembly.fa"
)
}