pax_global_header 0000666 0000000 0000000 00000000064 12455220076 0014515 g ustar 00root root 0000000 0000000 52 comment=c03974c6e1b639a407d699ffa0bec04e40f05d94
macsyfinder-macsyfinder-1.0.2/ 0000775 0000000 0000000 00000000000 12455220076 0016323 5 ustar 00root root 0000000 0000000 macsyfinder-macsyfinder-1.0.2/.gitignore 0000664 0000000 0000000 00000001275 12455220076 0020320 0 ustar 00root root 0000000 0000000 ######################
# Logs and databases #
######################
*\.log
.DS_Store
####################
# Eclipse metadata #
####################
\.project
\.pydevproject
\.settings/
#############
# vim files #
#############
*\.swp
*~
\#*\#
##########################
# Python complied source #
##########################
*\.pyc
*\.pyo
build/
dist/
doc/_build/
###################################
# MacsyFinder results directories #
###################################
bin/macsyfinder-*
bin/log*
bin/prru_psae_acav.*
bin/script.csh
log*
test/datatest/DEF_svg/
bin/formatdb.err
macsypy/*_svg
##############################
# MacsyFinder generated file #
##############################
MANIFEST
macsyfinder-macsyfinder-1.0.2/.travis.yml 0000664 0000000 0000000 00000001071 12455220076 0020433 0 ustar 00root root 0000000 0000000 language: python
python:
- "2.7"
# Apply only on main branches
branches:
except:
- /^feature.*$/
# command to install Ubuntu dependencies
before_install:
- sudo apt-get update -qq
- sudo apt-get install hmmer
- sudo apt-get install ncbi-blast+
# command to install python dependencies
install:
- "pip install coverage"
- "pip install python-coveralls"
# command to run tests
script:
- python setup.py build
- python setup.py test -vv
- cd test && coverage run --source ../macsypy main.py && coverage html
after_success:
- coveralls
macsyfinder-macsyfinder-1.0.2/CITATION 0000664 0000000 0000000 00000001426 12455220076 0017463 0 ustar 00root root 0000000 0000000 # How to cite macsyfinder
# below the citation informations in json format
authors:
- Abby SS.
- Néron B.
- Ménager H.
- Touchon M.
- Rocha EPC.
date: 2014
title: "MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems."
journal:
title: PLoS ONE
volume: 9
issue: 10
enumber: e110726.
doi: 10.1371/journal.pone.0110726
url: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0110726
# below a more human readable and traditional version
# Abby SS, Néron B, Ménager H, Touchon M, Rocha EPC (2014)
# MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems.
# PLoS ONE 9(10): e110726. doi:10.1371/journal.pone.0110726 macsyfinder-macsyfinder-1.0.2/COPYING 0000664 0000000 0000000 00000104513 12455220076 0017362 0 ustar 00root root 0000000 0000000 GNU GENERAL PUBLIC LICENSE
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PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
Copyright (C)
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see .
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
Copyright (C)
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
.
macsyfinder-macsyfinder-1.0.2/COPYRIGHT 0000664 0000000 0000000 00000005006 12455220076 0017617 0 ustar 00root root 0000000 0000000 MacSyFinder/MacSyView - Detection of macromolecular systems
in protein datasets using systems modelling and similarity search.
Copyright © 2014 Institut Pasteur (Paris) and CNRS.
------------------------------------------------------------------
Citation:
Abby SS, Néron B, Ménager H, Touchon M, Rocha EPC (2014). MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems. PLoS ONE 9(10): e110726. doi:10.1371/journal.pone.0110726
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0110726
------------------------------------------------------------------
The code includes contributions and input from:
Sophie Abby Microbial Evolutionary Genomics Unit, UMR CNRS 3525,
Institut Pasteur, Paris.
Bertrand Néron Biology IT Center, Institut Pasteur, Paris.
Hervé Ménager Biology IT Center, Institut Pasteur, Paris.
