#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
test empty
'''

import unittest
from pydna import Dseqrecord, Dseq, parse, read,  eq
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord as Srec

class test_dsdna(unittest.TestCase):

    def test_linear_circular(self):
        ''' test Dseqrecord linear & circular property'''
        a=Dseqrecord("attt")
        a.stamp()
        self.assertTrue( a.verify_stamp()  == True)
        a=Dseqrecord("attt", linear = True)
        self.assertTrue(a.linear     == True)
        self.assertTrue(a.circular   == False)
        self.assertTrue(a.rc().linear     == True)
        self.assertTrue(a.rc().circular   == False)
        self.assertTrue(a.seq.linear     == True)
        self.assertTrue(a.seq.circular   == False)

        a=Dseqrecord("attt", linear = False)
        self.assertTrue(a.linear     == False)
        self.assertTrue(a.circular   == True)
        self.assertTrue(a.rc().linear     == False)
        self.assertTrue(a.rc().circular   == True)
        self.assertTrue(a.seq.linear     == False)
        self.assertTrue(a.seq.circular   == True)

        a=Dseqrecord("attt", circular = True)
        self.assertTrue(a.linear     == False)
        self.assertTrue(a.circular   == True)
        self.assertTrue(a.rc().linear     == False)
        self.assertTrue(a.rc().circular   == True)
        self.assertTrue(a.seq.linear     == False)
        self.assertTrue(a.seq.circular   == True)

        a=Dseqrecord("attt", circular = False)
        self.assertTrue(a.linear     == True)
        self.assertTrue(a.circular   == False)
        self.assertTrue(a.rc().linear     == True)
        self.assertTrue(a.rc().circular   == False)
        self.assertTrue(a.seq.linear     == True)
        self.assertTrue(a.seq.circular   == False)

    def test_stamp(self):

        a=Dseqrecord("attt")
        a.stamp()
        self.assertTrue( a.verify_stamp()  == True)

    def test_revcomp(self):

        a=Dseqrecord("attt")

        rc = a.rc()

        self.assertTrue( str(rc.seq) == "aaat")

    def test_initialization(self):
        a=[]

        a.append(       Dseqrecord("attt")          )
        a.append(       Dseqrecord(Dseq("attt"))    )
        a.append(       Dseqrecord(Seq("attt"))     )
        a.append(       Dseqrecord(Srec(Seq("attt"))))
        a.append(       Dseqrecord(Dseqrecord("attt")) )

        for b in a:
           self.assertTrue( type(b.seq) == Dseq          )
           self.assertTrue( str(b.seq.watson) == "attt" )
           self.assertTrue( str(b.seq.crick)  == "aaat" )
           self.assertTrue( str(b.seq) == "attt"        )
           self.assertTrue( str(b.seq) == "attt"        )
           self.assertTrue(b.linear     == b.seq.linear  )
           self.assertTrue(b.linear     == True         )
           self.assertTrue(b.circular   == False        )
           self.assertTrue(b.seq.linear     == True     )
           self.assertTrue(b.seq.circular   == False    )

        a=[]
        a.append(       Dseqrecord("attt", circular=True)           )
        a.append(       Dseqrecord(Dseq("attt"), circular=True)     )
        a.append(       Dseqrecord(Seq("attt"), circular=True)      )
        a.append(       Dseqrecord(Srec(Seq("attt")), circular=True))
        a.append(       Dseqrecord(Dseqrecord("attt"), circular=True  ))

        for b in a:
           self.assertTrue( type(b.seq) == Dseq          )
           self.assertTrue( str(b.seq.watson) == "attt" )
           self.assertTrue( str(b.seq.crick)  == "aaat" )
           self.assertTrue( str(b.seq) == "attt"        )
           self.assertTrue( str(b.seq) == "attt"        )
           self.assertTrue(b.linear     == b.seq.linear  )
           self.assertTrue(b.linear     == False        )
           self.assertTrue(b.circular   == True         )
           self.assertTrue(b.seq.linear     == False    )
           self.assertTrue(b.seq.circular   == True     )

