#!/usr/bin/env python
# coding: utf-8

# # This notebook shows rich jupyter representations of Dseqrecord and derived classes
# 
# * Dseqrecord --> base class
# * GenbankRecord(Dseqrecord) --> read from Genbank link
# * GenbankFile(Dseqrecord) --> read from local file
# * Amplicon(Dseqrecord) --> PCR product
# * Contig(Dseqrecord) --> Produced through Assembly 

# In[1]:


try:
    from pydna.readers import read
    from pydna.parsers import parse_primers
    from pydna.dseqrecord import Dseqrecord
    from pydna.genbank import Genbank
    from pydna.amplify import pcr
    from pydna.assembly import Assembly
except ImportError:
    import sys, os

    sys.path.append(os.pardir)
    from pydna.readers import read
    from pydna.parsers import parse_primers
    from pydna.dseqrecord import Dseqrecord
    from pydna.genbank import Genbank
    from pydna.amplify import pcr
    from pydna.assembly import Assembly


# ### Dseqrecord

# In[2]:


ldsr = Dseqrecord("aaa")


# In[3]:


type(ldsr)


# In[4]:


ldsr


# In[5]:


[ldsr, ldsr]


# In[6]:


cdsr = Dseqrecord("aaa", circular=True)


# In[7]:


type(cdsr)


# In[8]:


cdsr


# In[9]:


[cdsr, cdsr]


# In[10]:


cdsr.reverse_complement()


# In[11]:


[cdsr.reverse_complement(), cdsr.reverse_complement()]


# In[12]:


fromstring = read(">string\naaaa")


# In[13]:


type(fromstring)


# In[14]:


fromstring


# In[15]:


[fromstring, fromstring]


# In[16]:


[fromstring.reverse_complement(), fromstring.reverse_complement()]


# ### GenbankRecord

# In[17]:


from pydna.genbankrecord import GenbankRecord


# In[18]:


# The GenbankRecord is not meant to be used directly
gbr = GenbankRecord("aaa", item="AccessionNumber", start=1, stop=3, circular=True)


# In[19]:


type(gbr)


# In[20]:


# This link is dead as expected
gbr


# In[21]:


gbr.hyperlink


# In[22]:


gbr.reverse_complement()


# In[23]:


gbr.reverse_complement().hyperlink


# In[24]:


gbr.reverse_complement().reverse_complement().hyperlink


# In[25]:


gb = Genbank("bjornjobb@gmail.com")


# In[26]:


gbr2 = gb.nucleotide("E05006")


# In[27]:


type(gbr2)


# In[28]:


gbr2


# In[29]:


gbr2.reverse_complement()


# In[30]:


gbr3 = gb.nucleotide("E05006 REGION: 5..15")


# In[31]:


type(gbr3)


# In[32]:


gbr4 = gb.nucleotide("E05006 REGION: complement(5..15)")


# In[33]:


type(gbr4)


# In[34]:


gbr4


# In[35]:


gbr4.reverse_complement()


# ### GenbankFile

# In[36]:


from pydna.genbankfile import GenbankFile


# In[37]:


gbf = GenbankFile("aaa")


# In[38]:


type(gbf)


# In[39]:


# The GenbankFile is not supposed to be used directly
# The link below is dead as expected
gbf


# In[40]:


gbf1 = read("sequence.gb")


# In[41]:


type(gbf1)


# In[42]:


gbf1


# In[43]:


gbf1.reverse_complement()


# In[44]:


gbf2 = read("subfolder/sequence.gb")


# In[45]:


type(gbf2)


# In[46]:


gbf2


# In[47]:


gbf2.reverse_complement()


# ### Amplicon

# In[48]:


from pydna.amplicon import Amplicon


# In[49]:


# The Amplicon class is not meant to be used directly, but it is possible
amp = Amplicon("aaa")


# In[50]:


type(amp)


# In[51]:


amp


# In[52]:


primers = parse_primers(
    '''
>ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg '''
)


# In[53]:


temp = Dseqrecord("gctactacacacgtactgactg" + "gatc" * 239 + "caagatagagtcagtaaccaca")


# In[54]:


prd = pcr(primers, temp)


# In[55]:


type(prd)


# In[56]:


prd.figure()


# In[57]:


prd.program()


# In[58]:


(prd, prd)


# In[59]:


prd.reverse_complement()


# In[60]:


(prd.reverse_complement(), prd.reverse_complement())


# In[61]:


prd.reverse_complement().figure()


# In[62]:


prd.reverse_complement().program()


# ### Contig

# In[63]:


from pydna.contig import Contig


# In[64]:


# Contig is not meant to be used directly, but it is possible
cnt = Contig("aaa")


# In[65]:


type(cnt)


# In[66]:


a = Dseqrecord("acgatgctatactaagCCCCtgtgctgtgctct", name="SequenceA")
b = Dseqrecord("tgtgctgtgctctTTTTTTTtattctggctgtat", name="SequenceB")
c = Dseqrecord("tattctggctgtatGGGGGtacgatgctatactaa", name="SequenceC")
x = Assembly((a, b, c), limit=13)


# In[67]:


x


# In[68]:


type(x)


# In[69]:


cnt = x.assemble_circular()[0]


# In[70]:


type(cnt)


# In[71]:


cnt


# In[72]:


cnt.detailed_figure()


# In[73]:


cnt.reverse_complement()


# In[74]:


cnt.reverse_complement().detailed_figure()