MacSyView also includes contributions from others, including
copyrighted and licensed code and technology:
- JQuery
Url: http://jquery.com/
Author:
License: MIT (see website for details)
- JQuery-mousewheel
Url: https://github.com/brandonaaron/jquery-mousewheel
Author: Brandon Aaron
License: MIT (see website for details)
- Raphael
Url: http://raphaeljs.com/
Author: Dmitry Baranovskiy
License: MIT (see website for details)
- Bootstrap
Url: http://getbootstrap.com/
Author: Mark Otto, Jacob Thornton
License: MIT (see website for details)
- Mustache
Url: http://github.com/janl/mustache.js
Author: Jan Lehnardt
License: MIT (see website for details)
- Raphael.export
Url: https://github.com/ElbertF/Raphael.Export
Author: ElbertF
License: MIT (see website for details)
-----------------------------------------------------------------
The source code of MacSyFinder and MacSyView is distributed
under the terms of the GNU GeneralPublic License.
See the file COPYING for details.
Thess programs are free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 3 of the License.
These programs are distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
A copy of the GNU General Public License is in the file COPYING. You
may also obtain a copy from .
macsyfinder-macsyfinder-1.0.2/INSTALL 0000664 0000000 0000000 00000005515 12455220076 0017362 0 ustar 00root root 0000000 0000000 INSTALLATION INSTRUCTIONS FOR MacSyFinder and MacSyView
*******************************************************
1 - Requirements :
==================
for MacSyFinder :
-----------------
- Any machine running a unix-like Operating System.
- Python, (>=2.7 & <3.0)
- makeblastdb (>= 2.2.28) or formatdb (>=2.2.26)
+ makeblastdb is a distribute with blastdb
(http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
+ formatdb
- hmmsearch 3.0 (http://hmmer.janelia.org/)
for MacSyView :
---------------
- chromium or firefox web browser.
2 - Archive overview:
=====================
bin => contain the executables (macsyfinder)
data => the hmm profiles and the systems definitions
doc => the documentation in html and pdf
etc => a template of macsyfinder configuration file
test => all needed for unit tests
macsypy => the macsyfinder python library
setup.py => the installation script
3 - Installation steps:
=======================
3.1 - Make sure every required dependence/software is present.
--------------------------------------------------------------
by default MacSyFinder will search if makeblastdb is on your PATH if not it will looking for formatdb.
if neither makeblastdb nor formatdb are in your path you have to set the absolute path toward one of
these tools in the configuration file.
by default MacSyFinder will try to use hmmsearch in your PATH, if hmmsearch is not in the PATH,
you have to set the absolute path to the hmmsearch in configuration.
If the tools are not in the path, some test will be skipped and a warning will be raised.
3.2 - Perform the installation.
-------------------------------
unpack the archive
tar -xzf macsyfinder-x.x.tar.gz
cd macsyfinder-x.x
macsyfinder installation follows classical "pythonic" installation procedure (see http://docs.python.org/2/install/):
python setup.py build
python setup.py test -vv
python setup.py install
if you have not the privileges to perform a system wide installation, you can use virtualenv
(http://www.virtualenv.org/en/latest/virtualenv.html).
or use the option --prefix
You can access all general cmd with python setup.py --help
and specific options with python setup.py cmd --help
4 Configuration.
================
macsyfinder have some options that can be set in configuration file
+ system wide $prefix/etc/macsyfinder/macsyfinder.conf
+ user wide ~/.macsyfinder/macsyfinder.conf
+ for project ./macsyfinder.conf
or on the command line.
