#!/usr/bin/python

import sys, time
from SOAPpy import WSDL

kingdom = sys.argv[1]
mol = sys.argv[2]

def revcompl(seq):
	#returns the reverse complement of the DNA
	revseq = ''
	for c in seq:
		revseq = c + revseq

	revcompseq = ''
	for base in revseq:
		if base == 'A':
			revcompseq += 'T'
		elif base == 'T':
			revcompseq += 'A'
		elif base == 'C':
			revcompseq += 'G'
		elif base == 'G':
			revcompseq += 'C'
	return revcompseq


# create SOAP services entry points
RNAmmerWSDL = 'http://www.cbs.dtu.dk/ws/RNAmmer/RNAmmer_1_2a.wsdl'

id = ""
genome = ""

#expect one fasta sequence from stdin
for line in sys.stdin:
	if line == "":
		break
	if line.startswith(">"):
		id = line.rstrip("\n").split(">")[1]
		pass
	else:
		genome = genome + line.rstrip("\n")

RmmerProxy = WSDL.Proxy(RNAmmerWSDL)

# input for RNAmmer
RmmerIn = {'kingdom' : kingdom, 'mol': mol, 'sequences' : {'entry': {'ident': id, 'seq': genome}}}


# this method returns a jobid, which can be used to get the results later
jobid = RmmerProxy.runService(RmmerIn)

print 'RNAmmer service launched with jobid: %s' % jobid.jobid

#set a loop for checking job status
job = RmmerProxy.pollQueue({'jobid' : jobid.jobid})

while job.status != 'FINISHED': 
	print 'The job is: %s' % job.status
	job = RmmerProxy.pollQueue({'jobid' : jobid.jobid})
	time.sleep(5)

print 'Job done, fetching results'

#when job is done fetch results
result = RmmerProxy.fetchResult({'jobid' : jobid.jobid})

for gene in result.entries.entry:
	sequence = gene.sequence
	#if gene.direction == "+":
	#	sequence = genome[int(gene.start)-501:int(gene.start)+500]
	#else:
	#	sequence = genome[int(gene.stop):int(gene.stop)+500]
	#	sequence = revcompl(sequence)
	print ">16SrRNA_%s..%s" % (gene.start, gene.stop)
	for i in range(0,len(sequence),60):
		print sequence[i:i+60]