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How to use resetall method in pytest-mock
Best Python code snippet using pytest-mock
__main__.py
Source:__main__.py 
1#!/usr/bin/env python2import os3import sys4import argparse5import shlex6import shutil7import time8import subprocess9import glob10import tempfile11import errno12import tarfile13import json14import pathlib15from . import __version__ as tool_version16from .helpers import bco, print_error, check_file_exists, check_file_doesnt_exists17import stag.align as align18import stag.create_db as create_db19import stag.classify as classify20import stag.check_create_db_input_files as check_create_db_input_files21import stag.correct_seq as correct_seq22import stag.unzip_db as unzip_db23import stag.classify_genome as classify_genome24import stag.train_genome as train_genome25import stag.convert_ali as convert_ali26def handle_error(error, help_f=None):27 if help_f:28 help_f()29 print_error()30 print(error, file=sys.stderr)31 sys.exit(1)32# ------------------------------------------------------------------------------33# print the help informations34# ------------------------------------------------------------------------------35class CapitalisedHelpFormatter(argparse.HelpFormatter):36 def add_usage(self, usage, actions, groups, prefix=None):37 if prefix is None:38 prefix = ''39 return super(CapitalisedHelpFormatter, self).add_usage(usage, actions, groups, prefix)40def msg(name=None):41 str_msg = f'''42\0043{bco.Cyan}Program:{bco.ResetAll} stag - Supervised Taxonomic Assignment of marker Genes44{bco.Cyan}Version:{bco.ResetAll} '''+tool_version+f'''45{bco.Cyan}Usage:{bco.ResetAll} stag <command> [options]46{bco.Cyan}Command:{bco.ResetAll}47 {bco.LightGreen}-- Single gene{bco.ResetAll}48 {bco.LightBlue}train{bco.ResetAll} Train a classifier and create a database49 {bco.LightBlue}classify{bco.ResetAll} Taxonomically annotate a gene50 {bco.LightBlue}align{bco.ResetAll} Align a sequence to a hmm or infernal model51 {bco.LightBlue}create_db{bco.ResetAll} Create a database given the aligned sequences52 {bco.LightBlue}check_input{bco.ResetAll} Check the input for the train command53 {bco.LightBlue}correct_seq{bco.ResetAll} Correct sequences that are in wrong orientation54 {bco.LightBlue}convert_ali{bco.ResetAll} Convert between 1-hot-encoding and fasta, and vice versa55 {bco.LightBlue}unzip_db{bco.ResetAll} Create a directory with the content of a database56 {bco.LightGreen}-- Genome{bco.ResetAll}57 {bco.LightBlue}train_genome{bco.ResetAll} Merge classifiers of single genes58 {bco.LightBlue}classify_genome{bco.ResetAll} Taxonomically annotate a genome (predict genes, extract59 the database marker genes and classify them)60Type stag <command> to print the help for a specific command61 '''62 return str_msg63# ------------------------------------------------------------------------------64def print_menu_align():65 sys.stderr.write("\n")66 sys.stderr.write(f"{bco.Cyan}Usage:{bco.ResetAll} {bco.Green}stag{bco.ResetAll} align {bco.LightBlue}-i{bco.ResetAll} <fasta_seqs> {bco.LightBlue}-a{bco.ResetAll} <hmmfile> [options]\n\n")67 sys.stderr.write(f" {bco.LightBlue}-i{bco.ResetAll} FILE sequences to be aligned (fasta format) {bco.LightMagenta}[required]{bco.ResetAll}\n")68 sys.stderr.write(f" {bco.LightBlue}-p{bco.ResetAll} FILE protein sequences, corresponding to -i {bco.LightMagenta}[None]{bco.ResetAll}\n")69 sys.stderr.write(f" {bco.LightBlue}-a{bco.ResetAll} FILE hmmfile or cmfile to use as template for the alignment {bco.LightMagenta}[required]{bco.ResetAll}\n")70 sys.stderr.write(f" {bco.LightBlue}-o{bco.ResetAll} FILE output file name {bco.LightMagenta}[stdout]{bco.ResetAll}\n")71 sys.stderr.write(f" {bco.LightBlue}-c{bco.ResetAll} set if you are using a cmfile\n")72 sys.stderr.write(f" {bco.LightBlue}-m{bco.ResetAll} INT threshold for the number of features per sequence (percentage) {bco.LightMagenta}[0]{bco.ResetAll}\n")73 sys.stderr.write(f" {bco.LightBlue}-t{bco.ResetAll} INT number of threads {bco.LightMagenta}[1]{bco.ResetAll}\n")74 sys.stderr.write(f" {bco.LightBlue}-v{bco.ResetAll} INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging {bco.LightMagenta}[3]{bco.ResetAll}\n\n")75 sys.stderr.write(f"{bco.Cyan}Note:{bco.ResetAll} if -p is provided, then the alignment will be done at the level\nof the proteins and then converted to gene alignment (from -i input).\nThe order of the sequences in -i and -p should be the same.\n\n")76# ------------------------------------------------------------------------------77def print_menu_create_db():78 sys.stderr.write("\n")79 sys.stderr.write(f"{bco.Cyan}Usage:{bco.ResetAll} {bco.Green}stag{bco.ResetAll} create_db {bco.LightBlue}-s{bco.ResetAll} <aligned_file> {bco.LightBlue}-x{bco.ResetAll} <taxonomy_file>\n")80 sys.stderr.write(f" {bco.LightBlue}-a{bco.ResetAll} <hmmfile> {bco.LightBlue}-o{bco.ResetAll} <output_DB> [options]\n\n")81 sys.stderr.write(f" {bco.LightBlue}-s{bco.ResetAll} FILE file with 1-hot encoding MSA (result from stag align) {bco.LightMagenta}[required]{bco.ResetAll}\n")82 sys.stderr.write(f" {bco.LightBlue}-a{bco.ResetAll} FILE hmmfile or cmfile to used as template for the alignment {bco.LightMagenta}[required]{bco.ResetAll}\n")83 sys.stderr.write(f" {bco.LightBlue}-c{bco.ResetAll} set if you are using a cmfile\n")84 sys.stderr.write(f" {bco.LightBlue}-x{bco.ResetAll} FILE taxonomy file (tab separated) {bco.LightMagenta}[required]{bco.ResetAll}\n")85 sys.stderr.write(f" {bco.LightBlue}-o{bco.ResetAll} FILE output file name (HDF5 format) {bco.LightMagenta}[required]{bco.ResetAll}\n")86 sys.stderr.write(f" {bco.LightBlue}-f{bco.ResetAll} force to rewrite output file\n")87 sys.stderr.write(f" {bco.LightBlue}-C{bco.ResetAll} FILE save intermediate cross validation results {bco.LightMagenta}[None]{bco.ResetAll}\n")88 sys.stderr.write(f" {bco.LightBlue}-p{bco.ResetAll} FILE protein sequences, if they were used for the alignment {bco.LightMagenta}[None]{bco.ResetAll}\n")89 sys.stderr.write(f" {bco.LightBlue}-e{bco.ResetAll} STR penalty for the logistic regression {bco.LightMagenta}[\"l1\"]{bco.ResetAll}\n")90 sys.stderr.write(f" {bco.LightBlue}-E{bco.ResetAll} STR solver for the logistic regression {bco.LightMagenta}[\"liblinear\"]{bco.ResetAll}\n")91 sys.stderr.write(f" {bco.LightBlue}-t{bco.ResetAll} INT number of threads {bco.LightMagenta}[1]{bco.ResetAll}\n")92 sys.stderr.write(f" {bco.LightBlue}-v{bco.ResetAll} INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging {bco.LightMagenta}[3]{bco.ResetAll}\n\n")93# ------------------------------------------------------------------------------94def print_menu_classify():95 sys.stderr.write("\n")96 sys.stderr.write(f"{bco.Cyan}Usage:{bco.ResetAll} {bco.Green}stag{bco.ResetAll} classify {bco.LightBlue}-d{bco.ResetAll} <database> [{bco.LightBlue}-i{bco.ResetAll}/{bco.LightBlue}-s{bco.ResetAll}] <seq_file> [options]\n\n")97 sys.stderr.write(f" {bco.LightBlue}-d{bco.ResetAll} FILE database created with create_db or train {bco.LightMagenta}[required]{bco.ResetAll}\n")98 sys.stderr.write(f" {bco.LightBlue}-i{bco.ResetAll} FILE sequences to taxonomically