        a=[]
        a.append(Dseqrecord(Dseq("attt",circular=True), circular=True))
        a.append(Dseqrecord(Dseq("attt",circular=False), circular=True))
        a.append(Dseqrecord(Dseq("attt",circular=True), circular=False))
        a.append(Dseqrecord(Dseq("attt",circular=False), circular=False))

        circular = [True,True,False,False]
        linear   = [False,False,True,True]

        for b,ci,li in zip(a,circular,linear):
           self.assertTrue( type(b.seq) == Dseq          )
           self.assertTrue( str(b.seq.watson) == "attt" )
           self.assertTrue( str(b.seq.crick)  == "aaat" )
           self.assertTrue( str(b.seq) == "attt"        )
           self.assertTrue( str(b.seq) == "attt"        )
           self.assertTrue(b.linear     == b.seq.linear  )
           self.assertTrue(b.linear     == li  )
           self.assertTrue(b.circular   == ci         )
           self.assertTrue(b.seq.linear     == li    )
           self.assertTrue(b.seq.circular   == ci     )

        a=[]
        ds = Dseq("attt", "taaa")
        self.assertTrue(ds.linear == True)
        self.assertTrue(ds.ovhg == -1)
        self.assertTrue( str(ds.watson) == "attt" )
        self.assertTrue( str(ds.crick) == "taaa" )

        #   attt
        #    aaat

        a.append(Dseqrecord(ds, circular = False))
        self.assertTrue(ds.linear == True)
        a.append(Dseqrecord(ds, linear  = True))
        self.assertTrue(ds.linear == True)

        a.append(Dseqrecord(ds, circular=True))
        self.assertTrue(ds.linear == True)
        a.append(Dseqrecord(ds, linear=False))
        self.assertTrue(ds.linear == True)

        circular = [False,False,True,True]
        linear   = [True,True,False,False]
        crick    = ["taaa","taaa","aaat","aaat"]
        sek = ["attta","attta","attt", "attt"]
        for b,ci,li,s,cri in zip(a,circular,linear, sek, crick):

           self.assertTrue( type(b.seq) == Dseq          )
           self.assertTrue( str(b.seq.watson) == "attt" )
           self.assertTrue( str(b.seq.crick)  == cri     )
           self.assertTrue( str(b.seq) == s              )

           self.assertTrue(b.linear     == b.seq.linear  )
           self.assertTrue(b.linear     == li  )
           self.assertTrue(b.circular   == ci         )
           self.assertTrue(b.seq.linear     == li    )
           self.assertTrue(b.seq.circular   == ci     )

        a=[]
        ds = Dseq("attt", "caaa")
        self.assertTrue(ds.linear == True)
        self.assertTrue(ds.ovhg == -1)

        a.append(Dseqrecord(ds, circular=False))
        self.assertTrue(ds.linear == True)
        a.append(Dseqrecord(ds, linear=True))
        self.assertTrue(ds.linear == True)

        with self.assertRaises(TypeError):
            Dseqrecord(ds, circular=True)

        self.assertTrue(ds.linear == True)

        with self.assertRaises(TypeError):
            Dseqrecord(ds, linear=False)

        self.assertTrue(ds.linear == True)

        with self.assertRaises(TypeError):
            b = Dseqrecord([])

        with self.assertRaises(TypeError):
            b = Dseqrecord(("a",))

        with self.assertRaises(TypeError):
            b = Dseqrecord(0)

        from pydna import read

        input =   '''
                LOCUS       New_DNA                    4 bp ds-DNA     linear       30-MAR-2013
                DEFINITION  .
                ACCESSION
                VERSION
                SOURCE      .
                  ORGANISM  .
                COMMENT
                COMMENT     ApEinfo:methylated:1
                FEATURES             Location/Qualifiers
                     misc_feature    2..3
                                     /label=NewFeature
                                     /ApEinfo_fwdcolor=cyan
                                     /ApEinfo_revcolor=green
                                     /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                                     width 5 offset 0
                ORIGIN
                        1 acgt
                //
                '''
        a = read(input)

        self.assertEqual( a.features[0].extract(a).seq.watson, "CG")


        b = a+a

        for f in b.features:
            self.assertEqual( b.features[0].extract(a).seq.watson, "CG")