for all options see documentation
+ ($prefix or /usr)/share/doc/macsyfinder/html/index.html
+ ($prefix or /usr)/share/doc/macsyfinder/pdf/Macsyfinder.pdf
5 Uninstalation.
================
To uninstall MacSyFinder (the last version installed), run:
(sudo) python setup.py uninstall
To get started after installation, see the Running MacSyFinder section in the
User's Guide (Userguide.pdf) macsyfinder-macsyfinder-1.0.2/MANIFEST.in 0000664 0000000 0000000 00000001311 12455220076 0020055 0 ustar 00root root 0000000 0000000 exclude macsypy/test_*.py
recursive-include doc/_build/html *
include doc/_build/latex/Macsyfinder.pdf
include data/DEF/*.xml
include data/profiles/*.hmm
include data/sequence_data/datatest_gembase.fasta*
include data/sequence_data/datatest_gembase.topology
include data/sequence_data/results.macsyfinder.json
include test/test_*.py
include test/main.py
include test/__init__.py
include test/datatest/DEF/*.xml
include test/datatest/base/*
include test/datatest/hmm/*
include test/datatest/profiles/*
include test/macsyfinder.conf
include etc/macsyfinder.conf
include INSTALL
include COPYING
include COPYRIGHT
include NEWS
include CITATION
recursive-include macsyview/app *
recursive-include macsyview/bin *
macsyfinder-macsyfinder-1.0.2/NEWS 0000664 0000000 0000000 00000000515 12455220076 0017023 0 ustar 00root root 0000000 0000000 CHANGES IN RELEASE 1.0.2
# Fix https://github.com/gem-pasteur/macsyfinder/issues/1
unit tests to fix "too many file open"
# add portability for windows
thank's to Francisco J. Ossandon
# add new option --dir-out
Path to the directory where to store results.
If out-dir is specified res-search-dir will be ignored. macsyfinder-macsyfinder-1.0.2/README.md 0000664 0000000 0000000 00000003235 12455220076 0017605 0 ustar 00root root 0000000 0000000 MacSyFinder
===========
MacSyFinder - Detection of macromolecular systems in protein datasets using systems modelling and similarity search.
Citation
--------
Abby SS, Néron B, Ménager H, Touchon M, Rocha EPC (2014). MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems. PLoS ONE 9(10): e110726. doi:10.1371/journal.pone.0110726
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0110726
Download distribution
---------------------
[](http://dl.bintray.com/gem-pasteur/MacSyFinder/macsyfinder-1.0.1.tar.gz)
Installation from distribution
------------------------------
1. Uncompress and untar the package:
tar -xzf macsyfinder-x.x.tar.gz
2. Go to the macsyfinder directory
cd macsyfinder-1.0
3. Build and install
python setup.py build
python setup.py test -vv
python setup.py install
to see all installation options "python setup.py --help"
See the INSTALL file for more details.
Installation from repository
----------------------------
Please be careful, MacSyView has its own repository: https://github.com/gem-pasteur/macsyview
Unit tests with Travis-CI
-------------------------
[](https://travis-ci.org/gem-pasteur/macsyfinder)
Documentation
-------------
You will find complete documentation for setting up your project at the Read the Docs site.
[![Doc] (https://readthedocs.org/projects/macsyfinder/badge/?version=latest)](http://macsyfinder.readthedocs.org/en/latest/#)
macsyfinder-macsyfinder-1.0.2/bin/ 0000775 0000000 0000000 00000000000 12455220076 0017073 5 ustar 00root root 0000000 0000000 macsyfinder-macsyfinder-1.0.2/bin/macsyfinder 0000775 0000000 0000000 00000044371 12455220076 0021336 0 ustar 00root root 0000000 0000000 #!/usr/bin/env python
# -*- coding: utf-8 -*-
################################################################################
# MacSyFinder - Detection of macromolecular systems in protein datasets #
# using systems modelling and similarity search. #
# Authors: Sophie Abby, Bertrand Néron #
# Copyright © 2014 Institut Pasteur, Paris. #
# See the COPYRIGHT file for details #
# #
# MacsyFinder is distributed under the terms of the GNU General Public License #
# (GPLv3). See the COPYING file for details. #
################################################################################
import sys
import os
import argparse
import logging
if 'MACSY_HOME' in os.environ:
MACSY_HOME = os.environ.get('MACSY_HOME')
MACSY_HOME = os.path.abspath(os.path.realpath(MACSY_HOME))
if MACSY_HOME not in sys.path:
sys.path.insert(0, MACSY_HOME)
try:
from macsypy.config import Config
except ImportError , err:
msg = "Cannot import macsypy, check your installation or your MACSY_HOME variable : {0!s}".format( err )
sys.exit( msg )
from operator import attrgetter # To be used with "sorted"
from textwrap import dedent
from macsypy.system_parser import SystemParser
from macsypy.search_genes import search_genes
from macsypy.database import Indexes
from macsypy.search_systems import search_systems
from macsypy.system import system_bank
from macsypy.gene import gene_bank
parser = argparse.ArgumentParser(epilog="For more details, visit the MacSyFinder website and see the MacSyFinder documentation.", formatter_class=argparse.RawDescriptionHelpFormatter,
description=dedent('''
* * * *
* * * * * * ** * *
** * * * * * * *
__ __ * ____ * * * * ** *
|| | \/ | __ _ ___ || / ___| _ _ || ___ _ _ *
|| | |\/| |/ _` |/ __| || \___ \| | | | || | __(_)_ _ __| |___ _ _
|| | | | | (_| | (__ || ___) | |_| | || | _|| | ' \/ _` / -_) '_|
|| |_| |_|\__,_|\___| || |____/ \__, | || |_| |_|_||_\__,_\___|_|
* * |___/ * *
* * * * * ** * * * *
* * * * * *
* * * * *
MacSyFinder is a tool for the detection of protein secretion systems
of diderm bacteria from a protein dataset.