annotate (fasta format) {bco.LightMagenta}[required]{bco.ResetAll}\n")99 sys.stderr.write(f" {bco.LightBlue}-s{bco.ResetAll} FILE aligned sequences, can be provided instead of -i {bco.ResetAll}\n")100 sys.stderr.write(f" {bco.LightBlue}-p{bco.ResetAll} FILE protein sequences, corresponding to -i {bco.LightMagenta}[None]{bco.ResetAll}\n")101 sys.stderr.write(f" {bco.LightBlue}-S{bco.ResetAll} FILE save intermediate alignment file {bco.LightMagenta}[None]{bco.ResetAll}\n")102 sys.stderr.write(f" {bco.LightBlue}-o{bco.ResetAll} FILE output file name {bco.LightMagenta}[stdout]{bco.ResetAll}\n")103 sys.stderr.write(f" {bco.LightBlue}-l{bco.ResetAll} long output (with more information about the classification)\n")104 sys.stderr.write(f" {bco.LightBlue}-m{bco.ResetAll} INT threshold for the number of features per sequence (percentage) {bco.LightMagenta}[0]{bco.ResetAll}\n")105 sys.stderr.write(f" {bco.LightBlue}-v{bco.ResetAll} INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging {bco.LightMagenta}[3]{bco.ResetAll}\n\n")106# ------------------------------------------------------------------------------107def print_menu_check_input():108 sys.stderr.write("\n")109 sys.stderr.write(f"{bco.Cyan}Usage:{bco.ResetAll} {bco.Green}stag{bco.ResetAll} check_input {bco.LightBlue}-i{bco.ResetAll} <fasta_seqs> {bco.LightBlue}-x{bco.ResetAll} <taxonomy_file>\n")110 sys.stderr.write(f" {bco.LightBlue}-a{bco.ResetAll} <hmmfile> [options]\n\n")111 sys.stderr.write(f" {bco.LightBlue}-i{bco.ResetAll} FILE sequences to be aligned (fasta format) {bco.LightMagenta}[required]{bco.ResetAll}\n")112 sys.stderr.write(f" {bco.LightBlue}-p{bco.ResetAll} FILE protein sequences, corresponding to -i {bco.LightMagenta}[None]{bco.ResetAll}\n")113 sys.stderr.write(f" {bco.LightBlue}-a{bco.ResetAll} FILE hmmfile or cmfile to used as template for the alignment {bco.LightMagenta}[required]{bco.ResetAll}\n")114 sys.stderr.write(f" {bco.LightBlue}-c{bco.ResetAll} set if you are using a cmfile\n")115 sys.stderr.write(f" {bco.LightBlue}-x{bco.ResetAll} FILE taxonomy file (tab separated) {bco.LightMagenta}[required]{bco.ResetAll}\n")116 sys.stderr.write(f" {bco.LightBlue}-w{bco.ResetAll} FILE save warning messages to a file {bco.LightMagenta}[None]{bco.ResetAll}\n")117 sys.stderr.write(f" {bco.LightBlue}-v{bco.ResetAll} INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging {bco.LightMagenta}[3]{bco.ResetAll}\n\n")118# ------------------------------------------------------------------------------119def print_menu_train():120 sys.stderr.write("\n")121 sys.stderr.write(f"{bco.Cyan}Usage:{bco.ResetAll} {bco.Green}stag{bco.ResetAll} train {bco.LightBlue}-i{bco.ResetAll} <fasta_seqs> {bco.LightBlue}-x{bco.ResetAll} <taxonomy_file>\n")122 sys.stderr.write(f" {bco.LightBlue}-a{bco.ResetAll} <hmmfile> {bco.LightBlue}-o{bco.ResetAll} <output_DB> [options]\n\n")123 sys.stderr.write(f" {bco.LightBlue}-i{bco.ResetAll} FILE sequences to be aligned (fasta format) {bco.LightMagenta}[required]{bco.ResetAll}\n")124 sys.stderr.write(f" {bco.LightBlue}-p{bco.ResetAll} FILE protein sequences, corresponding to -i {bco.LightMagenta}[None]{bco.ResetAll}\n")125 sys.stderr.write(f" {bco.LightBlue}-a{bco.ResetAll} FILE hmmfile or cmfile to used as template for the alignment {bco.LightMagenta}[required]{bco.ResetAll}\n")126 sys.stderr.write(f" {bco.LightBlue}-c{bco.ResetAll} set if you are using a cmfile\n")127 sys.stderr.write(f" {bco.LightBlue}-x{bco.ResetAll} FILE taxonomy file (tab separated) {bco.LightMagenta}[required]{bco.ResetAll}\n")128 sys.stderr.write(f" {bco.LightBlue}-o{bco.ResetAll} FILE output file name (HDF5 format) {bco.LightMagenta}[required]{bco.ResetAll}\n")129 sys.stderr.write(f" {bco.LightBlue}-f{bco.ResetAll} force to rewrite output file\n\n")130 sys.stderr.write(f" {bco.LightBlue}-S{bco.ResetAll} FILE save intermediate alignment file {bco.LightMagenta}[None]{bco.ResetAll}\n")131 sys.stderr.write(f" {bco.LightBlue}-C{bco.ResetAll} FILE save intermediate cross validation results {bco.LightMagenta}[None]{bco.ResetAll}\n")132 sys.stderr.write(f" {bco.LightBlue}-t{bco.ResetAll} INT number of threads {bco.LightMagenta}[1]{bco.ResetAll}\n")133 sys.stderr.write(f" {bco.LightBlue}-m{bco.ResetAll} INT threshold for the number of features per sequence (percentage) {bco.LightMagenta}[0]{bco.ResetAll}\n")134 sys.stderr.write(f" {bco.LightBlue}-v{bco.ResetAll} INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging {bco.LightMagenta}[3]{bco.ResetAll}\n\n")135 sys.stderr.write(f" {bco.LightBlue}-e{bco.ResetAll} STR penalty for the logistic regression {bco.LightMagenta}[\"l1\"]{bco.ResetAll}\n")136 sys.stderr.write(f" {bco.LightBlue}-E{bco.ResetAll} STR solver for the logistic regression {bco.LightMagenta}[\"liblinear\"]{bco.ResetAll}\n\n")137 sys.stderr.write(f"{bco.Cyan}Note:{bco.ResetAll} if -p is provided, then the alignment will be done at the level\nof the proteins and then converted to gene alignment (from -i input).\nThe order of the sequences in -i and -p should be the same.\n\n")138# ------------------------------------------------------------------------------139def print_menu_correct_seq():140 sys.stderr.write("\n")141 sys.stderr.write(f"{bco.Cyan}Usage:{bco.ResetAll} {bco.Green}stag{bco.ResetAll} correct_seq {bco.LightBlue}-i{bco.ResetAll} <fasta_seqs> {bco.LightBlue}-a{bco.ResetAll} <hmmfile> [options]\n\n")142 sys.stderr.write(f" {bco.LightBlue}-i{bco.ResetAll} FILE sequences to be aligned (fasta format) {bco.LightMagenta}[required]{bco.ResetAll}\n")143 sys.stderr.write(f" {bco.LightBlue}-a{bco.ResetAll} FILE hmmfile or cmfile to use as template for the alignment {bco.LightMagenta}[required]{bco.ResetAll}\n")144 sys.stderr.write(f" {bco.LightBlue}-o{bco.ResetAll} FILE output file name {bco.LightMagenta}[stdout]{bco.ResetAll}\n")145 sys.stderr.write(f" {bco.LightBlue}-c{bco.ResetAll} set if you are using a cmfile\n")146 sys.stderr.write(f" {bco.LightBlue}-m{bco.ResetAll} INT threshold for the number of features per sequence (percentage) {bco.LightMagenta}[5]{bco.ResetAll}\n")147 sys.stderr.write(f" {bco.LightBlue}-t{bco.ResetAll} INT number of threads {bco.LightMagenta}[1]{bco.ResetAll}\n")148 sys.stderr.write(f" {bco.LightBlue}-v{bco.ResetAll} INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging {bco.LightMagenta}[3]{bco.ResetAll}\n\n")149# ------------------------------------------------------------------------------150def print_menu_train_genome():151 sys.stderr.write("\n")152 sys.stderr.write(f"{bco.Cyan}Usage:{bco.ResetAll} {bco.Green}stag{bco.ResetAll} train_genome {bco.LightBlue}-i{bco.ResetAll} <list_gene_DBs> {bco.LightBlue}-T{bco.ResetAll} <gene_thresholds>\n {bco.LightBlue}-o{bco.ResetAll} <output_DB> {bco.LightBlue}-C{bco.ResetAll} <concat_genes_DB> [options]\n\n")153 sys.stderr.write(f" {bco.LightBlue}-i{bco.ResetAll} LIST list of single gene databases to use (comma separated) {bco.LightMagenta}[required]{bco.ResetAll}\n")154 sys.stderr.write(f" {bco.LightBlue}-T{bco.ResetAll} FILE hmm treshold for selecting the genes {bco.LightMagenta}[required]{bco.ResetAll}\n")155 sys.stderr.write(f" {bco.LightBlue}-C{bco.ResetAll} FILE stag