Helper Tool¶
macsyprofile¶
To help develop new models we provide the tool macsyprofile which is to be used as post treatement.
It is ran over a previous macsyfinder analysis:
it extracts from raw HMMER output files the hits and computes the profile coverage for each of them.
it enables to filter the hits in a user-defined manner, to test other values of filtering parameters than those used with the MacSyFinder run.
it writes down the results in a file in tsv format hmm_coverage.tsv.
usage: macsyprofile [-h] [--coverage-profile COVERAGE_PROFILE]
[--i-evalue-sel I_EVALUE_SEL]
[--best-hits {score,i_eval,profile_coverage}] [-p PATTERN]
[-o OUT] [-f] [-V] [-v] [--mute]
previous_run
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MacSyProfile - MacSyFinder profile helper tool
positional arguments:
previous_run The path to a macsyfinder results directory.
optional arguments:
-h, --help show this help message and exit
--coverage-profile COVERAGE_PROFILE
Minimal profile coverage required for the hit
alignment with the profile to allow the hit selection
for systems detection. (default no threshold)
--i-evalue-sel I_EVALUE_SEL
Maximal independent e-value for Hmmer hits to be
selected for systems detection. (default: no selection
based on i-evalue)
--best-hits {score,i_eval,profile_coverage}
If several hits match the same replicon, same gene.
Select only the best one (based on best 'score' or
'i_evalue' or 'profile_coverage')
-p PATTERN, --pattern PATTERN
pattern to filter the hmm files to analyse.
-o OUT, --out OUT the path to a file to write results.
--index-dir INDEX_DIR
Specifies the path to a directory to store/read the sequence index
when the sequence-db dir is not writable.
-f, --force force to write output even the file already exists
(overwrite it).
-V, --version show program's version number and exit
-v, --verbosity Increases the verbosity level. There are 4 levels:
Error messages (default), Warning (-v), Info (-vv) and
Debug.(-vvv)
--mute Mute the log on stdout. (continue to log on
macsyfinder.log) (default: False)
For more details, visit the MacSyFinder website and see the MacSyFinder documentation.
For instance:
>macsyprofile macsyfinder-2021XXXX_XX-XX-XX
will analyse the HMMER raw outputs stored in macsyfinder-2021XXXX_XX-XX-XX/hmmer_results directory and the results will be stored in macsyfinder-2021XXXX_XX-XX-XX/hmm_coverage.tsv file
Setting filtering parameters¶
This helper tool is designed to help the user test the relevance of the HMM profiles used, what filtering parameters for HMMER to be used, and understand why some components might be unexpectedly missing from the MacSyFinder results. This can thus help to improve the models - for instance for the genomic location parameters (is a component not found cause it should be listed as a loner?).
Therefore by default, the filtering parameters are very loose so that most hits found with HMMER will be reported, even the weakest ones.
However, it is possible to filter hits to be extracted based on the profile coverage with –coverage-profile or the i-evalue (–i-evalue-sel) to be a bit more stringent.
Also, it is possible to use the –best-hits in order to report only the best hit for a given protein sequence when several profiles were matching hit.
Using patterns with “–pattern”¶
If in previous_run/hmmer_results you have the following files:
previous_run/hmmer_results/Archaeal-T4P_arCOG11238.search_hmm.out
previous_run/hmmer_results/Archaeal-T4P_arCOG11520.search_hmm.out
previous_run/hmmer_results/Archaeal-T4P_arCOG11777.search_hmm.out
previous_run/hmmer_results/Archaeal-T4P_arCOG11778.search_hmm.out
previous_run/hmmer_results/Archaeal-T4P_arCOG11936.search_hmm.out
previous_run/hmmer_results/Archaeal-T4P_arCOG14515.search_hmm.out
previous_run/hmmer_results/ComM_comC.search_hmm.out
previous_run/hmmer_results/ComM_comEB.search_hmm.out
previous_run/hmmer_results/ComM_comEC.search_hmm.out
previous_run/hmmer_results/ComM_comGA.search_hmm.out
previous_run/hmmer_results/ComM_comGB.search_hmm.out
previous_run/hmmer_results/ComM_comGC.search_hmm.out
previous_run/hmmer_results/ComM_comGD.search_hmm.out
