[feature request] Import Blast tabular with comment lines

[ConYel]

Hello and thank you for this impressive package!
As I'm working with some genomic ranges lately I would like to include some results from BLAST.
At first, I thought that it would be quite easy to include the results as granges but until now I haven't found a function that imports a blast resulting file in tabular with comment lines format.

For the implementation, I used an example (with some changes) from here:
In my case I use docker to run BLAST, you can find all the corresponding code below:

Context

Import BLAST output as Genomic Ranges

Code

Run docker, download database and example, output the result to current directory

docker run --rm -ti -v $(pwd):/home/my_data  ncbi/blast

curl -O https://raw.githubusercontent.com/mhahsler/rBLAST/master/inst/examples/RNA_example.fasta

curl -O https://ftp.ncbi.nlm.nih.gov/blast/db/16S_ribosomal_RNA.tar.gz

mkdir 16SMicrobialDB

tar -zxvf 16S_ribosomal_RNA.tar.gz  -C 16SMicrobialDB

blastn -db 16SMicrobialDB/16S_ribosomal_RNA -query RNA_example.fasta -out "/home/my_data/results_blast.txt" -outfmt "7 delim=@ qseqid qlen sseqid slen qstart qend sstart send qseq sseq evalue bitscore score length pident nident mismatch positive ppos frames qframe sframe sstrand qcovs qcovhsp qcovus" -ungapped -num_threads 2

exit

Import results, check lengths of Genomic Ranges that are correct and provide a pseudo-function for later development.

suppressPackageStartupMessages({
library(tidyverse)
library(plyranges)
library(vroom)}
)

## find how many fields exist for the column names
blast_file <- file.path("results_blast.txt")

fourth_line_fields <-  blast_file %>% 
  vroom_lines() %>% 
  .[4] %>% 
  str_remove("# Fields: ") %>% 
  str_split(", ") %>% 
  unlist %>% 
  str_replace_all(" |/","_") %>% 
  str_replace("%","percent") %>% 
  str_remove("\\.")
  
## create basic columns for the creation of a GR object
blast_sequences <- blast_file %>% 
  read_delim(delim = "@", # here it should be made clear that the delim could be something else
             comment = "#", 
             col_names = fourth_line_fields) %>% 
  select(ends_with(c("start","end","seq","length","strand","subject_id"))) %>% 
  mutate(strand = if_else(subject_strand == "minus","-","+") %>% as_factor(),
         start = if_else(strand == "-", s_end, s_start),
         end = if_else(strand == "+", s_start, s_end),
         seqnames = subject_id)

## check if lengths are correct
blast_sequences %>% 
  mutate(qGR_len = abs(q_end-q_start )+1,
         sGR_len = abs(end-start)+1,
         qseq_len= str_length(query_seq), 
         sseq_len = str_length(subject_seq )) %>% 
  mutate(isittrue = qGR_len == sGR_len & qseq_len == sseq_len & qGR_len == sseq_len) %>% 
  count(isittrue)

#transform from tibble to Granges and then to tibble, check if lengths are correct again
blast_sequences %>% 
  mutate(qGR_len = abs(q_end-q_start )+1,
         sGR_len = abs(end-start)+1,
         qseq_len= str_length(query_seq), 
         sseq_len = str_length(subject_seq )) %>% 
  select(seqnames, start, end, strand, qGR_len:sseq_len) %>% 
  as_granges() %>% 
  as_tibble() %>% 
  mutate(isittrue = qGR_len == sGR_len & qseq_len == sseq_len & qGR_len == sseq_len & qGR_len == width ) %>% 
  count(isittrue)

# Function?
read_blast_tab_format <- function(blast_file, delim = "@"){
  fourth_line_fields <- blast_file %>% 
  vroom_lines() %>% 
  .[4] %>% 
  str_remove("# Fields: ") %>% 
  str_split(", ") %>% 
  unlist %>% 
  str_replace_all(" |/","_") %>% 
  str_replace("%","percent") %>% 
  str_remove("\\.")
  
  blast_sequences <- blast_file %>% 
  read_delim(delim = delim, # here it should be made clear that the delim could be something else
             comment = "#", 
             col_names = fourth_line_fields) %>% 
  mutate(strand = if_else(subject_strand == "minus","-","+") %>% as_factor(),
         start = if_else(strand == "-", s_end, s_start),
         end = if_else(strand == "+", s_start, s_end),
         seqnames = subject_id) %>% 
    as_granges()
  
  return(blast_sequences)
}

Small reproducible example

See above :)

R session information

Remember to include your full R session information.

Session info -------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 4.0.3 (2020-10-10)
 os       Windows 10 x64              
 system   x86_64, mingw32             
 ui       RStudio                     
 language (EN)                        
 collate  English_United Kingdom.1252 
 ctype    English_United Kingdom.1252 
 tz       Europe/Berlin               
 date     2021-06-05                  

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Cheers! 🍻