database for the concatenated genes{bco.LightMagenta}[required]{bco.ResetAll}\n")156 sys.stderr.write(f" {bco.LightBlue}-o{bco.ResetAll} FILE output file name (HDF5 format) {bco.LightMagenta}[required]{bco.ResetAll}\n")157 sys.stderr.write(f" {bco.LightBlue}-t{bco.ResetAll} INT number of threads {bco.LightMagenta}[1]{bco.ResetAll}\n")158 sys.stderr.write(f" {bco.LightBlue}-v{bco.ResetAll} INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging {bco.LightMagenta}[3]{bco.ResetAll}\n\n")159# ------------------------------------------------------------------------------160def print_menu_classify_genome():161 sys.stderr.write("\n")162 sys.stderr.write(f"{bco.Cyan}Usage:{bco.ResetAll} {bco.Green}stag{bco.ResetAll} classify_genome {bco.LightBlue}-d{bco.ResetAll} <genome_database> {bco.LightBlue}-o{bco.ResetAll} res_dir\n")163 sys.stderr.write(f" [{bco.LightBlue}-i{bco.ResetAll} <fasta_seq>/{bco.LightBlue}-D{bco.ResetAll} <directory>/{bco.LightBlue}-G{bco.ResetAll} <markers.json>] [options]\n\n")164 sys.stderr.write(f" {bco.LightBlue}-d{bco.ResetAll} FILE database created with train_genome {bco.LightMagenta}[required]{bco.ResetAll}\n")165 sys.stderr.write(f" {bco.LightBlue}-i{bco.ResetAll} FILE genome fasta file\n")166 sys.stderr.write(f" {bco.LightBlue}-D{bco.ResetAll} DIR directory containing genome fasta files (only fasta\n files will be used)\n")167 sys.stderr.write(f" {bco.LightBlue}-G{bco.ResetAll} FILE json file pointing at a marker gene set (in lieu of a full genome)\n")168 sys.stderr.write(f" {bco.LightBlue}-o{bco.ResetAll} DIR output directory {bco.LightMagenta}[required]{bco.ResetAll}\n")169 sys.stderr.write(f" {bco.LightBlue}-l{bco.ResetAll} long output (with more information about the classification) {bco.LightMagenta}[False]\n")170 sys.stderr.write(f" {bco.LightBlue}-v{bco.ResetAll} INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging {bco.LightMagenta}[3]{bco.ResetAll}\n")171 sys.stderr.write(f" {bco.LightBlue}-r{bco.ResetAll} use all genes above the filter {bco.LightMagenta}[False]{bco.ResetAll}\n\n")172 sys.stderr.write(f" {bco.LightBlue}-t{bco.ResetAll} INT number of threads {bco.LightMagenta}[1]{bco.ResetAll}\n")173# ------------------------------------------------------------------------------174def print_menu_convert_ali():175 sys.stderr.write("\n")176 sys.stderr.write(f"{bco.Cyan}Usage:{bco.ResetAll} {bco.Green}stag{bco.ResetAll} convert_ali {bco.LightBlue}-i{bco.ResetAll} <file_in> {bco.LightBlue}-o{bco.ResetAll} <file_out> [options]\n\n")177 sys.stderr.write(f" {bco.LightBlue}-i{bco.ResetAll} FILE Input file, either a 1-hot-encoding created by stag align,\n")178 sys.stderr.write(f" or a fasta file of aligned sequences created by hmmalign.\n")179 sys.stderr.write(f" The input type is detected automatically {bco.LightMagenta}[required]{bco.ResetAll}\n")180 sys.stderr.write(f" {bco.LightBlue}-o{bco.ResetAll} FILE A 1-hot-encoding if the input was fasta,\n")181 sys.stderr.write(f" or a fasta file if the input was 1-hot-encoding {bco.LightMagenta}[required]{bco.ResetAll}\n")182 sys.stderr.write(f" {bco.LightBlue}-v{bco.ResetAll} INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging {bco.LightMagenta}[3]{bco.ResetAll}\n\n")183# ------------------------------------------------------------------------------184def print_menu_unzip_db():185 sys.stderr.write("\n")186 sys.stderr.write(f"{bco.Cyan}Usage:{bco.ResetAll} {bco.Green}stag{bco.ResetAll} unzip_db {bco.LightBlue}-d{bco.ResetAll} <database> {bco.LightBlue}-o{bco.ResetAll} <dir_out> [options]\n\n")187 sys.stderr.write(f" {bco.LightBlue}-d{bco.ResetAll} FILE database created with create_db or train {bco.LightMagenta}[required]{bco.ResetAll}\n")188 sys.stderr.write(f" {bco.LightBlue}-o{bco.ResetAll} DIR create a dir with the unzipped database {bco.LightMagenta}[required]{bco.ResetAll}\n")189 sys.stderr.write(f" {bco.LightBlue}-v{bco.ResetAll} INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging {bco.LightMagenta}[3]{bco.ResetAll}\n\n")190# ------------------------------------------------------------------------------191# MAIN192# ------------------------------------------------------------------------------193def main(argv=None):194 parser = argparse.ArgumentParser(usage=msg(), formatter_class=CapitalisedHelpFormatter,add_help=False)195 parser.add_argument('command', action="store", default=None, help='mode to run stag',196 choices=['align','train','classify','create_db','check_input','correct_seq','train_genome',197 'classify_genome','test','convert_ali',"unzip_db"])198 parser.add_argument('-o', action="store", dest='output', default=None, help='name of output file')199 parser.add_argument('-t', type=int, action="store", dest='threads', default=1, help='Number of threads to be used.')200 parser.add_argument('-v', action='store', type=int, default=3, dest='verbose', help='Verbose levels', choices=list(range(1,5)))201 parser.add_argument('-c', action='store_true', dest='use_cm_align', help='Set if you want to use cmalign isntead of hmmalign')202 parser.add_argument('-s', action="store", default=None,dest='aligned_sequences', help='sequences that needs to be aligned')203 parser.add_argument('-a', action="store", default=None,dest='template_al', help='alignment template')204 parser.add_argument('-x', action="store", default=None,dest='taxonomy', help='taxonomy file path')205 parser.add_argument('-f', action='store_true', dest='force_rewrite', help='Set if you want to rewrite the file, even if it exists')206 parser.add_argument('-i', action="store", dest='fasta_input', default=None, help='input fasta sequences')207 parser.add_argument('-p', action="store", dest='protein_fasta_input', default=None, help='input fasta sequences, in protein format. Corresponding to the -i sequences')208 parser.add_argument('-w', action="store", dest='warning_file_check_input', default=None, help='for check_input there can be quite some warning messages. Use -w to save them to a file')209 parser.add_argument('-d', action="store", dest='database', default=None, help='file containing the database')210 parser.add_argument('-S', action="store", dest='intermediate_al', default=None, help='name of the file for the intermediate alignment')211 parser.add_argument('-C', action="store", dest='intermediate_cross_val', default=None, help='name of the file for the intermediate cross validation results')212 parser.add_argument('-m', action='store', type=int, default=None, dest='min_perc_state', help='Minimum number of mapping states, i.e. how many features of the classifier we cover')213 parser.add_argument('-l', action='store_true', dest='long_out', help='Print more columns for the classification pipeline')214 parser.add_argument('-r', action='store_true', dest='keep_all_genes', help='keep all genes when doing the classification of genomes')215 parser.add_argument('-D', action="store", dest='dir_input', default=None, help='input directory')216 parser.add_argument('-T', action="store", dest='file_thresholds', default=None, help='file with the thresholds for the genes in the genome classifier') # basically the minimum score required217 