Input and Options of MacSyFinder¶
Input dataset¶
The input dataset must be a set of protein sequences in Fasta format (see http://en.wikipedia.org/wiki/FASTA_format).
The base section in the configuration file (see Configuration file) 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 Command-line options (see 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 Gembase format.
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 Command-line options (see Input options), or in the configuration in the base section.
With the “gembase” format, it is possible to specify a topology per replicon with a topology file (see Gembase format and Topology files).
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
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)
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)
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
Configuration file¶
Options to run MacSyFinder can be specified in a configuration file. The 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’ 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:
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 the output section).