extract_fasta: Extract fasta sequences

In ArnaudDroitLab/wgs: Automate the downloading of genbank wgs

Description

Extract the sequences obtained after a blast analysis.

Usage

extract_fasta(blast_out, metadata, merged_fasta)

Arguments

blast_out	The filename of the blast results
metadata	The subset of the metadata obtained with the merge_files or the download_files functions.
merged_fasta	The fasta obtained with the merge_files function

Details

The blast results must contain an header with the following columns:

1. qseqid

2. sseqid

3. evalue

4. qlen

5. qlen

6. pident

7. qcovs

8. length

9. sstart

10. send

Value

TODO

Examples

## Not run: 
  metadata <- get_demo_metadata()
  extract_fasta("test.out", metadata, "merged.fna")

## End(Not run)

ArnaudDroitLab/wgs documentation built on June 21, 2019, 1:51 p.m.