# -*- coding: utf-8 -*- # (c) The James Hutton Institute 2016-2019 # (c) University of Strathclyde 2019-2020 # Author: Leighton Pritchard # # Contact: leighton.pritchard@strath.ac.uk # # Leighton Pritchard, # Strathclyde Institute for Pharmacy and Biomedical Sciences, # Cathedral Street, # Glasgow, # G4 0RE # Scotland, # UK # # The MIT License # # Copyright (c) 2016-2019 The James Hutton Institute # Copyright (c) 2019-2020 University of Strathclyde # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. """Code to support pyani with miscellaneous functions.""" import pandas as pd from . import pyani_config # Class to hold ANI dataframe results class ANIResults(object): """Holds ANI dataframe results.""" def __init__(self, labels, mode): """Initialise with four empty, labelled dataframes.""" self.alignment_lengths = pd.DataFrame(index=labels, columns=labels, dtype=float) self.similarity_errors = pd.DataFrame( index=labels, columns=labels, dtype=float ).fillna(0) self.percentage_identity = pd.DataFrame( index=labels, columns=labels, dtype=float ).fillna(1.0) self.alignment_coverage = pd.DataFrame( index=labels, columns=labels, dtype=float ).fillna(1.0) self.zero_error = False self.mode = mode def add_tot_length(self, qname, sname, value, sym=True): """Add a total length value to self.alignment_lengths.""" self.alignment_lengths.loc[qname, sname] = value if sym: self.alignment_lengths.loc[sname, qname] = value def add_sim_errors(self, qname, sname, value, sym=True): """Add a similarity error value to self.similarity_errors.""" self.similarity_errors.loc[qname, sname] = value if sym: self.similarity_errors.loc[sname, qname] = value def add_pid(self, qname, sname, value, sym=True): """Add a percentage identity value to self.percentage_identity.""" self.percentage_identity.loc[qname, sname] = value if sym: self.percentage_identity.loc[sname, qname] = value def add_coverage(self, qname, sname, qcover, scover=None): """Add percentage coverage values to self.alignment_coverage.""" self.alignment_coverage.loc[qname, sname] = qcover if scover: self.alignment_coverage.loc[sname, qname] = scover @property def hadamard(self): """Return Hadamard matrix (identity * coverage).""" return self.percentage_identity * self.alignment_coverage @property def data(self): """Return list of (dataframe, filestem) tuples.""" stemdict = { "ANIm": pyani_config.ANIM_FILESTEMS, "ANIb": pyani_config.ANIB_FILESTEMS, "ANIblastall": pyani_config.ANIBLASTALL_FILESTEMS, } return zip( ( self.alignment_lengths, self.percentage_identity, self.alignment_coverage, self.similarity_errors, self.hadamard, ), stemdict[self.mode], ) # return [(self.alignment_lengths, "ANIm_alignment_lengths"), # (self.percentage_identity, "ANIm_percentage_identity"), # (self.alignment_coverage, "ANIm_alignment_coverage"), # (self.similarity_errors, "ANIm_similarity_errors"), # (self.hadamard, "ANIm_hadamard")] # Class to hold BLAST functions class BLASTfunctions(object): """Class to hold BLAST functions.""" def __init__(self, db_func, blastn_func): """Initialise struct to hold BLAST functions.""" self.db_func = db_func self.blastn_func = blastn_func # Class to hold BLAST executables class BLASTexes(object): """Class to hold BLAST functions.""" def __init__(self, format_exe, blast_exe): """Initialise struct to hold BLAST functions.""" self.format_exe = format_exe self.blast_exe = blast_exe # Class to hold/build BLAST commands class BLASTcmds(object): """Holds BLAST command/database formatting commands.""" def __init__(self, funcs, exes, prefix, outdir): """Initialise BLASTcmds.""" self.funcs = funcs self.exes = exes self.prefix = prefix self.outdir = outdir def build_db_cmd(self, fname): """Return database format/build command.""" return self.funcs.db_func(fname, self.outdir, self.exes.format_exe)[0] def get_db_name(self, fname): """Return database filename.""" return self.funcs.db_func(fname, self.outdir, self.exes.format_exe)[1] def build_blast_cmd(self, fname, dbname): """Return BLASTN command.""" return self.funcs.blastn_func(fname, dbname, self.outdir, self.exes.blast_exe) # Read sequence annotations in from file def get_labels(filename, logger=None): r"""Return dictionary of alternative sequence labels, or None. - filename - path to file containing tab-separated table of labels Input files should be formatted as \t