SeqExtract -- In Progress ! ! !

Given a set of query sequences in FASTA format, BLAST for matches and extract matched sequences from target database using samtools.
Currently requires that the user download FASTA files of interest (reference genomes, etc) to their computer.

TODO

• Check that all issues are raised and resolved as expected ##DONE
  • checked for CLI mode
  • checked for GUI mode
• Interface directly with web databases
  • for NCBI databases, add option -remote to blast command; then clean up data
  • for others?
• Create a simple installer.sh to install BLAST, samtools, PySimpleGUI (if and as required)

Usage

$ cd SeqExtract

## run "chmod u+x ./SE_cli.sh" to use the following commands without specifying "bash"

## launch GUI
$ bash ./SE_cli.sh

## use CLI (absolute paths recommended)
$ bash ./SE_cli.sh -o path/to/output/dir -r path/to/database/dir -i path/to/query/file.fasta -q query_type -t target_type

Output Directory

|-coords/
 |--- queryid_1.coords_forward.txt
 |--- queryid_1.coords_reverse.txt
 |--- queryid_{n}.coords_forward.txt
 |--- queryid_{n}.coords_reverse.txt
|-db/
 |--- combinedrefs.fasta
 |--- {makeblastdb output files}
|-separated_results/
 |--- queryid_1.txt
 |--- queryid_{n}.txt
|-params.txt
|-queryid_1.sequences.txt
|-queryid_{n}.sequences.txt
|-SeqExt.{blast_type}.hits.outfmt6
|-SeqExtract.log-hh.mm.ss.txt

Pseudocode: SE_cli.sh

count number of options at launch
 if number of options == 0:
  pick runtype - GUI
 else:
  pick runtype - CLI
    
if runtype == "GUI":
  launch SE_gui.py
else:
  check number of arguments
  if correct number:
    collect inputs
    check inputs for issues and attempt to resolve
    pass inputs to params.txt
  else:
    print help and quit

Pseudocode: SE_gui.py

* import PySimpleGUI

generate form to collect user input
check inputs for issues
if issues:
  raise exceptions and attempt to resolve (with gui prompts)

pass inputs to params.txt

Pseudocode: SE_wrapper.sh

* source params.txt
clean up params.txt and move it to designated output path
read in variables
perform BLAST search
split BLAST output by query ID
get match start and end, examine if reverse-complement needed
collect coordinates to extract from database
samtools index into database and extract targets, reverse complement if needed
merge sequences into .sequences.txt