        feature = a.features[0]

        s = Dseq("agctt","agcta")
        #print s.fig()
        #Dseq(-6)
        # agctt
        #atcga
        b = Dseqrecord(s)
        b.features.append(feature)
        cb = Dseqrecord(b,circular=True)
        self.assertEqual(b.features[0].extract(b).seq.watson.lower(), cb.features[0].extract(b).seq.watson.lower() )
        self.assertEqual(b.features[0].extract(b).seq.crick.lower(),  cb.features[0].extract(b).seq.crick.lower() )

        s = Dseq("aagct","aagct")
        #print s.fig()
        #Dseq(-6)
        #aagct
        # tcgaa
        b = Dseqrecord(s)
        with self.assertRaises(TypeError):
            cb = Dseqrecord(b, circular=True)

        s = Dseq("agctt","agcta")
        #print s.fig()
        #Dseq(-6)
        # agcta
        #ttcga

        b = Dseqrecord(s)
        b.features.append(feature)
        cb = Dseqrecord(b,circular=True)
        self.assertEqual(b.features[0].extract(b).seq.watson.lower(), cb.features[0].extract(b).seq.watson.lower() )
        self.assertEqual(b.features[0].extract(b).seq.crick.lower(),  cb.features[0].extract(b).seq.crick.lower() )

    def test_Dseqrecord_cutting_circular(self):

        from Bio.Restriction import BsaI, KpnI, Acc65I

        test = "aaaaaaGGTACCggtctcaaaa"

        for i in range(len(test)):
            nt = test[i:]+test[:i]

            d = Dseqrecord(nt, circular = True).cut(Acc65I)[0]
            self.assertEqual(d.seq.watson.upper(), "GTACCGGTCTCAAAAAAAAAAG")
            self.assertEqual(d.seq.crick.upper(),  "GTACCTTTTTTTTTTGAGACCG")
            self.assertEqual(d.seq.ovhg, -4)

            d = Dseqrecord(nt, circular = True).cut(KpnI)[0]
            self.assertEqual(d.seq.watson.upper(), "CGGTCTCAAAAAAAAAAGGTAC")
            self.assertEqual(d.seq.crick.upper(), "CTTTTTTTTTTGAGACCGGTAC")
            self.assertEqual(d.seq.ovhg, 4)

            d = Dseqrecord(nt, circular = True).cut(BsaI)[0]
            self.assertEqual(d.seq.watson.upper(), "AAAAAAAAAGGTACCGGTCTCA")
            self.assertEqual(d.seq.crick.upper(), "TTTTTGAGACCGGTACCTTTTT")
            self.assertEqual(d.seq.ovhg, -4)


    def test_Dseq_cutting_adding(self):

        from Bio.Seq import Seq
        from Bio.Restriction import BamHI,EcoRI, PstI, EcoRV, SmaI
        from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
        from Bio.SeqUtils.CheckSum import seguid
        from pydna import Dseq


        a = Dseq('GGATCCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtGGATCC',
                 'CCTAGGagtagatgatagtagcatcgcatgactagataagacgacgagtagtagccatgagagatattaatatatatatacgcgcaCCTAGG'[::-1],
                 linear=True,
                 ovhg=0)

        b = a.cut(BamHI)[1]


        self.assertEqual( b.watson , "GATCCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtG")
        self.assertEqual( b.crick  , "GATCCacgcgcatatatatataattatagagagtaccgatgatgagcagcagaatagatcagtacgctacgatgatagtagatgaG")

        c = Dseq('nCTGCAGtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtGAATTCn',
                 'nGACGTCagtagatgatagtagcatcgcatgactagataagacgacgagtagtagccatgagagatattaatatatatatacgcgcaCTTAAGn'[::-1],
                 linear=True,
                 ovhg=0)

        f,d,l = c.cut((EcoRI, PstI))

        self.assertEqual( d.watson  , "GtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtG")
        self.assertEqual( d.crick   , "AATTCacgcgcatatatatataattatagagagtaccgatgatgagcagcagaatagatcagtacgctacgatgatagtagatgaCTGCA")


        e =    Dseq("nGAATTCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtCTGCAGn",
                    "nCTTAAGagtagatgatagtagcatcgcatgactagataagacgacgagtagtagccatgagagatattaatatatatatacgcgcaGACGTCn"[::-1],
                    linear=True,
                    ovhg=0)

        f = e.cut((EcoRI,PstI))[1]

        self.assertEqual( f.watson ,"AATTCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtCTGCA")
        self.assertEqual( f.crick  , "GacgcgcatatatatataattatagagagtaccgatgatgagcagcagaatagatcagtacgctacgatgatagtagatgaG")



