Welcome to schemarecomb’s documentation!¶
With schemarecomb, you can design easy-to-use recombinant protein libraries, even if you aren’t a computational expert.
Usage¶
Here’s a simple example:
>>> import schemarecomb as sr
>>> from Bio import SeqIO
>>>
>>> # pytest stuff, you can ignore this.
>>> getfixture('bgl3_mock_namespace')
>>> tempdir = getfixture('tmpdir')
>>> out_fn = tempdir / 'bgl3_dna_frags.fasta'
>>>
>>> # Create a parent alignment and get the closest PDB structure.
>>> fn = 'tests/fixtures/bgl3_1-parent/bgl3_p0.fasta'
>>> parents = sr.ParentSequences.from_fasta(fn)
>>> parents.obtain_seqs(6, 0.7) # BLAST takes about 10 minutes.
>>> parents.align() # MUSCLE takes about a minute.
>>> parents.get_PDB() # BLAST takes about 10 minutes.
>>>
>>> # Run SCHEMA-RASPP to get libraries.
>>> libraries = sr.generate_libraries(parents, 7)
>>>
>>> # Auto-select the best library and save the resulting DNA fragments.
>>> best_lib = max(libraries, key=lambda x: x.mutation_rate - x.energy)
>>>
>>> # Save the generated DNA fragments.
>>> SeqIO.write(best_lib.dna_blocks, out_fn, 'fasta')
42
With this simple script, we generated a six parent, seven block chimeric beta-glucosidase library. The saved DNA fragments can be ordered directly from a DNA synthesis provider and assembled with NEB’s Golden Gate Assembly Kit. There’s no worrying about adding restriction sites since schemarecomb automatically adds BsaI sites.
View the Quickstart Guide for more example scripts and the Reference Manual for more details on specific classes and modules.
If you would like to contribute, view the Contributing tutorial.
Biologist’s, Programmer’s, and Installation guides coming in version 0.2.0.