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Merge branch 'main' of gitlab.pasteur.fr:gem/macsylib
2 parents 0e01b2f + fcd9023 commit e6ec225

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Lines changed: 24736 additions & 3 deletions

‎doc/source/user_guide/new.rst‎

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What's new in MacSyLib
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**********************
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main
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====
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Bug fix
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-------
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The command line option `--no-cut-ga` supersed the *model.conf* `cut_ga` value.
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(see https://github.com/gem-pasteur/macsyfinder/issues/84)
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V 1.0.4
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=======

‎src/macsylib/config.py‎

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@@ -150,7 +150,7 @@ class Config:
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model_opts = ('itself', 'exchangeable', 'mandatory', 'accessory', 'neutral',
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'out_of_cluster', 'redundancy_penalty',
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'e_value_search', 'e_value_sel', 'coverage_profile', 'cut_ga')
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'e_value_search', 'e_value_sel', 'coverage_profile', 'cut_ga', 'no_cut_ga')
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path_opts = ('sequence_db', 'topology_file', 'cfg_file', 'log_file', 'models_dir', 'system_models_dir', 'out_dir',
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'profile_suffix', 'res_search_dir', 'res_search_suffix', 'res_extract_suffix', 'index_dir')
@@ -244,7 +244,6 @@ def __init__(self, defaults: MacsyDefaults, parsed_args: argparse.Namespace) ->
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# superseed options (potentially in model_conf)
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# by the values provided by previous-run, project conf, the users on the commandline
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self._options.update(self._tmp_opts)
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# check that hmmsearch exists
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if not self.hmmer():
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msg = "'hmmsearch' NOT found in your PATH, Please specify hmmsearch path with --hmmer opt " \
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args_dict = {k: v for k, v in vars(parsed_args).items() if not k.startswith('__') and v is not None}
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for opt in self.model_opts:
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if opt in args_dict:
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self._tmp_opts[opt] = args_dict[opt]
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if opt == 'no_cut_ga':
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self._tmp_opts['cut_ga'] = False
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else:
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self._tmp_opts[opt] = args_dict[opt]
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del args_dict[opt]
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self._set_options(args_dict)
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:return:
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:rtype:
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"""
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print(f'!!!!!!!!!!!!!! _set_no_cut_ga {value = } !!!!!!!!!!!!!!!!!!!!!!!!')
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self._options['cut_ga'] = not value
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print(f"!!!! {self._options['cut_ga'] = }")
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def models_dir(self) -> str | None:

‎tests/data/models/Model_conf_cutga/.gitignore‎

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.eggs
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######################
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# Logs and databases #
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######################
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*\.log
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.DS_Store
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#############
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# vim files #
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#############
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*\.swp
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*~
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\#*\#
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#################
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# pycharm files #
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#################
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\.idea
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##########################
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# Python complied source #
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##########################
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*\.pyc
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*\.pyo
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build/
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dist/
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doc/_build/
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‎tests/data/models/Model_conf_cutga/LICENSE‎

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This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
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To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/
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or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.

‎tests/data/models/Model_conf_cutga/README.md‎

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# Models to test model_conf with cut_ga
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check if cut-ga is take into account
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and more important if it s supersed by commandline --no-cut-ga option

‎tests/data/models/Model_conf_cutga/definitions/T2SS.xml‎

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<!--
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Authors: Remi Denise, Sophie Abby
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Copyright: 2018-2022 Institut Pasteur Paris, CNRS
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See the COPYRIGHT file for details
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This file is a part of TXSScan and TFFscan package.
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TXSScan and TFFscan are packages of models for macyfinder
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(https://github.com/gem-pasteur/macsyfinder)
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TXSScan and TFFscan are distributed under the terms of
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Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
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see LICENCE file ship with the package or visit
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http://creativecommons.org/licenses/by-nc-sa/4.0/
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for more details.
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-->
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<model inter_gene_max_space="5" min_mandatory_genes_required="3" min_genes_required="6" multi_loci="true" vers="2.1">
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<gene name="T2SS_gspC" presence="accessory"/>
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<gene name="T2SS_gspD" presence="mandatory" loner="true" multi_system="false"/>
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<gene name="T2SS_gspE" presence="mandatory" loner="true"/>
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<gene name="T2SS_gspF" presence="mandatory"/>
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<gene name="T2SS_gspG" presence="mandatory"/>
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<gene name="T2SS_gspH" presence="accessory"/>
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<gene name="T2SS_gspI" presence="accessory"/>
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<gene name="T2SS_gspJ" presence="accessory"/>
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<gene name="T2SS_gspK" presence="accessory"/>
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<gene name="T2SS_gspL" presence="accessory"/>
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<gene name="T2SS_gspM" presence="accessory"/>
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<gene name="T2SS_gspN" presence="accessory"/>
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<gene name="T2SS_gspO" presence="accessory" loner="true" multi_model="true">
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<exchangeables>
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<gene name="T4aP_pilD"/>
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<gene name="ComM_comC"/>
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</exchangeables>
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</gene>
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<gene name="T4aP_pilT" presence="forbidden"/>
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</model>

‎tests/data/models/Model_conf_cutga/definitions/T6SSiii.xml‎

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<!--
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Authors: Sophie Abby, Remi Denise, Youn Le Cras
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Copyright: 2014-2024 Institut Pasteur Paris, CNRS
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See the COPYRIGHT file for details
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This file is a part of TXSScan package.
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TXSScan is a package of models for macyfinder
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(https://github.com/gem-pasteur/macsyfinder)
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TXSScan is distributed under the terms of
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Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
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see LICENCE file shipped with the package or visit
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http://creativecommons.org/licenses/by-nc-sa/4.0/
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for more details.
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-->
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<model inter_gene_max_space="10" min_mandatory_genes_required="8" min_genes_required="8" multi_loci="1" vers="2.1">
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<gene name="T6SSiii_tssB" presence="mandatory" />
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<gene name="T6SSiii_tssC" presence="mandatory" />
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<gene name="T6SSiii_tssD" presence="mandatory" loner="1"/>
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<gene name="T6SSiii_tssE" presence="mandatory" />
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<gene name="T6SSiii_tssF" presence="mandatory" />
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<gene name="T6SSiii_tssG" presence="mandatory" />
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<gene name="T6SSiii_tssH" presence="mandatory" />
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<gene name="T6SSiii_tssI" presence="mandatory" loner="1"/>
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<gene name="T6SSiii_tssK" presence="mandatory" />
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<gene name="T6SSiii_tssN" presence="mandatory" />
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<gene name="T6SSiii_tssO" presence="mandatory" />
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<gene name="T6SSiii_tssP" presence="mandatory" />
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<gene name="T6SSiii_tssQ" presence="mandatory" />
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<gene name="T6SSiii_tssR" presence="mandatory" />
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</model>

‎tests/data/models/Model_conf_cutga/metadata.yml‎

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---
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maintainer:
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name: Bertrand Neron
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email: bneron@pasteur.fr
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short_desc: test models
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license: CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/)
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copyright: 2014-2026, Institut Pasteur, CNRS

‎tests/data/models/Model_conf_cutga/model_conf.xml‎

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<model_config>
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<filtering>
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<cut_ga>true</cut_ga>
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</filtering>
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</model_config>

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