#!/usr/bin/env python
#Lorenz 8-3-09,
# Quick script to run vienna findpath,
# by running executable accessFindPath.
# Inputs file formatted similar to fasta format,
# with lines as in the file example.faa, as well
# as the maxkeep parameter to the findPath algorithm.
#
# Displays to standard out barrier for each RNA and
# sequence pair in the input file.
# Outputs full paths to file ./fullPath.txt

from subprocess import Popen, PIPE
import sys, parseFaaForSeq

if len(sys.argv)!=3:
    output= """Usage: %s filename maxkeep"
    filename has format
    > fasta comment
    sequence
    struc1
    struc2
    Displays to standard out barrier for each RNA and
    sequence pair in the input file.
    Outputs full paths to file ./fullPath.txt"""
    print output % sys.argv[0]
    exit(1)

f=parseFaaForSeq.parseFaa(sys.argv[1])
maxkeep=int(sys.argv[2])
g=open("fullPath.txt", "w")
(seq, comment, struc1, struc2)=f.nextSeq2Str()
index=0
print "%20s %7s %s" %\
     ("name", "maxkeep", "FindPath barrier")
while (seq):
 max_list=[maxkeep]
 flag=False
 for maxkeep in max_list:
    p=Popen(["accessFindPath", seq, struc1, struc2, str(maxkeep)],
      stdin=PIPE, stdout=PIPE)
    #    print '%s %s "%s" "%s" %d' % ("accessFindPath", seq, struc1, struc2, maxkeep)
    (pout, perr)=p.communicate();
    g.write(comment+'\n'+seq+'\n'+pout)
    lines=pout.split('\n');
    maxE=-9999.
    init=True
    for line in lines:
        if len(line)<2:
            continue
        if len(line)>4 and line[:4]=="time":
          time=float(line.split()[-1])
          break
        E=float(line.split()[1])
        if (init):
           initE=E
           init=False
        maxE=max(maxE,E)
    print "%20s %7d %14.2f" %\
     (comment[:20], maxkeep, maxE-initE)
 index+=1
 (seq, comment, struc1, struc2)=f.nextSeq2Str()