.. 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. .. _input: ******************************** Input and Options of MacSyFinder ******************************** .. _input-dataset-label: Input dataset ============= The input dataset must be a set of protein sequences in **Fasta format** (see http://en.wikipedia.org/wiki/FASTA_format). The :ref:`base section` in the configuration file (see :ref:`config-definition-label`) can be used to specify **the path** and the **type of dataset** to deal with, as well as the `--sequence_db` and `--db_type` parameters respectively, described in the :ref:`command-line-label` (see :ref:`Input options `). Four types of protein datasets are supported: * *unordered* : a set of sequences (*e.g.* a metagenomic dataset) * *unordered_replicon* : a set of sequences corresponding to a complete genome (*e.g.* an unassembled complete genome) * *ordered_replicon* : a set of sequences corresponding to an ordered complete replicon (*e.g.* an assembled complete genome) * *gembase* : a set of multiple ordered replicons, which format follows the convention described in :ref:`gembase_convention`. For "ordered" ("ordered_replicon" or "gembase") datasets only, MacSyFinder can take into account the **shape of the genome**: "linear", or "circular" for detection. The default is set to "circular". This can be set with the `--replicon_topology` parameter from :ref:`command-line-label` (see :ref:`Input options `), or in the configuration in the :ref:`base section`. With the "gembase" format, it is possible to specify a topology per replicon with a topology file (see :ref:`gembase_convention` and :ref:`topology-files`). .. _command-line-label: Command-line options ==================== Positional arguments:: systems The systems to detect. This is an obligatory option with no keyword associated to it. To detect all systems described in .xml available, set to "all" (case insensitive). Otherwise, a single or multiple systems can be specified. For example: "SystemA SystemB". Optional arguments:: -h, --help Show the help message and exit .. _cmd-input-label: Input dataset options:: --sequence-db SEQUENCE_DB Path to the sequence dataset in fasta format. --db-type {unordered_replicon,ordered_replicon,gembase,unordered} 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" --replicon-topology {linear,circular} The topology of the replicons (this option is meaningful only if the db_type is 'ordered_replicon' or 'gembase' --topology-file TOPOLOGY-FILE 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: "RepliconA linear" --idx Forces to build the indexes for the sequence dataset even if they were presviously computed and present at the dataset location (default = False) .. _system-detect-options: Systems detection options:: --inter-gene-max-space SYSTEM VALUE 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 a system name, the second a number of components. This option can be repeated several times: "--inter-gene-max-space T3SS 12 --inter-gene-max-space Flagellum 20" --min-mandatory-genes-required SYSTEM VALUE 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: "--min-mandatory-genes-required T2SS 15 --min-mandatory-genes-required Flagellum 10" --min-genes-required SYSTEM VALUE 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: "--min-genes-required T2SS 15 --min-genes-required Flagellum 10" --max-nb-genes SYSTEM VALUE The maximal number of genes allowed in the system. --multi-loci SYSTEM Specifies if the system can be detected as a 'scattered' system. (default: False) .. _hmmer-options: Options for Hmmer execution and hits filtering:: --hmmer HMMER_EXE Path to the Hmmer program. --index-db INDEX_DB_EXE 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). --e-value-search E_VALUE_RES Maximal e-value for hits to be reported during Hmmer search. (default = 1) --i-evalue-select I_EVALUE_SEL Maximal independent e-value for Hmmer hits to be selected for system detection. (default = 0.001) --coverage-profile COVERAGE_PROFILE Minimal profile coverage required in the hit alignment to allow the hit selection for system detection. (default = 0.5) Path options:: -d DEF_DIR, --def DEF_DIR Path to the systems definition files. -o OUT_DIR, --out-dir OUT_DIR Path to the directory where to store results. If out-dir is specified res-search-dir will be ignored. -r RES_SEARCH_DIR, --res-search-dir RES_SEARCH_DIR Path to the directory where to store MacSyFinder search results directories. --res-search-suffix RES_SEARCH_SUFFIX The suffix to give to Hmmer raw output files. --res-extract-suffix RES_EXTRACT_SUFFIX The suffix to give to filtered hits output files. -p PROFILE_DIR, --profile-dir PROFILE_DIR Path to the profiles directory. --profile-suffix PROFILE_SUFFIX 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 in the specified folder 'profile_dir' and be named 'gspG.hmm3'. (default: ".hmm") General options:: -w WORKER_NB, --worker WORKER_NB Number of workers to be used by MacSyFinder. In the case the user wants to run MacSyFinder in a multi-thread mode. All workers can be used with the value '0'. (default = 1) -v, --verbosity