blast_to_mcl: Prepare BLAST results for MCL.

In joelnitta/baitfindR: Find Baits for Sequence Capture

Description

Converts the output of an all-by-all blast query into a format that can be parsed by mcl to find clusters.

Usage

blast_to_mcl(
  path_to_ys = pkgconfig::get_config("baitfindR::path_to_ys"),
  blast_results,
  hit_fraction_cutoff,
  echo = pkgconfig::get_config("baitfindR::echo", fallback = FALSE),
  ...
)

Arguments

path_to_ys	Character vector of length one; the complete path to the folder containing Y&S python scripts, e.g., "/Users/me/apps/phylogenomic_dataset_construction/"
blast_results	Character vector of length one; the complete path to the tab-separated text file containing the results from an all-by-all blast search. If blast searches were run separately (i.e., one for each sample), the results should be concatenated into a single file. For the blast search, the output format should specified as: -outfmt '6 qseqid qlen sseqid slen frames pident nident length mismatch gapopen qstart qend sstart send evalue bitscore'
hit_fraction_cutoff	Numeric between 0 and 1. Indicates the minimum percentage overlap between query and target in blast results to be retained in the output. According to Y&S, "A low hit-fraction cutoff will output clusters with more incomplete sequences and much larger and sparser alignments, whereas a high hit-fraction cutoff gives tighter clusters but ignores incomplete or divergent sequences."
echo	Logical; should the standard output and error be printed to the screen?
...	Other arguments. Not used by this function, but meant to be used by drake_plan for tracking during workflows.

Details

Wrapper for Yang and Smith (2014) blast_to_mcl.py

Value

A tab-separated text file with three columns: the first two are the matching query and target from the all-by-all blast, and the third is the negative log e-value for that match. This file is named <blast_results>.hit-frac<hit_fraction_cutoff>.minusLogEvalue, where <blast_results> and <hit_fraction_cutoff> correspond to the values of those arguments. If possible contaminants (i.e., identical sequences between different samples) were found, these are written to <blast_results>.ident.hit-frac<hit_fraction_cutoff>. Output files will be written to the same folder containing blast_results.

Author(s)

Joel H Nitta, [e-mail]

References

Yang, Y. and S.A. Smith. 2014. Orthology inference in non-model organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics. Molecular Biology and Evolution 31:3081-3092. https://bitbucket.org/yangya/phylogenomic_dataset_construction/overview

Examples

## Not run: blast_to_mcl(blast_results = "some/folder/blastresults.tab", hit_fraction_cutoff = 0.5)

joelnitta/baitfindR documentation built on May 7, 2020, 6:21 p.m.