        ''' blunt cloning '''


        pUC19 = read("./pUC19.gb")

        self.assertFalse( pUC19.linear )

        self.assertTrue( len(pUC19) == 2686 )
        self.assertTrue( len(pUC19.seq.watson) == 2686 )
        self.assertTrue( len(pUC19.seq.crick) == 2686 )

        self.assertTrue( pUC19.seq.circular == True)
        self.assertTrue( pUC19.seq.linear   == False)

        pUC19_SmaI = pUC19.cut(SmaI)
        self.assertTrue( len(pUC19_SmaI) == 1)
        pUC19_SmaI = pUC19_SmaI.pop()


        self.assertTrue( pUC19_SmaI.linear )
        self.assertTrue( len(pUC19_SmaI) == 2686 )
        self.assertTrue( pUC19_SmaI.linear )

        pUC19_SmaI_a = pUC19_SmaI.seq + a

        self.assertTrue(  pUC19_SmaI_a.linear   )
        self.assertFalse( pUC19_SmaI_a.circular )

        pUC19_SmaI_a=pUC19_SmaI_a.looped()
        self.assertTrue( len(pUC19_SmaI_a) == 2778 )

        self.assertTrue(  pUC19_SmaI_a.circular )
        self.assertFalse( pUC19_SmaI_a.linear   )
        self.assertTrue( eq(pUC19_SmaI_a, read("./pUC19-SmaI-a.gb")   ))

        ''' sticky end cloning '''

        pUC19_BamHI = pUC19.cut(BamHI)

        self.assertTrue( len(pUC19_BamHI) == 1)

        pUC19_BamHI = pUC19_BamHI.pop().seq

        self.assertTrue( len(pUC19_BamHI.watson) == len(pUC19_BamHI.crick) == 2686 )

        pUC19_BamHI_a = pUC19_BamHI+b

        self.assertTrue( len(pUC19_BamHI_a.watson) == len(pUC19_BamHI_a.crick) == 2772 )

        self.assertTrue( pUC19_BamHI_a.circular == False)
        self.assertTrue( pUC19_BamHI_a.linear   == True)

        pUC19_BamHI_a = pUC19_BamHI_a.looped()

        self.assertTrue( pUC19_BamHI_a.circular == True)
        self.assertTrue( pUC19_BamHI_a.linear   == False)

        self.assertTrue( eq(pUC19_BamHI_a, read("./pUC19-BamHI-a.gb")))

        pUC19_BamHI_a_rc = pUC19_BamHI+b.rc()

        pUC19_BamHI_a_rc = pUC19_BamHI_a_rc.looped()


        self.assertTrue( pUC19_BamHI_a.circular == True)
        self.assertTrue( pUC19_BamHI_a.linear   == False)
        self.assertTrue( eq(pUC19_BamHI_a_rc, read("./pUC19-BamHI-a-rc.gb")))

        ''' adding (ligating) dsDNA objects '''
        with self.assertRaisesRegexp(TypeError, "circular"):
            pUC19+a
        with self.assertRaisesRegexp(TypeError, "circular"):
            a+pUC19
        with self.assertRaisesRegexp(TypeError, "compatible"):
            a+b
        with self.assertRaisesRegexp(TypeError, "compatible"):
            b+a
        with self.assertRaisesRegexp(TypeError, "compatible"):
            d+d

