#! /usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function, absolute_import
# Third-party module
import numpy
# Local module
from .. import PB
def _assert_same_size(sequences):
"""
Raise an exception is all sequence are not the same length.
Parameters
----------
sequences
a list of sequences
Raises
------
pbxplore.PB.SizeError
not all the sequences are the same length.
"""
seq_size = len(sequences[0])
for seq in sequences:
if len(seq) != seq_size:
raise PB.SizeError
[docs]def count_matrix(pb_seq):
"""
Count the occurences of each block at each position.
The occurence matrix has one row per sequence, and one column per block.
The columns are ordered in as :const:`pbxplore.PB.NAMES`.
Parameters
----------
pb_seq
a list of PB sequences.
Returns
-------
pb_count : numpy array
The occurence matrix.
Raises
------
pbxplore.PB.InvalidBlockError
encountered an unexpected PB
"""
_assert_same_size(pb_seq)
pb_count = numpy.zeros((len(pb_seq[0]), len(PB.NAMES)))
for seq in pb_seq:
for idx, block in enumerate(seq):
if block in PB.NAMES:
pb_count[idx, PB.NAMES.index(block)] += 1.0
elif block not in ["Z", "z"]:
raise PB.InvalidBlockError(block=block)
return pb_count
[docs]def read_occurence_file(name):
"""
Read an occurence matrix from a file.
It will return the matrix as a numpy array and the indexes of residues.
Parameters
----------
name : str
Name of the file.
Returns
-------
count_mat : numpy array
the occurence matrix without the residue number
residues: list
the list of residues indexes
Raises
------
ValueError
when something is wrong about the file
"""
# load count file
# skip first row that contains PBs labels
try:
count = numpy.loadtxt(name, dtype=int, skiprows=1)
except:
raise ValueError("ERROR: {0}: wrong data format".format(name))
# determine number of sequences compiled
# use the sum of all residue at position 3
# since positions 1 and 2 have no PBs assignement
# and begin at 1 to not sum the index of the line (here is 3)
sequence_number = sum(count[2, 1:])
if sequence_number == 0:
raise ValueError("ERROR: counting 0 sequences!")
# read residues number
residues = count[:, 0]
# remove residue numbers (first column)
count = count[:, 1:]
# get index of first residue
try:
int(residues[0])
except:
raise ValueError("""ERROR: cannot read index of first residue.
Wrong data format in {0}""".format(name))
return count, residues