''') )
#, formatter_class=argparse.RawDescriptionHelpFormatter)
#, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("systems",
nargs = '+',
help = "The systems to detect. This is an obligatory option with no keyword associated to it. To detect all the protein secretion systems and related appendages: set to \"all\" (case insensitive). Otherwise, a single or multiple systems can be specified. For example: \"T2SS T4P\". ")
genome_options = parser.add_argument_group(title = "Input dataset options")
genome_options.add_argument("--sequence-db",
action = 'store',
dest = 'sequence_db',
help = "Path to the sequence dataset in fasta format.")
genome_options.add_argument("--db-type" ,
choices = ['unordered_replicon', 'ordered_replicon', 'gembase', 'unordered'],
dest = "db_type",
default = None,
help = "The type of dataset to deal with. \"unordered_replicon\" corresponds to a non-assembled genome, \"unordered\" to a metagenomic dataset, \"ordered_replicon\" to an assembled genome, and \"gembase\" to a set of replicons where sequence identifiers follow this convention: \">RepliconName SequenceID\"." )
genome_options.add_argument("--replicon-topology" ,
choices = ['linear', 'circular'],
dest = "replicon_topology",
default = None,
help = "The topology of the replicons (this option is meaningful only if the db_type is 'ordered_replicon' or 'gembase'. ")
genome_options.add_argument("--topology-file" ,
dest = "topology_file",
default = None,
help = "Topology file path. The topology file allows to specify a topology (linear or circular) for each replicon (this option is meaningful only if the db_type is 'ordered_replicon' or 'gembase'. A topology file is a tabular file with two columns: the 1st is the replicon name, and the 2nd the corresponding topology:\n\"RepliconA\tlinear\" ")
genome_options.add_argument("--idx" ,
action = 'store_true',
dest = "build_indexes",
default = False,
help = "Forces to build the indexes for the sequence dataset even if they were presviously computed and present at the dataset location (default = False)")
system_options = parser.add_argument_group(title = "Systems detection options")
system_options.add_argument("--inter-gene-max-space",
action = 'append',
nargs = 2,
dest = 'inter_gene_max_space',
default = None,
help = "Co-localization criterion: maximum number of components non-matched by a profile allowed between two matched components for them to be considered contiguous. Option only meaningful for 'ordered' datasets. The first value must match to a system, the second to a number of components.\
This option can be repeated several times:\n \"--inter-gene-max-space T2SS 12 --inter-gene-max-space Flagellum 20\""
)
system_options.add_argument("--min-mandatory-genes-required",
action = 'append',
nargs = 2,
dest = 'min_mandatory_genes_required',
default = None,
help = "The minimal number of mandatory genes required for system assessment. The first value must correspond to a system name, the second value to an integer.\
This option can be repeated several times:\n \"--min-mandatory-genes-required T2SS 15 --min-mandatory-genes-required Flagellum 10\""
)
system_options.add_argument("--min-genes-required",
action = 'append',
nargs = 2,
dest = 'min_genes_required',
default = None,
help = "The minimal number of genes required for system assessment (includes both 'mandatory' and 'accessory' components). The first value must correspond to a system name, the second value to an integer.\
This option can be repeated several times:\n \"--min-genes-required T2SS 15 --min-genes-required Flagellum 10\""
)
system_options.add_argument("--max-nb-genes",
action = 'append',
nargs = 2,
dest = 'max_nb_genes',
default = None,
help = "The maximal number of genes required for system assessment. The first value must correspond to a system name, the second value to an integer.\
This option can be repeated several times:\n \"--max-nb-genes T2SS 5 --max-nb-genes Flagellum 10"
)
system_options.add_argument("--multi-loci",
action = 'store',
dest = 'multi_loci',
default = None,
help = "Allow the storage of multi-loci systems for the specified systems.\
The systems are specified as a comma separated list (--multi-loci sys1,sys2) default is False"
)
hmmer_options = parser.add_argument_group(title = "Options for Hmmer execution and hits filtering")
hmmer_options.add_argument('--hmmer',
action = 'store',
dest = 'hmmer_exe',
default = None,
help = 'Path to the Hmmer program.')