        ''' directional cloning '''

        pUC19_EcoRI_PstI = pUC19.cut(EcoRI, PstI).pop(0)

        with self.assertRaisesRegexp(TypeError, "compatible"):
            pUC19_EcoRI_PstI + d

        pUC19_EcoRI_PstI_d = pUC19_EcoRI_PstI + d.rc()

        pUC19_EcoRI_PstI_d =  pUC19_EcoRI_PstI_d.looped()

        self.assertTrue( eq(pUC19_EcoRI_PstI_d,      read("./pUC19-EcoRI_PstI-d-rc.gb")))
        self.assertTrue( eq(pUC19_EcoRI_PstI_d.rc(), read("./pUC19-EcoRI_PstI-d-rc.gb")))


    def test_Dseqrecord_cutting_adding(self):
        from Bio.Restriction import Bsu36I, BstAPI
        pCAPs = read("./pCAPs.gb")
        a,b = pCAPs.cut(Bsu36I, BstAPI)
        c=(a+b).looped()
        self.assertTrue( eq(c, pCAPs) )


        a = (Dseqrecord( Dseq(  'AATTCACANGGTACCNGGTACCNGCGGATATC',
                                 'GTGTNCCATGGNCCATGGNCGCCTATAG'[::-1], -4)),

             Dseqrecord( Dseq(      'CACANGGTACCNGGTACCNGCGGATATC',
                                 'GTGTNCCATGGNCCATGGNCGCCTATAG'[::-1], 0)),

             Dseqrecord( Dseq(    'CACANGGTACCNGGTACCNGCGGATATC',
                           'AATTGTGTNCCATGGNCCATGGNCGCCTATAG'[::-1], 4)),)

        from Bio.Restriction import KpnI, Acc65I, NlaIV

        enzymes = [Acc65I, NlaIV, KpnI]

        for enz in enzymes:
            for f in a:
                b,c,d = f.cut(enz)
                e=b+c+d
                assert str(e.seq).lower() == str(f.seq).lower()



        #from pydna import *
        #from pydna_helper import gb, ape
        from Bio.Restriction import KpnI, BamHI, Acc65I, NlaIV, EcoRI, EcoRV

        a=read('''

    LOCUS       New_DNA                   10 bp ds-DNA     linear       02-APR-2013
    DEFINITION
    ACCESSION   New_DNA
    VERSION     New_DNA
    KEYWORDS    .
    SOURCE
      ORGANISM  . .
    COMMENT
    COMMENT     ApEinfo:methylated:1
    FEATURES             Location/Qualifiers
         misc_feature    1..1
                         /label=1
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
         misc_feature    2..2
                         /label=2
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
         misc_feature    3..3
                         /label=3
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
         misc_feature    4..4
                         /label=4
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
         misc_feature    5..5
                         /label=5
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
         misc_feature    6..6
                         /label=6
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
         misc_feature    7..7
                         /label=7
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
         misc_feature    8..8
                         /label=8
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
         misc_feature    9..9
                         /label=9
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
         misc_feature    10..10
                         /label=10
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
    ORIGIN
            1 ttGGTACCgg
    //''')

        b,c = a.cut(Acc65I)

        self.assertEqual( [f.qualifiers["label"] for f in b.features], [['1'], ['2'], ['3'], ['4'], ['5'], ['6'], ['7']])
        self.assertEqual( [f.qualifiers["label"] for f in c.features], [['4'], ['5'], ['6'], ['7'], ['8'], ['9'], ['10']])




        a=read('''

    LOCUS       New_DNA                   33 bp ds-DNA     linear       08-NOV-2012
    DEFINITION  .
    ACCESSION
    VERSION
    SOURCE      .
      ORGANISM  .
    COMMENT
    COMMENT     ApEinfo:methylated:1
    FEATURES             Location/Qualifiers
         misc_feature    1..11
                         /label=Acc65I-1
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
         misc_feature    12..18
                         /label=Acc65I-2
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
         misc_feature    19..33
                         /label=Acc65I-3
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
         misc_feature    1..15
                         /label=KpnI-1
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
         misc_feature    16..22
                         /label=KpnI-2
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
         misc_feature    23..33
                         /label=KpnI-3
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
         misc_feature    1..13
                         /label=NlaIV-1
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
         misc_feature    14..20
                         /label=NlaIV-2
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
         misc_feature    21..33
                         /label=NlaIV-3
                         /ApEinfo_fwdcolor=cyan
                         /ApEinfo_revcolor=green
                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                         width 5 offset 0
    ORIGIN
            1 GAATTCacan ggtaccnGGT ACCngcgGAT ATC
    //