previous_run/hmmer_results/ComM_comGE.search_hmm.out
previous_run/hmmer_results/MSH_mshA.search_hmm.out
previous_run/hmmer_results/MSH_mshB.search_hmm.out
previous_run/hmmer_results/MSH_mshC.search_hmm.out
But you are interested only in ComM family genes, you can specify the option --pattern 'ComM*'
For instance:
>macsyprofile --pattern 'ComM*' macsyfinder-2021XXXX_XX-XX-XX
parsing macsyfinder-2021XXXX_XX-XX-XX/hmmer_results/ComM_comB.search_hmm.out
parsing macsyfinder-2021XXXX_XX-XX-XX/hmmer_results/ComM_comC.search_hmm.out
parsing macsyfinder-2021XXXX_XX-XX-XX/hmmer_results/ComM_comEA.search_hmm.out
parsing macsyfinder-2021XXXX_XX-XX-XX/hmmer_results/ComM_comEB.search_hmm.out
parsing macsyfinder-2021XXXX_XX-XX-XX/hmmer_results/ComM_comEC.search_hmm.out
parsing macsyfinder-2021XXXX_XX-XX-XX/hmmer_results/ComM_comGA.search_hmm.out
parsing macsyfinder-2021XXXX_XX-XX-XX/hmmer_results/ComM_comGB.search_hmm.out
parsing macsyfinder-2021XXXX_XX-XX-XX/hmmer_results/ComM_comGC.search_hmm.out
parsing macsyfinder-2021XXXX_XX-XX-XX/hmmer_results/ComM_comGD.search_hmm.out
parsing macsyfinder-2021XXXX_XX-XX-XX/hmmer_results/ComM_comGE.search_hmm.out
found 79 hits
result is in 'macsyfinder-2021XXXX_XX-XX-XX/hmm_coverage.tsv'
Note
The patterns available are the glob patterns (the jokers usable with unix ls command )
>macsyprofile --pattern 'ComM_com?C' -f macsyfinder-2021XXXX_XX-XX-XX
parsing macsyfinder-2021XXXX_XX-XX-XX/hmmer_results/ComM_comEC.search_hmm.out
parsing macsyfinder-2021XXXX_XX-XX-XX/hmmer_results/ComM_comGC.search_hmm.out
found 16 hits
result is in 'macsyfinder-2021XXXX_XX-XX-XX/hmm_coverage.tsv'
A useful example for modellers?¶
>macsyprofile --best-hits i_eval --i-evalue-sel 0.001 --coverage-profile 0.5 -o msf_GCF_003149495.1_ASM314949v1_tff-sf/hmm_coverage_best-hits_ieval_default_filter_MSF.tsv msf_GCF_003149495.1_ASM314949v1_tff-sf
found 221 hits
result is in 'msf_GCF_003149495.1_ASM314949v1_tff-sf/hmm_coverage_best-hits_ieval_default_filter_MSF.tsv'
This command line might be useful to macsy-models modellers, as it consists in extracting all relevant hits that are used by the MacSyFinder engine to search systems, when using the default parameters:
the proteins are assigned with their best hits (i-evalue based) when they match several profiles (–best-hits i_eval option)
the default filtering parameters (i-evalue and profile coverage) are used (–i-evalue-sel and –coverage-profile options)
By using this command line that lists all hits available for MacSyFinder to search for systems, one could be interested in comparing this list to the list of hits that end in being assigned to systems (listed e.g. in best_solution.tsv). This can help to determine why a component is missing from a system: is it because there are no good hits for it, or is it because it does not comply to the co-localization rules defined in the systems’ model?
Parsing macsyprofile outputs¶
The macsyprofile output is a tabulated separated values (.tsv) files The first lines which are comments (starting with ‘#’) display the tool version and the complete command line used. Then follow the results. The first line of results is a header line.
# macsyprofile 2.0rc1
# macsyprofile --pattern ComM* --coverage-profile 0.5 macsyfinder-20201202_15-17-46/
hit_id replicon_name position_hit hit_sequence_length gene_name i_eval score profile_coverage sequence_coverage begin end
GCF_000006745_021980 GCF_000006745 2198 291 ComM_comC 2.500e-40 136.400 0.942 0.708 62 267
GCF_000006745_007650 GCF_000006745 765 253 ComM_comC 9.600e-31 105.100 0.937 0.798 43 244
...
Note
This file can be easily parsed using the Python pandas library.
import pandas as pd
systems = pd.read_csv("path/to/hmm_coverage.tsv", sep='\t', comment='#')
Warning
The macsyprofile tool is not compliant with results produced with macsyfinder v1.
If you get Cannot find models in conf file XXX. May be these results have been generated with an old version of macsyfinder.
Check the configuration file, if [models] section contains models_1 = XXX YYY remove the _1 from models
models = XXX YYY