Increases the verbosity level. There are 4 levels: Error messages (default), Warning (-v), Info (-vv) and Debug(-vvv). --log LOG_FILE Path to the directory where to store the 'macsyfinder.log' log file. --config CFG_FILE Path to a putative MacSyFinder configuration file to be used. --previous-run PREVIOUS_RUN 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. It is in conflict with options: --config, --sequence_db, --profile-suffix, --res-extract-suffix, --e-value-res, --db-type, --hmmer .. _config-definition-label: Configuration file ================== Options to run MacSyFinder can be specified in a configuration file. The :ref:`Config ` handles all configuration options for MacSyFinder. Three locations are parsed to find configuration files: * $PREFIX/etc/macsyfinder/macsyfinder.conf * $(HOME)/.macsyfinder/macsyfinder.conf * ./macsyfinder.conf Moreover these three locations options can be passed on the command-line. Each file can define options, at the end all options are added. If an option is specified several times: .. note:: The precedence rules from the less important to the more important are: $PREFIX/etc/macsyfinder/macsyfinder.conf < $(HOME)/.macsyfinder/macsyfinder.conf < ./macsyfinder.conf < "command-line" options This means that command-line options will always bypass those from the configuration files. In the same flavor, options altering the definition of systems found in the command-line or the configuration file will always overwhelm values from systems' :ref:`XML definition files `. The configuration files must follow the Python "ini" file syntax. The Config object provides some default values and performs some validations of the values, for instance: In MacSyFinder, five sections are defined: .. _config-base-label: * **base** : all information related to the protein dataset under study * *file* : the path to the dataset in Fasta format (*no default value*) * *type* : the type of dataset to handle, four types are supported: * *unordered* : a set of sequences (*e.g.* a metagenomic dataset) * *unordered_replicon* : a set of sequences corresponding to a complete replicon (*e.g.* an unassembled complete genome) * *ordered_replicon* : a set of sequences corresponding to a complete replicon ordered (*e.g.* an assembled complete genome) * *gembase* : a set of multiple ordered replicons. (*no default value*) * *replicon_topology* : the topology of the replicon under study. Two topologies are supported: 'linear' and 'circular' (*default* = 'circular') This option will be ignored if the dataset type is not ordered (*i.e.* "unordered_replicon" or "unordered"). * **system** * *inter_gene_max_space* = list of system name and integer separated by spaces. These values will supersede the values found in the system definition file. * *min_mandatory_genes_required* = list of system name and integer separated by spaces. These values will supersede the values found in the system definition file. * *min_genes_required* = list of system name and integer separated by spaces. These values will supersede the values found in the system definition file. * **hmmer** * *hmmer_exe* (default= *hmmsearch* ) * *index_db_exe* the executable to use to build the index for the hmm. The value can be 'makeblastdb' or 'formatdb' or the absolute path toward one of these two binaries (default= *makeblastdb* ) * *e_value_res* = (default= *1* ) * *i_evalue_sel* = (default= *0.5* ) * *coverage_profile* = (default= *0.5* ) * **directories** * *res_search_dir* = (default= *./datatest/res_search* ) * *res_search_suffix* = (default= *.search_hmm.out* ) * *profile_dir* = (default= *./profiles* ) * *profile_suffix* = (default= *.fasta-aln_edit.hmm* ) * *res_extract_suffix* = (default= *.res_hmm_extract* ) * *def_dir* = (default= *./DEF/* ) * **general** * *log_level*: (default= *debug* ) This corresponds to an integer code: ======== ========== Level Numeric value ======== ========== CRITICAL 50 ERROR 40 WARNING 30 INFO 20 DEBUG 10 NOTSET 0 ======== ========== * *log_file* = (default = macsyfinder.log in directory of the run) Example of a configuration file:: [base] prefix = /path/to/macsyfinder/home/ file = %(prefix)s/dataset/prru_psae.001.c01.fasta type = gembase replicon_topology = circular [system] inter_gene_max_space = T2SS 22 Flagellum 44 min_mandatory_genes_required = T2SS 6 Flagellum 4 min_genes_required = T2SS 8 Flagellum 4 [hmmer] hmmer_exe = hmmsearch index_db_exe = makeblastdb e_value_res = 1 i_evalue_sel = 0.5 coverage_profile = 0.5 [directories] prefix = /path/to/macsyfinder/home/ def_dir = %(prefix)s/data/DEF res_search_dir = %(prefix)s/dataset/res_search/ res_search_suffix = .raw_hmm profile_dir = %(prefix)s/data/profiles profile_suffix = .fasta-aln.hmm res_extract_suffix = .res_hmm [general] log_level = debug .. note:: After a run, the corresponding configuration file ("macsyfinder.conf") is generated as a (re-usable) output file that stores every options used in the run. It is stored in the results' directory (see :ref:`the output section `). In-house input files ==================== .. toctree:: :maxdepth: 1 gembase_convention