        ''')

        self.assertTrue( a.seguid()=="di3hL8t2G4iQQsxlm/CtvnUMBz8" )

        self.assertTrue( ([x.qualifiers["label"][0] for x in a.features] ==
        ['Acc65I-1', 'Acc65I-2', 'Acc65I-3', 'KpnI-1', 'KpnI-2',
         'KpnI-3', 'NlaIV-1', 'NlaIV-2', 'NlaIV-3']))

        b,c,d = a.cut(Acc65I)

        self.assertTrue( [x.qualifiers["label"][0] for x in b.features] == ['Acc65I-1', 'KpnI-1', 'NlaIV-1'])
        self.assertTrue( [x.qualifiers["label"][0] for x in c.features] == ['Acc65I-2', 'KpnI-2', 'NlaIV-2'])
        self.assertTrue( [x.qualifiers["label"][0] for x in d.features] == ['Acc65I-3', 'KpnI-3', 'NlaIV-3'])
        e = b+c+d
        self.assertTrue( sorted([x.qualifiers["label"][0] for x in e.features])  == [x.qualifiers["label"][0] for x in a.features])
        self.assertTrue( str(a.seq)==str(e.seq))

        b,c,d = a.cut(KpnI)
        self.assertTrue( [x.qualifiers["label"][0] for x in b.features] == ['Acc65I-1', 'KpnI-1', 'NlaIV-1'])
        self.assertTrue( [x.qualifiers["label"][0] for x in c.features] == ['Acc65I-2', 'KpnI-2', 'NlaIV-2'])
        self.assertTrue( [x.qualifiers["label"][0] for x in d.features] == ['Acc65I-3', 'KpnI-3', 'NlaIV-3'])
        e = b+c+d
        self.assertTrue( sorted([x.qualifiers["label"][0] for x in e.features])  == [x.qualifiers["label"][0] for x in a.features])

        b,c,d = a.cut(NlaIV)
        self.assertTrue( [x.qualifiers["label"][0] for x in b.features] == ['Acc65I-1', 'NlaIV-1'])
        self.assertTrue( [x.qualifiers["label"][0] for x in c.features] == ['NlaIV-2'])
        self.assertTrue( [x.qualifiers["label"][0] for x in d.features] == [ 'KpnI-3', 'NlaIV-3'])
        e = b+c+d
        self.assertTrue( str(a.seq)==str(e.seq))

        b,c = a.cut(EcoRI)
        e = b+c
        self.assertTrue( str(a.seq)==str(e.seq))

        b,c = a.cut(EcoRV)
        e = b+c
        self.assertTrue( str(a.seq)==str(e.seq))

        b,c,d = a.cut(EcoRI,EcoRV)
        e = b+c+d

        self.assertTrue( str(a.seq)==str(e.seq))

        b,c,d, f = a.cut(Acc65I,EcoRI)
        e = b+c+d+f
        self.assertTrue( str(a.seq)==str(e.seq))

        b,c,d, f = a.cut(EcoRI,Acc65I)
        e = b+c+d+f
        self.assertTrue( str(a.seq)==str(e.seq))




    def test_Dseq_slicing(self):
        from Bio.Restriction import BamHI
        a=Dseq("ggatcc","ggatcc",0)

        self.assertEqual( a[:].watson, a.watson )
        self.assertEqual( a[:].crick, a.crick )
        self.assertEqual( a.ovhg, a[:].ovhg )

        b,c = a.cut(BamHI)
        d = b[1:5]
        e = d.rc()
        self.assertEqual( d+e, Dseq("gatc","gatc",0))



    def test_Dseq_slicing2(self):

        from Bio.Restriction import BamHI, EcoRI, KpnI

        a = Dseq("aaGGATCCnnnnnnnnnGAATTCccc", circular=True)

        self.assertEqual( a.cut(EcoRI, BamHI, KpnI,), a.cut(BamHI, EcoRI, KpnI,))

        a = Dseqrecord("aaGGATCCnnnnnnnnnGAATTCccc", circular=True)