hmmer_options.add_argument('--index-db',
action = 'store',
dest = 'index_db_exe',
default = None,
help = "The indexer to be used for Hmmer. The value can be either 'makeblastdb' or 'formatdb' or the path to one of these binary (default = makeblastb)")
hmmer_options.add_argument('--e-value-search',
action = 'store',
dest = 'e_value_res',
type = float,
default = None,
help = 'Maximal e-value for hits to be reported during Hmmer search. (default = 1)')
hmmer_options.add_argument('--i-evalue-select',
action = 'store',
dest = 'i_evalue_sel',
type = float,
default = None ,
help = 'Maximal independent e-value for Hmmer hits to be selected for system detection. (default = 0.001)')
hmmer_options.add_argument('--coverage-profile',
action = 'store',
dest = 'coverage_profile',
type = float,
default = None ,
help = 'Minimal profile coverage required in the hit alignment to allow the hit selection for system detection. (default = 0.5)')
dir_options = parser.add_argument_group(title = "Path options", description = None)
dir_options.add_argument('-d', '--def',
action = 'store',
dest = 'def_dir',
default = None,
help = 'Path to the systems definition files.')
dir_options.add_argument('-o', '--out-dir',
action = 'store',
dest = 'out_dir',
default = None,
help = 'Path to the directory where to store results. if out-dir is specified res-search-dir will be ignored.')
dir_options.add_argument('-r', '--res-search-dir',
action = 'store',
dest = 'res_search_dir',
default = None,
help = 'Path to the directory where to store MacSyFinder search results directories (default current working directory).')
dir_options.add_argument('--res-search-suffix',
action = 'store',
dest = 'res_search_suffix',
default = None,
help = 'The suffix to give to Hmmer raw output files.')
dir_options.add_argument('--res-extract-suffix',
action = 'store',
dest = 'res_extract_suffix',
default = None,
help = 'The suffix to give to filtered hits output files.')
dir_options.add_argument('-p', '--profile-dir',
action = 'store',
dest = 'profile_dir',
default = None,
help = 'Path to the profiles directory.')
dir_options.add_argument('--profile-suffix',
action = 'store',
dest = 'profile_suffix',
default = None,
help = "The suffix of profile files. For each 'Gene' element, the corresponding profile is searched in the 'profile_dir', in a file which name is based on the Gene name + the profile suffix. For instance, if the Gene is named 'gspG' and the suffix is '.hmm3', then the profile should be placed at the specified location and be named 'gspG.hmm3'")
general_options = parser.add_argument_group(title = "General options", description = None)
general_options.add_argument("-w", "--worker",
action = 'store',
dest = 'worker_nb',
type = int,
default = None,
help = "Number of workers to be used by MacSyFinder. In the case the user wants to run MacSyFinder in a multi-thread mode. (0 mean all cores will be used, default 1)")
general_options.add_argument("-v" , "--verbosity",
action= "count",
dest = "verbosity",
default = 0,
help = "Increases the verbosity level. There are 4 levels: Error messages (default), Warning (-v), Info (-vv) and Debug.(-vvv)")
general_options.add_argument("--log",
action = 'store',
dest = 'log_file',
default = None,
help = "Path to the directory where to store the 'macsyfinder.log' log file.")