parser.add_argument('-e', action="store", default="l1", dest='penalty_logistic', help='penalty for the logistic regression',choices=['l1','l2','none'])218 parser.add_argument('-E', action="store", default="liblinear", dest='solver_logistic', help='solver for the logistic regression',choices=['newton-cg', 'lbfgs', 'liblinear', 'sag', 'saga'])219 parser.add_argument('-G', action="store", dest="marker_genes", default=None, help="Set of identified marker genes in lieu of a genomic sequence")220 parser.add_argument('--version', action='version', version='%(prog)s {0} on python {1}'.format(tool_version, sys.version.split()[0]))221 args = parser.parse_args()222 # --------------------------------------------------------------------------223 # TEST routine224 # --------------------------------------------------------------------------225 if args.command == 'test':226 popenCMD = "stag_test"227 child = subprocess.Popen(popenCMD)228 child.communicate()229 rc = child.wait()230 return(rc)231 # --------------------------------------------------------------------------232 # set defaults for the parameters233 # --------------------------------------------------------------------------234 if args.command == 'correct_seq':235 if (args.min_perc_state is None): args.min_perc_state = 5236 else:237 if (args.min_perc_state is None): args.min_perc_state = 0238 if args.threads < 1:239 handle_error("number of threads (-t) is less than 1", None)240 if args.min_perc_state < 0 or args.min_perc_state > 100:241 handle_error("-m should be between 0 and 100. It represents the percentage\n"242 "of internal states covered by the sequence (i.e. the number of features).", None)243 # --------------------------------------------------------------------------244 # ALIGN routine245 # --------------------------------------------------------------------------246 error = ""247 if args.command == 'align':248 # check that '-i' and '-a' have been provided249 if not args.fasta_input:250 error = "missing <seqfile> (-i)"251 elif not args.template_al:252 error = "missing <hmmfile>/<cmfile> (-a)"253 if error:254 handle_error(error, print_menu_align)255 # check that '-s' and '-a' are files256 check_file_exists(args.fasta_input, isfasta = True)257 check_file_exists(args.template_al, isfasta = False)258 # if -p is provided, then check that it is a fasta file259 if args.protein_fasta_input:260 check_file_exists(args.protein_fasta_input, isfasta = True)261 # call the function262 if args.output is None:263 for ali in align.align_generator(args.fasta_input, args.protein_fasta_input, args.template_al,264 args.use_cm_align, args.threads, args.verbose, False, args.min_perc_state):265 print(ali)266 else:267 align.align_file(args.fasta_input, args.protein_fasta_input, args.template_al, args.use_cm_align, args.threads,268 args.verbose, args.output, args.min_perc_state)269 # --------------------------------------------------------------------------270 # CREATE_DB routine271 # --------------------------------------------------------------------------272 elif args.command == 'create_db':273 if not args.aligned_sequences:274 # check that '-s' has been provided (alignment produced by stag align)275 error = "missing <aligned_file> (-s)"276 elif not args.taxonomy:277 # check that '-x' has been provided (taxonomy file)278 error = "missing <taxonomy_file> (-x)"279 elif not args.template_al:280 # check that the hmm file is provided281 error = "missing <hmmfile>/<cmfile> (-a)"282 elif not args.output:283 # check that output is set284 error = "missing <output_DB> (-o)"285 if error:286 handle_error(error, print_menu_create_db)287 # check that '-s' and '-a' are files288 check_file_exists(args.aligned_sequences, isfasta = False)289 check_file_exists(args.taxonomy, isfasta = False)290 check_file_exists(args.template_al, isfasta = False)291 if not args.force_rewrite:292 check_file_doesnt_exists(args.output)293 # call the function to create the database294 create_db.create_db(args.aligned_sequences, args.taxonomy, args.verbose, args.output, args.use_cm_align,295 args.template_al, args.intermediate_cross_val, args.protein_fasta_input,296 args.penalty_logistic, args.solver_logistic, procs=args.threads)297 # --------------------------------------------------------------------------298 # TRAIN routine299 # --------------------------------------------------------------------------300 elif args.command == 'train':301 # check that '-i' and '-a' have been provided302 if not args.fasta_input:303 error = "missing <seqfile> (-i)"304 elif not args.template_al:305 error = "missing <hmmfile>/<cmfile> (-a)"306 elif not args.taxonomy:307 # check that '-x' has been provided (taxonomy file)308 error = "missing <taxonomy_file> (-x)"309 elif not args.output:310 # check that output is set311 error = "missing <output_DB> (-o)"312 if error:313 handle_error(error, print_menu_train)314 # check that '-s' and '-a' are files315 check_file_exists(args.fasta_input, isfasta = True)316 check_file_exists(args.template_al, isfasta = False)317 # if -p is provided, then check that it is a fasta file318 if args.protein_fasta_input:319 check_file_exists(args.protein_fasta_input, isfasta = True)320 check_file_exists(args.taxonomy, isfasta = False)321 if not args.force_rewrite:322 check_file_doesnt_exists(args.output)323 # FIRST: ALIGN ---------------------------------------------------------324 # we create a temporary file that will contain the alignments325 al_file = tempfile.NamedTemporaryFile(delete=False, mode="w")326 os.chmod(al_file.name, 0o644)327 # call the function328 align.align_file(args.fasta_input, args.protein_fasta_input, args.template_al, args.use_cm_align,329 args.threads, args.verbose, al_file.name, args.min_perc_state)330 # SECOND: CREATE_DB ----------------------------------------------------331 # call the function to create the database332 create_db.create_db(al_file.name, args.taxonomy, args.verbose, args.output, args.use_cm_align,333 args.template_al, args.intermediate_cross_val, args.protein_fasta_input,334 args.penalty_logistic, args.solver_logistic, procs=args.threads)335 # what to do with intermediate alignment -------------------------------336 if not args.intermediate_al:337 # remove it338 os.remove(al_file.name)339 else:340 # save it341 shutil.move(al_file.name, args.intermediate_al)342 # --------------------------------------------------------------------------343 # CLASSIFY routine344 # --------------------------------------------------------------------------345 elif args.command == 'classify':346 # check that '-i' has been provided (alignment produced by stag align)347 if not args.fasta_input and not args.aligned_sequences:348 error = "missing <fasta_seqs> (-i) or <aligned_seq> (-s)"349 elif not args.database:350 # check that '-d' has been provided (taxonomy file)351 error = "missing <database> (-d)"352 if error:353 handle_error(error, print_menu_classify)354 # check that they are files355 if args.fasta_input:356 check_file_exists(args.fasta_input, isfasta = True)357 check_file_exists(args.database, isfasta = False)358 # if -p is provided, then check that it is a fasta file359 if args.protein_fasta_input:360 