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"""
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
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