general_options.add_argument("--config",
action = 'store',
dest = 'cfg_file',
default = None,
help = "Path to a putative MacSyFinder configuration file to be used.")
general_options.add_argument("--previous-run",
action = 'store',
dest = 'previous_run',
default = None,
help = """Path to a previous MacSyFinder run directory. It allows to skip the Hmmer search step on same dataset, as it uses previous run results and thus parameters regarding Hmmer detection. The configuration file from this previous run will be used.
(conflict with options --config, --sequence-db, --profile-suffix, --res-extract-suffix,
--e-value-res, --db-type, --hmmer)""")
args = parser.parse_args()
if args.previous_run and (args.cfg_file or
args.sequence_db or
args.profile_suffix or
args.profile_dir or
args.res_extract_suffix or
args.e_value_res or
args.db_type or
args.hmmer_exe):
parser.error(""" --previous-run conficts with --config, --sequence-db, --profile-suffix, --res-extract-suffix, --e-value-res, --db-type, --hmmer""")
sh_formatter = logging.Formatter("%(levelname)-8s : L %(lineno)d : %(message)s")
sh = logging.StreamHandler(sys.stderr)
sh.setFormatter(sh_formatter)
if args.verbosity == 0:
log_level = None
elif args.verbosity == 1:
log_level = logging.WARNING
elif args.verbosity == 2:
log_level = logging.INFO
elif args.verbosity == 3:
log_level = logging.DEBUG
config = Config(previous_run = args.previous_run,
cfg_file = args.cfg_file,
sequence_db = args.sequence_db,
db_type = args.db_type,
build_indexes = args.build_indexes,
replicon_topology = args.replicon_topology,
topology_file = args.topology_file,
inter_gene_max_space = args.inter_gene_max_space,
min_mandatory_genes_required = args.min_mandatory_genes_required,
min_genes_required = args.min_genes_required,
max_nb_genes = args.max_nb_genes,
multi_loci = args.multi_loci,
hmmer_exe = args.hmmer_exe,
index_db_exe = args.index_db_exe,
e_value_res = args.e_value_res,
i_evalue_sel = args.i_evalue_sel,
coverage_profile = args.coverage_profile,
def_dir = args.def_dir,
res_search_dir = args.res_search_dir,
out_dir = args.out_dir,
res_search_suffix = args.res_search_suffix,
profile_dir = args.profile_dir,
profile_suffix = args.profile_suffix,
res_extract_suffix = args.res_extract_suffix,
log_level = log_level,
log_file = args.log_file,
worker_nb = args.worker_nb
)
logger = logging.getLogger('macsyfinder')
config.save(config.working_dir)
#build indexes
idx = Indexes(config)
idx.build(force = config.build_indexes)
parser = SystemParser(config, system_bank, gene_bank)
if ('all' or 'All' or 'ALL') in args.systems:
import glob
systems_name_to_detect = glob.glob(os.path.join(config.def_dir, '*.xml'))
systems_name_to_detect = [os.path.basename(s)[:-4] for s in systems_name_to_detect]
else:
systems_name_to_detect = args.systems
parser.parse(systems_name_to_detect)
out_logger = logging.getLogger('macsyfinder.out')
out_logger.info("MacSyFinder's results will be stored in {0}".format(config.working_dir))
out_logger.info("Analysis launched on {0} for system(s):".format(config.sequence_db))
for s in systems_name_to_detect:
out_logger.info("\t- {}".format(s))
systems_to_detect = [system_bank[system_name] for system_name in systems_name_to_detect]
all_genes = []
for system in systems_to_detect:
genes = system.mandatory_genes + system.accessory_genes + system.forbidden_genes
# Exchangeable homologs/analogs are also added cause they can "replace" an important gene...
ex_genes = []
for g in genes:
if g.exchangeable:
h_s = g.get_homologs()
ex_genes += h_s
a_s = g.get_analogs()
ex_genes += a_s
all_genes += (genes + ex_genes)
#############################################
# this part of code is executed in parallel
#############################################
all_reports = search_genes(all_genes, config)
#############################################
# end of parallel code
#############################################
all_hits = [hit for subl in [report.hits for report in all_reports ] for hit in subl]
if len(all_hits) > 0:
all_hits = sorted(all_hits, key = attrgetter('score'), reverse = True)
all_hits = sorted(all_hits, key = attrgetter('replicon_name', 'position'))
systems_to_detect = sorted(systems_to_detect, key = attrgetter('name'))
search_systems(all_hits, systems_to_detect, config)
else:
logger.info("No hits found in this dataset.")
