#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
utils tests
'''
import pytest
import sys

from pydna import eq, shift_origin, read, Dseqrecord
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord



def test_eq():
    ''' test eq'''
    assert   eq( "AAA" ,"TTT", linear   = True )
    assert  eq( "AAA" ,"TTT", linear   = False)

    assert  eq( "aAA" ,"TtT", linear   = True )
    assert  eq( "AAa" ,"TtT", linear   = False)


    assert  eq( "ATA" ,"AAT", circular = True )
    assert not eq( "ATA" ,"AAT", circular = False)
    assert  eq( "AAA" ,"AAA", linear   = True ) 
    assert  eq( "AAA" ,"AAA", linear   = False) 

    assert  eq( "ATA" ,Seq("AAT"), circular = True ) 
    assert not eq( "ATA" ,Seq("AAT"), circular = False) 
    assert  eq( "AAA" ,Seq("AAA"), linear   = True ) 
    assert  eq( "AAA" ,Seq("AAA"), linear   = False) 

    assert  eq( "ATA" ,SeqRecord("AAT"), circular = True ) 
    assert not eq( "ATA" ,SeqRecord("AAT"), circular = False)
    assert  eq( "AAA" ,SeqRecord("AAA"), linear   = True ) 
    assert  eq( "AAA" ,SeqRecord("AAA"), linear   = False) 

    assert  eq( "ATA" ,Dseqrecord("AAT"), circular = True ) 
    assert not eq( "ATA" ,Dseqrecord("AAT"), circular = False) 
    assert  eq( "AAA" ,Dseqrecord("AAA"), linear   = True ) 
    assert  eq( "AAA" ,Dseqrecord("AAA"), linear   = False) 

    assert  eq( Seq("ATA") ,SeqRecord("AAT"), circular = True )
    assert not eq( Seq("ATA") ,SeqRecord("AAT"), circular = False)
    assert  eq( Seq("AAA") ,SeqRecord("AAA"), linear   = True )
    assert  eq( Seq("AAA") ,SeqRecord("AAA"), linear   = False)

    assert  eq( Seq("ATA") ,Dseqrecord("AAT"), circular = True )
    assert not eq( Seq("ATA") ,Dseqrecord("AAT"), circular = False)
    assert  eq( Seq("AAA") ,Dseqrecord("AAA"), linear   = True ) 
    assert  eq( Seq("AAA") ,Dseqrecord("AAA"), linear   = False) 

    assert  eq( Dseqrecord("AAA",circular=False) ,Dseqrecord("AAA",circular=False)) 
    assert  eq( Dseqrecord("AAA",circular=True)  ,Dseqrecord("AAA",circular=True))   
    assert not eq( Dseqrecord("ATA",circular=False) ,Dseqrecord("AAT",circular=False)) 
    assert  eq( Dseqrecord("ATA",circular=True)  ,Dseqrecord("AAT",circular=True)) 


def test_shift_origin():

    pCAPs   = read("pCAPs.gb")
    assert pCAPs.circular
    pCAPs_b = shift_origin(pCAPs, 200)
    assert len(pCAPs) == len(pCAPs_b)
    assert pCAPs_b.circular
    assert eq(pCAPs, pCAPs_b)
    pCAPs_b_linear = pCAPs_b.tolinear()
    assert eq(pCAPs, pCAPs_b_linear, circular=True)
    pCAPs_c = pCAPs[200:]+pCAPs[:200]
    assert eq(pCAPs, pCAPs_c, circular=True)
    #with self.assertRaisesRegex(ValueError, "shift"):
    #    pCAPs_b = shift_origin(pCAPs, 20000)


def test_copy_features():

    from pydna.utils import seguid
    from pydna import read,copy_features
    a=read("pCAPs.gb")
    b=read("pCAPs_fasta.txt")

    for sh in [1,2,3,3127,3128,3129]:
        newb = (b[sh:]+b[:sh]).looped()
        copy_features(a, newb)
        #print "a",[len(str(f.extract(a).seq.lower()) for f in a.features if len(f)>10]
        #print "b",[len(str(f.extract(newb).seq).lower()) for f in newb.features]
        x= sorted([str(f.extract(a).seq).lower() for f in a.features if len(f)>10],key=len)
        y= sorted([str(f.extract(newb).seq).lower() for f in newb.features],key=len)
        assert x==y

    b=b.rc()

    for sh in [1,2,3,3127,3128,3129]:
        newb = b[sh:]+b[:sh]
        copy_features(a, newb)
        
        
        x = sorted([str(f.extract(a).seq).lower() for f in a.features if len(f)>10],key=len)
        y = sorted([str(f.extract(newb).seq).lower() for f in newb.features],key=len)
        assert x==y

    seguid_bla = "riT98j2v4NxVS8sbw_Q8epCwQwo"
    seguid_cre = "xLZ2xs2O8CUMmWh2OrhmNFp5ZLg"

