Quickstart

Installation

Just pull the repo and cd into the jdna directory.

pip install .

or

pipenv install .

Examples

from jdna import Sequence

seq = Sequence("AGTCAGTA")
print(seq)

seq = Sequence.random(300)

s1 = Sequence.random(300)
s2 = s1.copy().reverse_complement()

s1.print_alignment(s2)

s1 = Sequence.random(300).complement()

s1 = Sequence.random(550)
s1.annotate(100, 300, "GFP")
# ..
s1.print()

                                                            ----------------GFP----------------
                                                            |<START
                                                            ----      -----------RFP-----------
0         CCCAGGACTAGCGACTTTCCGTAACGCGACCTAACACCGGCCGTTCCTTCGAGCCAGGCAAATGTTACGTCACTTCCTTAGATTT
          GGGTCCTGATCGCTGAAAGGCATTGCGCTGGATTGTGGCCGGCAAGGAAGCTCGGTCCGTTTACAATGCAGTGAAGGAATCTAAA

          ------GFP------
          -----------------------------------------RFP-----------------------------------------
85        TGAACAGCGCCGTACCCCGATATGATATTTAGATATATAGCAGTTACACTTGGGGTTGCTATGGACTTAGATCTGCTGTATGTTT
          ACTTGTCGCGGCATGGGGCTATACTATAAATCTATATATCGTCAATGTGAACCCCAACGATACCTGAATCTAGACGACATACAAA

          -----------------------------------------RFP-----------------------------------------
170       TCTTACCTTCCGCATCAGGGGACAATTCGCCAGTAGAATTCAGTTTGTGCGTGAGAACATAAGATTGAATCCCACGCAGGCACAA
          AGAATGGAAGGCGTAGTCCCCTGTTAAGCGGTCATCTTAAGTCAAACACGCACTCTTGTATTCTAACTTAGGGTGCGTCCGTGTT

          ---------------------RFP----------------------
255       GCAGGGCGGGCAGACTCTATAGGTCCTAAGACCCTGAGACTGCGTCCTCAAGATACAGGTTAACAATCCCCGTATGGAGCCGTTC
          CGTCCCGCCCGTCTGAGATATCCAGGATTCTGGGACTCTGACGCAGGAGTTCTATGTCCAATTGTTAGGGGCATACCTCGGCAAG

340       TTAGCATGACCCGACAGGTGGGCTTGGCTCGCGTAAGTTGAGTGTTGCAGATACCTGCTGCTGCGCGGTCTAGGGGGAATCGCCG
          AATCGTACTGGGCTGTCCACCCGAACCGAGCGCATTCAACTCACAACGTCTATGGACGACGACGCGCCAGATCCCCCTTAGCGGC

425       ATTTTGACGTAGGATCGGTAATGGGCAGTAAACCCGCAACTATTTTCAGCACCAGATGCAAGTTTCCCTAGAAAGCGTCATGGTT
          TAAAACTGCATCCTAGCCATTACCCGTCATTTGGGCGTTGATAAAAGTCGTGGTCTACGTTCAAAGGGATCTTTCGCAGTACCAA

510       TGCAATCTCCTTAGGTCACAGCAAACATAGCAGCCCCTGT
          ACGTTAGAGGAATCCAGTGTCGTTTGTATCGTCGGGGACA

s1 = Sequence.random(300)
s2 = s1.copy().reverse_complement()
s3 = s1 + s2[:30] + s2[-10:] + s2[::-1]

from jdna import Reaction, Sequence

Reaction.cyclic_assembly()