#!/usr/bin/env ruby
# you need install soap4r to run this program.Please make sure soap4r is installed.
require 'soap/wsdlDriver'
# read WSDL file
wsdl = "http://www.bioinfo.tsinghua.edu.cn/~tigerchen/SubLoc.wsdl"
# connect SOAP server
serv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver
serv.generate_explicit_type = true

# if uncommented, you can see transactions for debug
#serv.wiredump_dev = STDERR

# name_search
res = serv.name_search('p53')
# get the number of matched entries
print res.length
# get each entry's content
res.each do |each|
    print each["ID"]
    print each["OS"]
    print each["LC"]
    print each["CX"]
    print each["DE"]
    print each["SQ"]
end

#id_search
res = serv.id_search("SWISSPROT","O03978")
# get the number of matched entries
print res.length
# get each entry's content
res.each do |each|
    print each["ID"]
    print each["OS"]
    print each["LC"]
    print each["CX"]
    print each["DE"]
    print each["SQ"]
end

res = serv.id_search("DBSubLoc","10043258")
# get the number of matched entries
print res.length
# get each entry's content
res.each do |each|
    print each["ID"]
    print each["OS"]
    print each["LC"]
    print each["CX"]
    print each["DE"]
    print each["SQ"]
end

# search by GO ID
# Caution!Search by GO ID may return many many entries, please be patient, thanks
#res = serv.id_search("GO","0005739")
# get the number of matched entries
print res.length
# get each entry's content
res.each do |each|
    print each["ID"]
    print each["OS"]
    print each["LC"]
    print each["CX"]
    print each["DE"]
    print each["SQ"]
end


####################
# blast_search
seq="TKRFFNKNNRLNKGYAKTFSINEPDNNFYRKKFEHILPPVDLISEYESIYPGTLQELMHMAQKEQAHKHAIDLKNLKIQERIAKLTRICLLIFGIGLVVLIFLKLLK"
res = serv.blast_search("all","full",seq,"1")
# we provide two kinds of output formats: original BLAST output and parsed results by BioPerl's BPlite, users could choose one they like.
#get the original output of BLAST program, you could use BioRuby to parse it quite easily. There are many example scripts on the Internet.
print res["plain"]
# or you can get the parsed result (using BioPerl's BPlite)
# the parsed output's fields, every field is separated by a TAB. 
#HIT_NUM    SCORE   BITS    PERCENT EXPECT  SUBJECT_NAME    IDENTITIES	MATCH_LENGTH	QUERY_START QUERY_END	SUBJECT_START	SUBJECT_END
print res["parsed"]
# the parsed output's fields
#HIT_NUM    SCORE   BITS    PERCENT EXPECT  SUBJECT_NAME    IDENTITIES	MATCH_LENGTH	QUERY_START QUERY_END	SUBJECT_START	SUBJECT_END

############### SubLoc prediction by SVM
# for more details about the method, please see:
#Hua, S. and Sun, Z. (2001). Support vector machine approach for protein subcellular localization prediction. Bioinformatics 17, 721-8.
# for prokaryotic organisms 
seq="TKRFFNKNNRLNKGYAKTFSINEPDNNFYRKKFEHILPPVDLISEYESIYPGTLQELMHMAQKEQAHKHAIDLKNLKIQERIAKLTRICLLIFGIGLVVLIFLKLLK"
pre= serv.pro_predict(seq)
# get sequence
#print pre["Seq"]
# get predicted location
print pre["Prediction"]
print "\t"
# get expected accuracy
print pre["ExpectAcc"]
print "\t"
# get reliability index
print pre["RI"]
print "\t"

# for eukaryotic organisms
pre= serv.eu_predict(seq)
# get sequence
#print pre["Seq"]
# get predicted location
print pre["Prediction"]
print "\t"
# get expected accuracy
print pre["ExpectAcc"]
print "\t"
# get reliability index
print pre["RI"]
print "\t"

######################################################################
################# SubLoc prediction by PSORT
# for more details about PSORT, please refer:
# Nakai, K. and Horton, P. (1999). PSORT: a program for detecting sorting signals in proteins and
# predicting their subcellular localization. Trends Biochem Sci 24, 34-6.

pre= serv.psort_predict(seq)
# get predicted location
print pre["Prediction"]
# get all output information of PSORT
print pre["Detail"]

########################################################################
################## Submit new entries by users
ID="test"
DE="pseudo-entry for test"
OS="human"
LC="cytoplasmic"
CX="unknown"
SQ="XXXXXXXXXXXXXXXXXX"
feed = serv.feed_entry(ID,DE,OS,LC,CX,SQ)
print feed