rime_mmseqs

#!/bin/bash

# Check for help argument or no arguments
if [[ "$1" == "-h" || "$1" == "--help" || $# -lt 2 ]]; then
    echo "Usage: rime_msa <fasta_file> <output_dir>"
    echo "Example: rime_msa input.fasta results_dir"
    echo 
    echo "Arguments:"
    echo "  <fasta_file>   Path to the input FASTA file"
    echo "  <output_dir>   Directory where the results will be extracted"
    echo
    echo "Set up help:"
    echo "1) Make sure you do give this file the correct persmissions. You can do that with the following command"
    echo "chmod 775 rime_mmseqs" 
    echo "2) Add this file's directory to your path. If you want it here, copy-paste this line to your bashrc file: "
    echo "export PATH=$(pwd):\$PATH"
    echo
    echo "Description:"
    echo "This function uploads a FASTA file to Rime for MSA generation and downloads the results."
    echo "input.fasta can *and should* have multiple sequences in the single fasta - this is VERY efficent!"
    echo 
    exit 0
fi

fasta_file=$1
output_dir=$2

red=$'\e[31m' 
none=$'\e[0m'  

if [ -e ./result.zip ]; then
    echo -e "${red}Warning: result.zip detected! Changed name to result.backup.jderoo123changeme.zip ${none}"
    mv result.zip result.backup.jderoo123changeme.zip
fi

PORT_NUMBER=12345
curl -X POST -F "fasta=@$fasta_file" http://rime.engr.colostate.edu:${PORT_NUMBER}/run_alignment --output result.zip


if [ ! -e ./result.zip ]; then
    echo -e "${red}Warning: api call failed. Try again later, or ask Chris to investigate ${none}"
else
    unzip result.zip -d $output_dir
    rm result.zip
fi