check_file_exists(args.protein_fasta_input, isfasta = True)361 # if -S is provided, we remove the file if it exists, since in the362 # function it appends only363 if args.intermediate_al:364 if os.path.isfile(args.intermediate_al):365 os.remove(args.intermediate_al)366 # call the function367 classify.classify(args.database, fasta_input=args.fasta_input, protein_fasta_input=args.protein_fasta_input, 368 verbose=args.verbose, threads=args.threads, output=args.output, long_out=args.long_out, 369 current_tool_version=tool_version, aligned_sequences=args.aligned_sequences,370 save_ali_to_file=args.intermediate_al, min_perc_state=args.min_perc_state)371 # --------------------------------------------------------------------------372 # CHECK_INPUT routine373 # --------------------------------------------------------------------------374 elif args.command == 'check_input':375 if not args.fasta_input:376 error = "missing <fasta_seqs> (-i)"377 elif not args.taxonomy:378 error = "missing <taxonomy_file> (-x)"379 elif not args.template_al:380 error = "missing <hmmfile>/<cmfile> (-a)"381 if error:382 handle_error(error, print_menu_check_input)383 check_create_db_input_files.check_input_files(args.fasta_input, args.protein_fasta_input, args.taxonomy,384 args.template_al, args.use_cm_align, args.warning_file_check_input)385 # --------------------------------------------------------------------------386 # CORRECT_SEQ routine387 # --------------------------------------------------------------------------388 # check if the sequences are in correct orientation, if they are not, then389 # take reverse complement. Save to -o all the seqeunces is correct order390 elif args.command == 'correct_seq':391 # check that '-i' and '-a' have been provided392 if not args.fasta_input:393 error = "missing <seqfile> (-i)"394 elif not args.template_al:395 error = "missing <hmmfile>/<cmfile> (-a)"396 if error:397 handle_error(error, print_menu_correct_seq)398 # check that '-s' and '-a' are files399 check_file_exists(args.fasta_input, isfasta = True)400 check_file_exists(args.template_al, isfasta = False)401 # call the function402 correct_seq.correct_seq(args.fasta_input, args.template_al, args.use_cm_align, args.threads, args.verbose,403 args.min_perc_state, args.output)404 # --------------------------------------------------------------------------405 # CONVERT_ALI routine406 # --------------------------------------------------------------------------407 elif args.command == 'convert_ali':408 # check that '-i' and '-o' have been provided409 if not args.fasta_input:410 error = "missing <file_in> (-i)"411 elif not args.output:412 error = "missing <file_out> (-o)"413 if error:414 handle_error(error, print_menu_convert_ali)415 # check that '-i' is a file416 check_file_exists(args.fasta_input, isfasta = False)417 # call function418 convert_ali.convert_ali(args.fasta_input, args.output, args.verbose)419 # --------------------------------------------------------------------------420 # UNZIP_db routine421 # --------------------------------------------------------------------------422 elif args.command == 'unzip_db':423 # check that '-d' and '-o' have been provided424 if not args.database:425 error = "missing <database> (-d)"426 elif not args.output:427 error = "missing <dir_out> (-o)"428 if error:429 handle_error(error, print_menu_unzip_db)430 # check that '-d' is a file431 check_file_exists(args.database, isfasta = False)432 # call function433 unzip_db.unzip_db(args.database, args.verbose, args.output)434 # --------------------------------------------------------------------------435 # TRAIN_GENOME routine436 # --------------------------------------------------------------------------437 # We want to have a database for classifying genomes. It will contains the438 # calssifiers for the seingle genes439 # Input: single gene databases440 # Output: a database file (hdf5) that can be used by stag classify_genome441 elif args.command == 'train_genome':442 # check that parameters are set ----------------------------------------443 if not args.output:444 error = "missing <output_DB> (-o)"445 elif not args.fasta_input:446 error = "missing <list_gene_DBs> (-i)"447 elif not args.file_thresholds:448 error = "missing <gene_thresholds> (-T)"449 elif not args.intermediate_cross_val:450 error = "missing <concat_genes_DB> (-C)"451 if error:452 handle_error(error, print_menu_train_genome)453 # call the function454 train_genome.train_genome(args.output, args.fasta_input, args.file_thresholds,455 args.threads, args.verbose, args.intermediate_cross_val)456 # --------------------------------------------------------------------------457 # CLASSIFY_GENOME routine458 # --------------------------------------------------------------------------459 if args.command == 'classify_genome':460 # check input461 if not args.database:462 error = "missing <database> (-d)"463 elif not any((args.fasta_input, args.dir_input, args.marker_genes)):464 error = "you need to provide at least -i, -D, or -G."465 elif sum(map(bool, (args.fasta_input, args.dir_input, args.marker_genes))) != 1:466 error = "options -i, -D, and -G are mutually exclusive"467 elif args.dir_input and not os.path.isdir(args.dir_input):468 error = "-D is not a directory."469 elif args.marker_genes and not os.path.isfile(args.marker_genes):470 error = "-G is not a valid file."471 elif not args.output:472 # check that output dir is defined473 error = "missing output directory (-o)"474 if error:475 handle_error(error, print_menu_classify_genome)476 # find files to classify477 marker_genes, list_files = list(), list()478 if args.fasta_input:479 check_file_exists(args.fasta_input, isfasta = True)480 list_files.append(args.fasta_input)481 elif args.marker_genes:482 marker_genes = [args.marker_genes]483 else:484 for f in os.listdir(args.dir_input):485 f = os.path.join(args.dir_input, f)486 try:487 if os.path.isfile(f) and open(f).read(1)[0] == ">":488 list_files.append(f)489 except Exception as e:490 if args.verbose > 1:491 sys.stderr.write("[W::main] Warning: ")492 sys.stderr.write("Cannot open file: {}\n".format(f))493 if not list_files:494 handle_error("no fasta files found in the directory.", None)495 sys.stderr.write(" Found "+str(len(list_files))+" fasta files\n")496 if os.path.isdir(args.output):497 if args.force_rewrite:498 shutil.rmtree(args.output)499 else:500 handle_error("output directory (-o {}) exists already.".format(args.output), None)501 # create output dir502 try:503 pathlib.Path(args.output).mkdir(exist_ok=True, parents=True)504 except:505 handle_error("creating the output directory (-o {}).".format(args.output), None)506 if list_files:507 from stag.classify_genome import validate_genome_files508 validate_genome_files(list_files)509 # call the function510 classify_genome.classify_genome(args.database, genome_files=list_files, marker_genes=marker_genes,511 verbose=args.verbose, threads=args.threads,512 output=args.output, long_out=args.long_out, keep_all_genes=args.keep_all_genes)513 return None # success514#-------------------------------- run main -------------------------------------515if __name__ == '__main__':...