        self.assertEqual( a.cut( EcoRI, BamHI,  KpnI,)[0].seq, a.cut( BamHI, EcoRI,  KpnI,)[0].seq)



    def test_rogerstager(self):

        from Bio.Seq import Seq
        from Bio.Restriction import BsaI

        answ = []
        answ.append( Dseq('aaaaaaaaaaaaggtctca', 'ttttttttccagagttttt'[::-1]) )
        answ.append( Dseq('aaaaaaaaaggtctca', 'tttttccagagttttt'[::-1]) )

        tests = [Seq("aaaaaaggtctcaaaaaaa"),
                 Seq("aaaaaaggtctcaaaa")  ]
        for s in tests:
            d = Dseqrecord(s).looped()
            for f in d.cut(BsaI):
                a = answ.pop(0)
                self.assertTrue( f.seq.watson == a.watson )
                self.assertTrue( f.seq.crick  == a.crick )
                self.assertTrue( f.seq.ovhg == a.ovhg )
                self.assertTrue( eq(f.seq, a) )



    def test_cut_around_and_religate(self):

        from Bio.Restriction import KpnI, BamHI, Acc65I

        def cut_and_religate_Dseq(seq_string, enz, top):
            ds = Dseq(seq_string, linear=top)
            frags = ds.cut(enz)
            if not frags:
                return
            a = frags.pop(0)
            for f in frags:
                a+=f
            if not top:
                a=a.looped()
            self.assertTrue( eq(a,ds) )

        seqs = [
                ("aaaGGTACCcccGGTACCCgggGGTACCttt", BamHI,  False),
                ("aaaGGTACCcccGGTACCCgggGGTACCttt", Acc65I, False),
                ("aaaGGTACCcccGGTACCCgggGGTACCttt", KpnI,   False),

                ("aaaGGTACCcccGGTACCCgggGGTACCttt", Acc65I, True),
                ("aaaGGTACCcccGGTACCCgggGGTACCttt", KpnI,   True),
                ("aaaGGTACCcccGGTACCCgggGGTACCttt", BamHI,  True),

                ("aaaGGTACCcccGGATCCCgggGGTACCttt", [Acc65I, BamHI], False),
                ("aaaGGTACCcccGGATCCCgggGGTACCttt", [KpnI, BamHI],   False),
                ("aaaGGTACCcccGGATCCCgggGGTACCttt", [BamHI,Acc65I],  False),
                ("aaaGGTACCcccGGATCCCgggGGTACCttt", [BamHI,KpnI],    False),

                ("aaaGGTACCcccGGATCCCgggGGTACCttt", [Acc65I, BamHI], True),
                ("aaaGGTACCcccGGATCCCgggGGTACCttt", [KpnI, BamHI],   True),
                ("aaaGGTACCcccGGATCCCgggGGTACCttt", [BamHI,Acc65I],  True),
                ("aaaGGTACCcccGGATCCCgggGGTACCttt", [BamHI,KpnI],    True),

                ]

        for s in seqs:
            sek, enz, lin = s
            for i in range(len(sek)):
                zek = sek[i:]+sek[:i]
                cut_and_religate_Dseq(zek, enz, lin)
                
                
    def test_features_change_ori(self):

        s = read('''
                    LOCUS       New_DNA                   13 bp ds-DNA     circular     12-NOV-2013
                    DEFINITION  .
                    ACCESSION   
                    VERSION     
                    SOURCE      .
                    ORGANISM  .
                    COMMENT     
                    COMMENT     ApEinfo:methylated:1
                    FEATURES             Location/Qualifiers
                         misc_feature    join(9..10,12..13,1..1,3..6)
                                         /label=hej
                                         /ApEinfo_fwdcolor=cyan
                                         /ApEinfo_revcolor=green
                                         /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                                         width 5 offset 0
                    ORIGIN
                            1 gattttaatc acc    
                    //''')