logger.debug("END")
macsyfinder-macsyfinder-1.0.2/data/ 0000775 0000000 0000000 00000000000 12455220076 0017234 5 ustar 00root root 0000000 0000000 macsyfinder-macsyfinder-1.0.2/data/DEF/ 0000775 0000000 0000000 00000000000 12455220076 0017632 5 ustar 00root root 0000000 0000000 macsyfinder-macsyfinder-1.0.2/data/DEF/CAS-TypeIA.xml 0000664 0000000 0000000 00000002410 12455220076 0022110 0 ustar 00root root 0000000 0000000
macsyfinder-macsyfinder-1.0.2/data/DEF/CAS-TypeIB.xml 0000664 0000000 0000000 00000002653 12455220076 0022122 0 ustar 00root root 0000000 0000000
macsyfinder-macsyfinder-1.0.2/data/DEF/CAS-TypeIC.xml 0000664 0000000 0000000 00000001751 12455220076 0022121 0 ustar 00root root 0000000 0000000
macsyfinder-macsyfinder-1.0.2/data/DEF/CAS-TypeID.xml 0000664 0000000 0000000 00000001705 12455220076 0022121 0 ustar 00root root 0000000 0000000
macsyfinder-macsyfinder-1.0.2/data/DEF/CAS-TypeIE.xml 0000664 0000000 0000000 00000001520 12455220076 0022115 0 ustar 00root root 0000000 0000000
macsyfinder-macsyfinder-1.0.2/data/DEF/CAS-TypeIF.xml 0000664 0000000 0000000 00000001554 12455220076 0022125 0 ustar 00root root 0000000 0000000
macsyfinder-macsyfinder-1.0.2/data/DEF/CAS-TypeIIA.xml 0000664 0000000 0000000 00000001325 12455220076 0022225 0 ustar 00root root 0000000 0000000
macsyfinder-macsyfinder-1.0.2/data/DEF/CAS-TypeIIB.xml 0000664 0000000 0000000 00000001325 12455220076 0022226 0 ustar 00root root 0000000 0000000
macsyfinder-macsyfinder-1.0.2/data/DEF/CAS-TypeIIIA.xml 0000664 0000000 0000000 00000004271 12455220076 0022341 0 ustar 00root root 0000000 0000000
macsyfinder-macsyfinder-1.0.2/data/DEF/CAS-TypeIIIB.xml 0000664 0000000 0000000 00000004326 12455220076 0022343 0 ustar 00root root 0000000 0000000
macsyfinder-macsyfinder-1.0.2/data/DEF/CAS-TypeIIIU.xml 0000664 0000000 0000000 00000004360 12455220076 0022364 0 ustar 00root root 0000000 0000000
macsyfinder-macsyfinder-1.0.2/data/DEF/CAS-TypeIIU.xml 0000664 0000000 0000000 00000001501 12455220076 0022245 0 ustar 00root root 0000000 0000000
macsyfinder-macsyfinder-1.0.2/data/DEF/CAS-TypeIU.xml 0000664 0000000 0000000 00000002151 12455220076 0022136 0 ustar 00root root 0000000 0000000
macsyfinder-macsyfinder-1.0.2/data/DEF/CAS-TypeU.xml 0000664 0000000 0000000 00000001672 12455220076 0022034 0 ustar 00root root 0000000 0000000
macsyfinder-macsyfinder-1.0.2/data/DEF/CAS.xml 0000664 0000000 0000000 00000014633 12455220076 0020771 0 ustar 00root root 0000000 0000000