"""
Wrap RNAfold command
"""
import os
import subprocess
import pybedtools
import re

def run_rnafold(seqs):
    out = structure = 0
    cmd = ("echo {seqs} | RNAfold").format(**locals())
    if len(seqs) < 200:
        process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True, close_fds=True)
        for line in iter(process.stdout.readline, ''):
            line = line.decode('utf-8')
            if line.find(" ") > -1:
                structure = line.split(" ")[0]
                out = float(re.search(' \((.+)\)', line).group(1))
                return {"structure": structure, "e": out}
    return {"structure": 'none', 'e': 'na'}

def calculate_structure(loci_file):
    structure_file = os.path.splitext(loci_file)[0] + "-fold.tsv"
    loci_bed = pybedtools.BedTool(loci_file)
    # getfasta with reference fasta
    # for line: get fasta -> run_rnafold -> add value to out_file
    return structure_file