stag_test.py
Source:stag_test.py
1#!/usr/bin/env python2# ============================================================================ #3# stag_test Run stag tests4#5# Author: Alessio Milanese (milanese@embl.de)6#7# ============================================================================ #8import time9import os10import sys11import tempfile12import subprocess13import shlex14import errno15import pkg_resources16import urllib.request17import hashlib18from pathlib import Path19import shutil20from .helpers import bco, is_tool, is_tool_and_return021TEST_DATA_PATH = pkg_resources.resource_filename("stag", "test")22# check md523def md5(fname):24 hash_md5 = hashlib.md5()25 with open(fname, "rb") as f:26 for chunk in iter(lambda: f.read(4096), b""):27 hash_md5.update(chunk)28 return hash_md5.hexdigest()29# download a file if it's not there30def download_file(url, filename):31 downloaded_correct = True32 try:33 urllib.request.urlretrieve(url, filename)34 except:35 downloaded_correct = False36 if downloaded_correct:37 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll}\n")38 else:39 sys.stderr.write(f"{bco.Yellow}{bco.Bold} error{bco.ResetAll}\n")40# function to download and decompress a tar.gz41def download_and_checkmd5_and_decompress(url, filename, md5_db, destination):42 # we remove a dir if it exist already43 shutil.rmtree(filename[0:-7], ignore_errors=True)44 # check if the file is already downloaded45 my_file = Path(filename)46 if my_file.is_file():47 sys.stderr.write(" â already downloaded\n")48 else:49 sys.stderr.write(" â download file: ")50 download_file(url, filename)51 # check md552 sys.stderr.write(" â check md5: ")53 current_md5 = md5(filename)54 if current_md5 == md5_db:55 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll}\n")56 else:57 sys.stderr.write(f"{bco.Yellow}{bco.Bold} different{bco.ResetAll}\n")58 sys.stderr.write(" â Re-download file: ")59 download_file(url, filename)60 sys.stderr.write(" â check md5: ")61 current_md5 = md5(filename)62 if current_md5 == md5_db:63 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll}\n")64 else:65 sys.stderr.write(f"{bco.Yellow}{bco.Bold} different{bco.ResetAll}\n")66 # decompress67 sys.stderr.write(" â Unzip file: ")68 extract_cmd = "tar -zxvf "+filename+" -C "+destination69 try:70 FNULL = open(os.devnull, 'w')71 process = subprocess.Popen(extract_cmd.split(),stderr=FNULL,stdout=FNULL)72 output, error = process.communicate()73 except:74 sys.stderr.write(f"{bco.Yellow}{bco.Bold} error{bco.ResetAll}\n")75 if process.returncode:76 sys.stderr.write(f"{bco.Yellow}{bco.Bold} error{bco.ResetAll}\n")77 else:78 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll}\n")79 # we return the reulting directory, which should have the same name as80 # the file downloaded minus ".tar.gz"81 return filename[0:-7]+"/"82# ------------------------------------------------------------------------------83# MAIN84# ------------------------------------------------------------------------------85def main(argv=None):86 sys.stderr.write(f"{bco.Blue}{bco.Bold} ------------------------------------------------------------------------------{bco.ResetAll}\n")87 sys.stderr.write(f"{bco.Blue}{bco.Bold}|{bco.Green} TEST STAG {bco.Blue}|{bco.ResetAll}\n")88 sys.stderr.write(f"{bco.Blue}{bco.Bold} ------------------------------------------------------------------------------{bco.ResetAll}\n")89 error_found = False90 # CHECK TOOLS ==============================================================91 sys.stderr.write(f"{bco.Cyan}{bco.Bold}1-- Tools and versions:{bco.ResetAll}\n")92 # check python version -----------------------------------------------------93 sys.stderr.write(" â python: ")94 python_version = sys.version_info95 if(python_version >= (3,0,0)):96 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll}\n")97 else:98 sys.stderr.write(f"{bco.Yellow}{bco.Bold} WARNING: python2 is not supported{bco.ResetAll}\n\n")99 error_found = True100 # check hmmer --------------------------------------------------------------101 sys.stderr.write(" â hmmalign: ")102 if is_tool("hmmalign"):103 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll}\n")104 else:105 sys.stderr.write(f"{bco.Yellow}{bco.Bold} WARNING. HMMER3 is not in the path{bco.ResetAll}\n\n")106 error_found = True107 # check Easel --------------------------------------------------------------108 sys.stderr.write(" â esl-reformat: ")109 if is_tool("esl-reformat"):110 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll}\n")111 else:112 sys.stderr.write(f"{bco.Yellow}{bco.Bold} WARNING. EASEL is not in the path{bco.ResetAll}\n\n")113 error_found = True114 # check Easel --------------------------------------------------------------115 sys.stderr.write(" â seqtk: ")116 if is_tool("seqtk"):117 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll}\n")118 else:119 sys.stderr.write(f"{bco.Yellow}{bco.Bold} WARNING. seqtk is not in the path{bco.ResetAll}\n\n")120 error_found = True121 # Python libraries:122 sys.stderr.write(" â (L)numpy: ") #------------------------------------123 library_correct = True124 try:125 import numpy126 except ImportError as e:127 library_correct = False128 if library_correct:129 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll}\n")130 else:131 sys.stderr.write(f"{bco.Yellow}{bco.Bold} WARNING. numpy is missing{bco.ResetAll}\n\n")132 error_found = True133 sys.stderr.write(" â (L)pandas: ") #------------------------------------134 library_correct = True135 try:136 import pandas137 except ImportError as e:138 library_correct = False139 if library_correct:140 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll}\n")141 else:142 sys.stderr.write(f"{bco.Yellow}{bco.Bold} WARNING. pandas is missing{bco.ResetAll}\n\n")143 error_found = True144 sys.stderr.write(" â (L)sklearn: ") #------------------------------------145 library_correct = True146 try:147 import sklearn148 except ImportError as e:149 library_correct = False150 if library_correct:151 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll}\n")152 else:153 sys.stderr.write(f"{bco.Yellow}{bco.Bold} WARNING. sklearn is missing{bco.ResetAll}\n\n")154 error_found = True155 sys.stderr.write(" â (L)h5py: ") #------------------------------------156 library_correct = True157 try:158 import h5py159 except ImportError as e:160 library_correct = False161 if library_correct:162 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll}\n")163 else:164 sys.stderr.write(f"{bco.Yellow}{bco.Bold} WARNING. h5py is missing{bco.ResetAll}\n\n")165 error_found = True166 # TRY TO RUN STAG ==========================================================167 sys.stderr.write(f"{bco.Cyan}{bco.Bold}2-- Run stag:{bco.ResetAll}\n")168 sys.stderr.write(" â train: ") #--------------------------------------169 sys.stderr.flush()170 seq_file = os.path.join(TEST_DATA_PATH, "sequences.fasta")171 tax_file = os.path.join(TEST_DATA_PATH, "sequences.taxonomy")172 hmm_file = os.path.join(TEST_DATA_PATH, "gene.hmm")173 temp_file_db = tempfile.NamedTemporaryFile(delete=False, mode="w")174 t0 = time.time()175 stag_command = "stag train -f -o "+temp_file_db.name+" -i "+seq_file+" -x "+tax_file+" -a "+hmm_file176 process = subprocess.run(stag_command.split())177 runtime = time.time() - t0178 if process.returncode:179 sys.stderr.write(f"{bco.Red}{bco.Bold} Error{bco.ResetAll} ({runtime:.3f}s)\n")180 sys.exit(1)181 else:182 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll} ({runtime:.3f}s)\n")183 sys.stderr.write(" â classify: ") #--------------------------------------184 sys.stderr.flush()185 temp_file_res = tempfile.NamedTemporaryFile(delete=False, mode="w")186 t0 = time.time()187 stag_command = "stag classify -v 1 -d "+temp_file_db.name+" -i "+seq_file+" -o "+temp_file_res.name188 process = subprocess.run(stag_command.split())189 runtime = time.time() - t0190 if process.returncode:191 sys.stderr.write(f"{bco.Red}{bco.Bold} Error{bco.ResetAll} ({runtime:.3f}s)\n")192 sys.exit(1)193 else:194 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll} ({runtime:.3f}s)\n")195 # remove temp file196 os.remove(temp_file_db.name+".log")197 os.remove(temp_file_db.name)198 # CHECK THE RESULTING FILE =================================================199 sys.stderr.write(f"{bco.Cyan}{bco.Bold}3-- Check result of the classification:{bco.ResetAll}\n")200 sys.stderr.write(" â taxonomy of classified sequences: ")201 sys.stderr.flush()202 o = open(tax_file,"r")203 correct_tax = dict()204 for i in o:205 vals = i.rstrip().split("\t")206 correct_tax[vals[0]] = vals[1]207 o.close()208 o = open(temp_file_res.name,"r")209 o.readline() # remove header210 pred_tax = dict()211 for i in o:212 vals = i.rstrip().split("\t")213 if len(vals) < 2:214 sys.stderr.write(f"{bco.Red}{bco.Bold} Error: less than two values ("+str(vals)+f"){bco.ResetAll}\n")215 os.remove(temp_file_res.name)216 sys.exit(1)217 pred_tax[vals[0]] = vals[1]218 o.close()219 # remove temp file220 os.remove(temp_file_res.name)221 # let's check the values222 if not set(pred_tax.keys()) == set(correct_tax.keys()):223 sys.stderr.write(f"{bco.Red}{bco.Bold} Error: different number of predicted genes{bco.ResetAll}\n")224 print(len(pred_tax), len(correct_tax), file=sys.stderr)225 print(*pred_tax.keys(), sep="\n")226 print("****")227 print(*correct_tax.keys(), sep="\n")228 sys.exit(1)229 # if we arrive here, we have the same set of predicted genes230 # let's check the predicted taxonomies231 error_flag = False232 for i in pred_tax:233 if pred_tax[i] != correct_tax[i]:234 error_flag = True235 sys.stderr.write(f"{bco.Red}{bco.Bold} Error: different taxonomy for "+i+"(correct:'"+correct_tax[i]+"', predicted:'"+pred_tax[i]+"')"+f"{bco.ResetAll}\n")236 if not error_flag:237 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll}\n")238 if error_found or error_flag:239 sys.exit(1)240 ############################################################################241 sys.stderr.write(f"{bco.Blue}{bco.Bold} ------------------------------------------------------------------------------{bco.ResetAll}\n")242 sys.stderr.write(f"{bco.Blue}{bco.Bold}|{bco.Green} LONG STAG TEST {bco.Blue}|{bco.ResetAll}\n")243 sys.stderr.write(f"{bco.Blue}{bco.Bold} ------------------------------------------------------------------------------{bco.ResetAll}\n")244 # long test part 1: test building genome DB --------------------------------245 sys.stderr.write(f"{bco.Cyan}{bco.Bold}1-- Build genome database:{bco.ResetAll}\n")246 # prepare data247 link_db = "https://zenodo.org/record/4626959/files/train_genome_files.tar.gz"248 db_name = os.path.join(TEST_DATA_PATH, "train_genome_files.tar.gz")249 md5_db = "5ec5a527d25cc6d1f11a8ec50cd252a7"250 this_dir = download_and_checkmd5_and_decompress(link_db, db_name, md5_db, TEST_DATA_PATH)251 # train genome252 sys.stderr.write(" â train genome DB: ")253 sys.stderr.flush()254 gene_files = this_dir + "COG0012," + this_dir + "COG0016," + this_dir + "COG0018"255 merged_db = this_dir + "genes_ali.stagDB"256 thresholds = this_dir + "gene_thresholds"257 result_genome_DB = this_dir + "TEST_DB.stagDB"258 t0 = time.time()259 stag_command = "stag train_genome -v 1 -o "+result_genome_DB+" -i "+gene_files+" -T "+thresholds+" -C "+merged_db260 process = subprocess.run(stag_command.split())261 runtime = time.time() - t0262 if process.returncode:263 sys.stderr.write(f"{bco.Red}{bco.Bold} Error{bco.ResetAll} ({runtime:.3f}s)\n")264 sys.exit(1)265 else:266 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll} ({runtime:.3f}s)\n")267 # long test part 2: test classify genome -----------------------------------268 sys.stderr.write(f"{bco.Cyan}{bco.Bold}2-- Test genome classification:{bco.ResetAll}\n")269 # prepare data270 link_db = "https://zenodo.org/record/4626959/files/classify_genome_files.tar.gz"271 db_name = os.path.join(TEST_DATA_PATH, "classify_genome_files.tar.gz")272 md5_db = "819cc77d463a797a330d8d1d9437feca"273 this_dir = download_and_checkmd5_and_decompress(link_db, db_name, md5_db, TEST_DATA_PATH)274 # train genome275 sys.stderr.write(" â classify 2 genomes: ")276 sys.stderr.flush()277 genome_files = this_dir + "genomes"278 result = this_dir + "RESULT_TEMP"279 t0 = time.time()280 stag_command = "stag classify_genome -v 1 -o "+result+" -d "+result_genome_DB+" -D "+genome_files281 process = subprocess.run(stag_command.split())282 runtime = time.time() - t0283 if process.returncode:284 sys.stderr.write(f"{bco.Red}{bco.Bold} Error{bco.ResetAll} ({runtime:.3f}s)\n")285 sys.exit(1)286 else:287 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll} ({runtime:.3f}s)\n")288 # check result of the classification ---------------------------------------289 sys.stderr.write(" â check result: ")290 # correct annotation291 o = open(this_dir + "CORRECT_ASSIGNMENT/genome_annotation")292 o.readline()293 correct_classification = dict()294 all_genomes = dict()295 for line in o:296 vals = line.rstrip().split("\t")297 correct_classification[vals[0]] = vals[1]298 all_genomes[vals[0]] = False299 o.close()300 # this annotation301 o = open(this_dir + "RESULT_TEMP/genome_annotation")302 o.readline()303 for line in o:304 vals = line.rstrip().split("\t")305 vals[0] = vals[0].split("/")[-1]306 all_genomes[vals[0]] = True307 if not vals[0] in correct_classification:308 sys.stderr.write(f"{bco.Red}{bco.Bold} Error, too many lines{bco.ResetAll}\n")309 sys.stderr.write(f"{bco.Red}{bco.Bold} Check "+ this_dir + f"RESULT_TEMP/genome_annotation {bco.ResetAll}\n")310 sys.exit(1)311 else:312 if