        #from pydna_helper import ape

        for i in range(1, len(s)):
            b=s.shifted(i)
            self.assertTrue(  str(b.features[0].extract(b).seq).lower()=="tcccgtttt")
    
        s = read('''
                LOCUS       New_DNA                   21 bp ds-DNA     circular     03-APR-2013
                DEFINITION  a
                ACCESSION
                VERSION
                SOURCE      .
                  ORGANISM  .
                COMMENT
                COMMENT     ApEinfo:methylated:1
                FEATURES             Location/Qualifiers
                     misc_feature    join(18..21,1..4)
                                     /label=bb
                                     /ApEinfo_fwdcolor=cyan
                                     /ApEinfo_revcolor=green
                                     /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                                     width 5 offset 0
                     misc_feature    5..17
                                     /label=ins
                                     /ApEinfo_fwdcolor=#e03c2b
                                     /ApEinfo_revcolor=green
                                     /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                                     width 5 offset 0
                ORIGIN
                        1 aaaGGTACCt ttGGATCCggg
                //
            ''')

        self.assertTrue( str(s.features[0].extract(s).seq)  == "CGGGAAAG" )
        self.assertTrue( str(s.features[1].extract(s).seq)  == "GTACCTTTGGATC" )
    
        for i in range(1, len(s)):
        
            b = s.shifted(i)
            self.assertTrue( [str(f.extract(b).seq) for f in b.features if f.qualifiers["label"][0]=='ins'][0] == "GTACCTTTGGATC" )
            self.assertTrue( [str(f.extract(b).seq) for f in b.features if f.qualifiers["label"][0]=='bb'][0] == "CGGGAAAG" )
        
        from Bio.Restriction import Acc65I,KpnI, BamHI

        bb1, ins1 = sorted(s.cut(Acc65I, BamHI), key=len, reverse=True)

        for i in range(1, len(s)):
            b = s.shifted(i)

            bb, ins = sorted(b.cut(Acc65I, BamHI), key=len, reverse=True)

            self.assertTrue( eq(bb1, bb) )
            self.assertTrue( eq(ins1,ins) )

            self.assertTrue( bb.features[0].extract(bb).seq.watson == "CGGGAAAG" )
            self.assertTrue( bb.features[0].extract(bb).seq.crick  == "CTTTCCCG" )

            self.assertTrue( eq(bb.features[0].extract(bb), s.features[0].extract(s) ) )

            self.assertTrue( ins.features[0].extract(ins).seq.watson == "GTACCTTTG" )
            self.assertTrue( ins.features[0].extract(ins).seq.crick  == "GATCCAAAG" )

            self.assertTrue( str(ins.features[0].extract(ins).seq) == str(s.features[1].extract(s).seq) )


    def test_synced(self):
        pUC19        = read("./pUC19.gb")
        pUC19_LAC4   = read("./pUC_LAC4.gb")
        pUC19_LAC4_c = read("pUC_LAC4_correct_rotation.gb")
        
        correct = str(pUC19_LAC4_c.seq).upper()
        
        for i in range(1, len(pUC19_LAC4), 500):
            cand = pUC19_LAC4.shifted(i)
            self.assertEqual(str(cand.synced("tcgcgcgtttcggtgatgacggtga").seq).upper(),
                             correct,
                             str(pUC19_LAC4.synced(pUC19).seq).upper())
            print i,
        print
        


    def test_synced3(self):
        pGUP1 = read("pGUP1_correct.gb")
        pGREG505 = read("pGREG505.gb")
        pGUP1_not_synced =  read("pGUP1_not_synced.gb")
        self.assertEqual(pGUP1_not_synced.synced(pGREG505).seguid(), '42wIByERn2kSe/Exn405RYwhffU')

class test_sync(unittest.TestCase):

    def test_synced2(self):
        pUC19            = read("./pUC19.gb")
        pUC19_small_gene = read("./pUC19_small_gene.gb")
        
        correct = str(pUC19_small_gene.seq).upper()
        
        for i in range(1, len(pUC19_small_gene), 500):
            cand = pUC19_small_gene.shifted(i)
            self.assertEqual(str(cand.synced("tcgcgcgtttcggtgatgacggtga").seq).upper(),
                             correct,
                             str(cand.synced(pUC19).seq).upper())
            print i,
        print

if __name__ == '__main__':
    runner = unittest.TextTestRunner(verbosity = 3)
    unittest.main(testRunner=runner)