    copy_features(a, b)
    assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_cre, seguid_cre, seguid_bla, seguid_bla]

    b=read("pCAPs_fasta.txt").looped()

    b=b.synced("attaacgagtgccgtaaacgacgatggttttacc")

    copy_features(a, b)
    assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_cre,seguid_cre,seguid_bla,seguid_bla]

    b=read("pCAPs_fasta.txt").looped()
    b=b.synced("ttaacgagtgccgtaaacgacgatggttttacc")

    copy_features(a, b)
    assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_cre,seguid_cre,seguid_bla,seguid_bla]

    b=read("pCAPs_fasta.txt").looped()
    b=b.synced("taacgagtgccgtaaacgacgatggttttacc")

    copy_features(a, b)
    assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_bla,seguid_bla]

    b=read("pCAPs_fasta.txt").looped()
    b=b.synced("gttaccaatgcttaatcagtgaggcacctatctcagc")

    copy_features(a, b)
    assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_cre,seguid_cre,seguid_bla,seguid_bla]

    b=read("pCAPs_fasta.txt").looped()
    b=b.synced("ttaccaatgcttaatcagtgaggcacctatctcagc")

    copy_features(a, b)
    assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_cre,seguid_cre,seguid_bla,seguid_bla]

    b=read("pCAPs_fasta.txt").looped()
    b=b.synced("taccaatgcttaatcagtgaggcacctatctcagc")

    copy_features(a, b)
    assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_cre,seguid_cre,]


def test_cseguid():
    from pydna.utils import cseguid
    x="tcgcgcgtttcggtgatgacggtgaaaacctctgacacatgcagctcccggagacggtcacagcttgtctgtaagcggatgccgggagcagacaagcccgtcagggcgcgtcagcgggtgttggcgggtgtcggggctggcttaactatgcggcatcagagcagattgtactgagagtgcaccatatgcggtgtgaaataccgcacagatgcgtaaggagaaaataccgcatcaggcgccattcgccattcaggctgcgcaactgttgggaagggcgatcggtgcgggcctcttcgctattacgccagctggcgaaagggggatgtgctgcaaggcgattaagttgggtaacgccagggttttcccagtcacgacgttgtaaaacgacggccagtgaattcgagctcggtacccgggGATCTATGAATATGGATCCGACTTACTGCAGGAATTCAAGCTACTGTTAGAgatcctctagagtcgacctgcaggcatgcaagcttggcgtaatcatggtcatagctgtttcctgtgtgaaattgttatccgctcacaattccacacaacatacgagccggaagcataaagtgtaaagcctggggtgcctaatgagtgagctaactcacattaattgcgttgcgctcactgcccgctttccagtcgggaaacctgtcgtgccagctgcattaatgaatcggccaacgcgcggggagaggcggtttgcgtattgggcgctcttccgcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccataggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagttaccaatgcttaatcagtgaggcacctatctcagcgatctgtctatttcgttcatccatagttgcctgactccccgtcgtgtagataactacgatacgggagggcttaccatctggccccagtgctgcaatgataccgcgagacccacgctcaccggctccagatttatcagcaataaaccagccagccggaagggccgagcgcagaagtggtcctgcaactttatccgcctccatccagtctattaattgttgccgggaagctagagtaagtagttcgccagttaatagtttgcgcaacgttgttgccattgctacaggcatcgtggtgtcacgctcgtcgtttggtatggcttcattcagctccggttcccaacgatcaaggcgagttacatgatcccccatgttgtgcaaaaaagcggttagctccttcggtcctccgatcgttgtcagaagtaagttggccgcagtgttatcactcatggttatggcagcactgcataattctcttactgtcatgccatccgtaagatgcttttctgtgactggtgagtactcaaccaagtcattctgagaatagtgtatgcggcgaccgagttgctcttgcccggcgtcaatacgggataataccgcgccacatagcagaactttaaaagtgctcatcattggaaaacgttcttcggggcgaaaactctcaaggatcttaccgctgttgagatccagttcgatgtaacccactcgtgcacccaactgatcttcagcatcttttactttcaccagcgtttctgggtgagcaaaaacaggaaggcaaaatgccgcaaaaaagggaataagggcgacacggaaatgttgaatactcatactcttcctttttcaatattattgaagcatttatcagggttattgtctcatgagcggatacatatttgaatgtatttagaaaaataaacaaataggggttccgcgcacatttccccgaaaagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcacgaggccctttcgtc"
    assert cseguid(x) == cseguid(x.upper()) == cseguid(x.lower()) == 'JgiKgBksd2v3q99NStKLepoQCm8'
    from Bio.SeqUtils.CheckSum  import seguid as base64_seguid



if __name__ == '__main__':
    pytest.cmdline.main([__file__, "-v", "-s"])