correct_classification[vals[0]] != vals[1]:313 sys.stderr.write(f"{bco.Red}{bco.Bold} Error, wrong calssification{bco.ResetAll}\n")314 sys.stderr.write(f"{bco.Red}{bco.Bold} Check "+ this_dir + f"RESULT_TEMP/genome_annotation {bco.ResetAll}\n")315 sys.exit(1)316 o.close()317 # check that all the genomes were profiled318 for genome in all_genomes:319 if not all_genomes[genome]:320 sys.stderr.write(f"{bco.Red}{bco.Bold} Error, some genomes are missing{bco.ResetAll}\n")321 sys.stderr.write(f"{bco.Red}{bco.Bold} Check "+ this_dir + f"RESULT_TEMP/genome_annotation {bco.ResetAll}\n")322 sys.exit(1)323 # if we arrive till here, then it's correct324 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll}\n")325 # long test part 3: test gene train and classification with real data ------326 sys.stderr.write(f"{bco.Cyan}{bco.Bold}3-- Test real genes:{bco.ResetAll}\n")327 # prepare data328 link_db = "https://zenodo.org/record/4626959/files/test_gene.tar.gz"329 db_name = os.path.join(TEST_DATA_PATH, "test_gene.tar.gz")330 md5_db = "bee91d9dc06fae153502af386c29ca5c"331 this_dir = download_and_checkmd5_and_decompress(link_db, db_name, md5_db, TEST_DATA_PATH)332 # train genome333 sys.stderr.write(" â train database: ")334 sys.stderr.flush()335 seq_file = this_dir + "train.fna"336 protein_file = this_dir + "train.faa"337 tax_file = this_dir + "train.tax"338 hmm_file = this_dir + "COG0012.hmm"339 trained_db = this_dir + "TRAINED_TEMP"340 temp_file_db = tempfile.NamedTemporaryFile(delete=False, mode="w")341 t0 = time.time()342 stag_command = "stag train -f -o "+trained_db+" -i "+seq_file+" -p "+protein_file+" -x "+tax_file+" -a "+hmm_file + " -t 2"343 process = subprocess.run(stag_command.split())344 runtime = time.time() - t0345 if process.returncode:346 sys.stderr.write(f"{bco.Red}{bco.Bold} Error{bco.ResetAll} ({runtime:.3f}s)\n")347 sys.exit(1)348 else:349 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll} ({runtime:.3f}s)\n")350 sys.stderr.write(" â classify: ") #--------------------------------------351 sys.stderr.flush()352 res_classification = this_dir + "RES_TEMP"353 seq_file = this_dir + "test.fna"354 protein_file = this_dir + "test.faa"355 t0 = time.time()356 stag_command = "stag classify -v 1 -d "+trained_db+" -i "+seq_file+" -p "+protein_file+" -o "+res_classification357 process = subprocess.run(stag_command.split())358 runtime = time.time() - t0359 if process.returncode:360 sys.stderr.write(f"{bco.Red}{bco.Bold} Error{bco.ResetAll} ({runtime:.3f}s)\n")361 sys.exit(1)362 else:363 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll} ({runtime:.3f}s)\n")364 # check result of the classification ---------------------------------------365 sys.stderr.write(" â check result: ")366 # correct annotation367 o = open(this_dir + "test.CORRECT_ASSIGNMENT")368 o.readline()369 correct_classification = dict()370 all_genomes = dict()371 for line in o:372 vals = line.rstrip().split("\t")373 correct_classification[vals[0]] = vals[1]374 all_genomes[vals[0]] = False375 o.close()376 # this annotation377 o = open(res_classification)378 o.readline()379 for line in o:380 vals = line.rstrip().split("\t")381 all_genomes[vals[0]] = True382 if not vals[0] in correct_classification:383 sys.stderr.write(f"{bco.Red}{bco.Bold} Error, too many lines{bco.ResetAll}\n")384 sys.stderr.write(f"{bco.Red}{bco.Bold} Check "+ res_classification + f"{bco.ResetAll}\n")385 sys.exit(1)386 else:387 if correct_classification[vals[0]] != vals[1]:388 sys.stderr.write(f"\n{bco.Yellow} Corr: "+correct_classification[vals[0]]+f"{bco.ResetAll}\n")389 sys.stderr.write(f"{bco.Yellow} Pred: "+vals[1]+f"{bco.ResetAll}\n")390 else:391 sys.stderr.write(f"\n{bco.LightGreen} Corr: "+correct_classification[vals[0]]+f"{bco.ResetAll}\n")392 sys.stderr.write(f"{bco.LightGreen} Pred: "+vals[1]+f"{bco.ResetAll}\n")393 o.close()394 # check that all the genomes were profiled395 for genome in all_genomes:396 if not all_genomes[genome]:397 sys.stderr.write(f"{bco.Red}{bco.Bold} Error, some genomes are missing{bco.ResetAll}\n")398 sys.stderr.write(f"{bco.Red}{bco.Bold} Check "+ res_classification + f"{bco.ResetAll}\n")399 sys.exit(1)400 # if we arrive till here, then it's correct401 sys.stderr.write(f"{bco.Green}{bco.Bold} correct{bco.ResetAll}\n")402 # print(*all_genomes.items(), sep="\n")403 return None # success404#-------------------------------- run main -------------------------------------405if __name__ == '__main__':...
Color.py
Source:Color.py
1class Color_Manager:2 class BG:3 Black = '\033[40m'4 Red = '\033[41m'5 Green = '\033[42m'6 Yellow = '\033[43m'7 Blue = '\033[44m'8 Magenta = '\033[45m'9 Cyan = '\033[46m'10 White = '\033[47m'11 Reset = '\033[49m'12 class FG:13 Black = '\033[30m'14 Red = '\033[31m'15 Green = '\033[32m'16 Yellow = '\033[33m'17 Blue = '\033[34m'18 Magenta = '\033[35m'19 Cyan = '\033[36m'20 White = '\033[37m'21 Reset = '\033[39m'22 class BRIGHT:23 dim = '\033[2m'24 normal = '\033[22m'25 class EFFECT:26 ResetAll = '\033[0m'27 Italic = '\033[3m'28 Underline = '\033[4m'29 Bold = '\033[1m'30 @classmethod31 def FgPrint(cls, str, color):32 if color == 'Black':33 print(cls.FG.Black + cls.EFFECT.Bold + str + cls.EFFECT.ResetAll, end = ' ')34 elif color == 'Red':35 print(cls.FG.Red + cls.EFFECT.Bold + str + cls.EFFECT.ResetAll, end = ' ')36 elif color == 'Green':37 print(cls.FG.Green + cls.EFFECT.Bold + str + cls.EFFECT.ResetAll, end = ' ')38 elif color == 'Yellow':39 print(cls.FG.Yellow + cls.EFFECT.Bold + str + cls.EFFECT.ResetAll, end = ' ')40 elif color == 'Blue':41 print(cls.FG.Blue + cls.EFFECT.Bold + str + cls.EFFECT.ResetAll, end = ' ')42 elif color == 'Magenta':43 print(cls.FG.Magenta + cls.EFFECT.Bold + str + cls.EFFECT.ResetAll, end = ' ')44 elif color == 'Cyan':45 print(cls.FG.Cyan + cls.EFFECT.Bold + str + cls.EFFECT.ResetAll, end = ' ')46 elif color == 'White':47 print(cls.FG.White + cls.EFFECT.Bold + str + cls.EFFECT.ResetAll, end = ' ')48 @classmethod49 def BgPrint(cls, str, color):50 if color == 'Black':51 print(cls.BG.Black + cls.EFFECT.Bold + str + cls.EFFECT.ResetAll, end = ' ')52 elif color == 'Red':53 print(cls.BG.Red + cls.EFFECT.Bold + str + cls.EFFECT.ResetAll, end = ' ')54 elif color == 'Green':55 print(cls.BG.Green + cls.EFFECT.Bold + str + cls.EFFECT.ResetAll, end = ' ')56 elif color == 'Yellow':57 print(cls.BG.Yellow + cls.EFFECT.Bold + str + cls.EFFECT.ResetAll, end = ' ')58 elif color == 'Blue':59 print(cls.BG.Blue + cls.EFFECT.Bold + str + cls.EFFECT.ResetAll, end = ' ')60 elif color == 'Magenta':61 print(cls.BG.Magenta + cls.EFFECT.Bold + str + cls.EFFECT.ResetAll, end = ' ')62 elif color == 'Cyan':63 print(cls.BG.Cyan + cls.EFFECT.Bold + str + cls.EFFECT.ResetAll, end = ' ')64 elif color == 'White':...
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