Carrying models from v1 to v2¶
Models from v1 are not compatible straight away with v2. For those who had designed MacSyFinder’s models for Version 1 and would like to carry them for Version 2, here are the changes to consider:
the keyword “system” was changed: <system> ::arrow:: <model>
the keyword <system_ref> was removed. For a given systems’ package, each gene has to be defined only once in a macsy-model. There is no need anymore to reference which model it is from, when used as a component in another system’s model.
now the version of the macsy-models’ type has to be documented as a feature of the “model” keyword, like this: vers = “2.0”
the following keywords have been replaced (but see below for more details):
homologs => exchangeables
analogs => exchangeables
Note
“exchangeable” is not a feature anymore, but is replaced by the keyword “exchangeables”.
Note
These changes in the grammar used to specify model is also accompanied by a change on how to organize folders with models and profiles. In particular, the new file architecture enables an easier shipping of the developed macsy-models. See here for more details.
Here follow some examples of updates from v1 to v2.
1. A very simple model.¶
T1SS.xml under v1:
<system inter_gene_max_space="5" min_mandatory_genes_required="3" min_genes_required="3">
<gene name="T1SS_abc" presence="mandatory"/>
<gene name="T1SS_mfp" presence="mandatory"/>
<gene name="T1SS_omf" presence="mandatory" loner="1" multi_system="1"/>
</system>
T1SS.xml under v2:
<model inter_gene_max_space="5" min_mandatory_genes_required="3" min_genes_required="3" vers = "2.0">
<gene name="T1SS_abc" presence="mandatory"/>
<gene name="T1SS_mfp" presence="mandatory"/>
<gene name="T1SS_omf" presence="mandatory" loner="1" multi_system="1"/>
</model>
Note
In a nutshell, the minimal changes from v1 to v2 for a simple macsy-model listing components are the following:
<system> => <model>
vers = “2.0”
2. A model with homologs.¶
Tad.xml under v1:
<system inter_gene_max_space="5" min_mandatory_genes_required="4" min_genes_required="6" multi_loci="0">
<gene name="Tad_rcpA" presence="mandatory">
<homologs>
<gene name="T2SS_gspD" system_ref="T2SS"/>
<gene name="T4P_pilQ" system_ref="T4P"/>
<gene name="T3SS_sctC" system_ref="T3SS"/>
</homologs>
</gene>
<gene name="Tad_tadA" presence="mandatory"/>
<gene name="Tad_tadB" presence="mandatory"/>
<gene name="Tad_tadC" presence="mandatory"/>
<gene name="Tad_tadV" presence="mandatory"/>
<gene name="Tad_tadZ" presence="mandatory"/>
<gene name="Tad_flp" presence="accessory"/>
<gene name="Tad_tadE" presence="accessory"/>
<gene name="Tad_tadF" presence="accessory"/>
</system>
Tad.xml under v2:
<model inter_gene_max_space="5" min_mandatory_genes_required="4" min_genes_required="6" multi_loci="0" vers="2.0">
<gene name="Tad_rcpA" presence="mandatory"/>
<gene name="Tad_tadA" presence="mandatory"/>
<gene name="Tad_tadB" presence="mandatory"/>
<gene name="Tad_tadC" presence="mandatory"/>
<gene name="Tad_tadV" presence="mandatory"/>
<gene name="Tad_tadZ" presence="mandatory"/>
<gene name="Tad_flp" presence="accessory"/>
<gene name="Tad_tadE" presence="accessory"/>
<gene name="Tad_tadF" presence="accessory"/>
</model>
Note
The homologs and analogs keyword having disappeared, it is not necessary anymore to list homologous components (e.g., those that may match several HMM profiles during the sequence similarity search), unless they are exchangeables.
3. A model with exchangeable homologs.¶
T3SS.xml under v1:
<system inter_gene_max_space="10" min_mandatory_genes_required="7" min_genes_required="7" multi_loci="1">
<gene name="T3SS_sctC" presence="mandatory" exchangeable="1">
<homologs>
<gene name="T2SS_gspD" system_ref="T2SS"/>
<gene name="T4P_pilQ" system_ref="T4P"/>
<gene name="Tad_rcpA" system_ref="Tad"/>
</homologs>
</gene>
<gene name="T3SS_sctJ" presence="mandatory">
<homologs>
<gene name="Flg_sctJ_FLG" system_ref="Flagellum"/>
</homologs>
</gene>
<gene name="T3SS_sctN" presence="mandatory">
<homologs>
<gene name="Flg_sctN_FLG" system_ref="Flagellum"/>
</homologs>
</gene>
<gene name="T3SS_sctQ" presence="mandatory">
<homologs>
<gene name="Flg_sctQ_FLG" system_ref="Flagellum"/>
</homologs>
</gene>
<gene name="T3SS_sctR" presence="mandatory">
<homologs>
<gene name="Flg_sctR_FLG" system_ref="Flagellum"/>
</homologs>
</gene>
<gene name="T3SS_sctS" presence="mandatory">
<homologs>
<gene name="Flg_sctS_FLG" system_ref="Flagellum"/>
</homologs>
</gene>
<gene name="T3SS_sctT" presence="mandatory">
<homologs>
<gene name="Flg_sctT_FLG" system_ref="Flagellum"/>
</homologs>
</gene>
<gene name="T3SS_sctU" presence="mandatory">
<homologs>
<gene name="Flg_sctU_FLG" system_ref="Flagellum"/>
</homologs>
</gene>
<gene name="T3SS_sctV" presence="mandatory">
<homologs>
<gene name="Flg_sctV_FLG" system_ref="Flagellum"/>
</homologs>
</gene>
<gene name="Flg_fliE" presence="forbidden" system_ref="Flagellum"/>
<gene name="Flg_flgB" presence="forbidden" system_ref="Flagellum"/>
<gene name="Flg_flgC" presence="forbidden" system_ref="Flagellum"/>
</system>
T3SS.xml under v2:
<model inter_gene_max_space="10" min_mandatory_genes_required="7" min_genes_required="7" multi_loci="1" vers="2.0">
<gene name="T3SS_sctC" presence="mandatory">
<exchangeables>
<gene name="T2SS_gspD"/>
<gene name="T4P_pilQ"/>
<gene name="Tad_rcpA"/>
</exchangeables>
</gene>
<gene name="T3SS_sctJ" presence="mandatory"/>
<gene name="T3SS_sctN" presence="mandatory"/>
<gene name="T3SS_sctQ" presence="mandatory"/>
<gene name="T3SS_sctR" presence="mandatory"/>
<gene name="T3SS_sctS" presence="mandatory"/>
<gene name="T3SS_sctT" presence="mandatory"/>
<gene name="T3SS_sctU" presence="mandatory"/>
<gene name="T3SS_sctV" presence="mandatory"/>
<gene name="Flg_fliE" presence="forbidden"/>
<gene name="Flg_flgB" presence="forbidden"/>
<gene name="Flg_flgC" presence="forbidden"/>
</model>
Note
As only the secretin component ‘T3SS_sctC’ was exchangeable in its role within T3SS with its homologs T2SS_gspD, T4P_pilQ and Tad_rcpA, these three components are now set as exchangeables (they can functionally replace the component ‘T3SS_sctC’), and all other homologs do not need to be listed anymore.
The keyword system_ref is not needed anymore. Therefore, the v2 definition of T3SS is way more compact than that for v1.
