bioviper

Warning: this code is still under development - while most parts are functional, there are still likely bugs and features that are yet to be implemented. Make a pull request if you have an issue!

A set of classes and functions built on top of Biopython to make working with biological data - primarily sequence alignments, protein structures and phylogenetic trees - simpler and more straightforward.

The core of this code is a set of three new classes: a MultipleSequenceAlignment class, a SequenceArray class (for unaligned sequences) and a ProteinStructure class.

I am working on a set of Jupyter notebooks that should explain the basic usage of these objects.

Installation

bioviper is now on PyPI and can be installed with pip or conda install:

pip install bioviper

However, for the last development version which may have some bugs fixed or new funcitonality being tested, I recommend using:

pip install git+https://github.com/samberry19/bioviper/

for the time being.

Basics

To load an alignment from a file:

msa = readAlignment("alignment.fa", format="fasta")

Much like a traditional Biopython MSA, this object is essentially a list of Bio.SeqRecord.SeqRecord objects, but it can do a few nice new things:

msa.ids                      # gives you all of the ids in the sequence alignment
msa.matrix                   # gives you the alignment as a 2D numpy array
msa[np.array([3,5,6,9])]     # gives a new MSA with the 3rd, 5th, 6th and 9th sequences
msa[:,np.array([3,5,6,9])]   # gives a new MSA with the 3rd, 5th, 6th and 9th columns
msa.calc_coverage()          # calculates the alignment coverage and stores it as msa.coverage
msa.calc_frequencies()       # calculates the frequency of each amino acid and stores it as msa.frequencies
msa.search_id("HUMAN")       # returns all sequences with "HUMAN" in the id
msa.search_sequence("ACYWL") # searches for sequence record(s) with the following subsequence
msa.sequence_lengths()       # returns the length of each sequence in the alignment, not countin gaps
msa.dealign()                # gives you all dealigned sequences (gaps removed)
msa.save(filename)           # saves to a file

To load a structure from a file:

structure = readPDB("6bu5.pdb", name="Nramp outward-open", model=0, chain="A")

There is no easy-to-use protein structure object in Biopython, so this one has mostly entirely new functionality (while incorporating Biopython residue and atom objects). Simple usage includes:

structure.sequence              # the full sequence from the PDB file
structure.ordered_sequence      # the part of the sequence for which there is structural data (the ordered residues)
structure.xyz                   # the xyz coordinates of the structure as a 2D numpy array
structure.residues              # a list of all of the residue objects
structure.atoms                 # a list of all of the atom objects
structure[np.array([3,5,6,9])   # returns a ProteinStructure with only the 34d, 5th, 6th and 9th residues 
structure.select_atoms("CA")    # returns a ProteinStructure with only the C-alpha atoms
structure.distance_matrix()     # calculates (if new) or returns (if already calculated) a distance matrix for the structure
                                   # by default, does so for only the C-alphas, but can also accept other arguments (see notebooks)
structure.contacts(7)           # returns all structural contacts within 7 Å (based on the distance matrix)
structure.assign_ss()           # assign secondary structures using DSSP (requires DSSP to be installed)
structure.save(filename.pdb)    # saves the structure as a pdb file

Attaching structures to a sequence alignment

One new feature of this code is that structures and phylogenetic trees can be "attached" to a multiple sequence alignment in order to facilitate analysis that integrates the different pieces of information.

A structure can be attached to first sequence of the MSA with msa.attach_structure(structure, 0). If you don't provide a sequence number, the program will attempt to find a matching sequence using msa.search_sequence() - this requires that the structure not have any sequence mutations. Multiple structures can be attached to the same sequence and can be accessed with msa[0].structures; if a single structure is attached, this will be found at msa[0].structures[0]. The structure's sequence will be automatically aligned to its sequence in the MSA and the corresponding MSA positions to each position in the structure can be accessed with structure._alipos, which is used in functions such as distance_difference.

Attaching phylogenetic trees to a sequence alignment

A phylogenetic tree with terminal ids matching the ids in the sequence alignment can be loaded as follows:

tree = Phylo.read("example_tree.nwk", "newick")
msa.attach_tree(tree)

Both the tree and the MSA's sequence records will now gain new attributes. For each sequence record that corresponded to a branch in the tree, that branch can now be accessed as record.branch. For each branch in the tree, the index of its corresponding sequence is stored in terminal_node.nseq. In order to select a portion of the MSA based on a clade in the tree, you can call e.g. msa.subset_by_clade(msa.tree.clade[0][0][1]).

One note to keep in mind is that if you subset the sequences in the MSA, it will pass along the branch attributes but not automically correct the nseq values in the tree or prune the tree to contain only the sequences in the new MSA. This can be done, however, by calling msa.fix_tree() on the new alignment; it is only not implemented by default because for larger alignments this may be relatively slow.