Commit 708920ac authored by TURPIN Laurent's avatar TURPIN Laurent
Browse files

Simplify examples and update tests

parent 5dcfca6b
......@@ -13,13 +13,6 @@ doc/user_guide/user_manual.pdf
doc/user_guide/user_manual.synctex.gz
doc/user_guide/user_manual.toc
# in the `examples` directory, ignore generated files
# i.e. ignore everything under `examples` directory...
examples/*/**
# ... except: don't ignore param.in files
!examples/**/param.in
!examples/**/README
# ignore IDE files and folders
.vscode
.idea/
\ No newline at end of file
......@@ -39,12 +39,12 @@ This command will compile 4 executables:
## How to run an expriment?
To run an example, e.g. basic, assuming you're in Aevol root directory:
```shell
cd examples/basic
../../build/bin/module_create ../basic.json #1
../../build/bin/module_run -b 0 -e 100 result.json #2
../../build/bin/module_lineage -I 0 -e 100 result.json #3
cd examples
../build/bin/module_create basic.json #1
../build/bin/module_run -b 0 -e 100 result.json #2
../build/bin/module_lineage -I 0 -e 100 result.json #3
mkdir stats
../../build/bin/module_anc_stat -Mv -j result.json lineage-b000000000-e000000100-i0.ae #4
../build/bin/module_anc_stat -Mv -j result.json lineage-b000000000-e000000100-i0.ae #4
```
Command by command:
......
# Set default behaviour depending on configure options
if WANT_DOXYGEN
all: doxygen
else
all:
endif
# Man pages
dist_man1_MANS = aevol_create.1 aevol_run.1 aevol_modify.1 aevol_propagate.1
dist_man1_MANS += aevol_misc_lineage.1 aevol_misc_ancstats.1
dist_man1_MANS += aevol_misc_robustness.1 aevol_misc_compute_pop_stats.1
dist_man1_MANS += aevol_misc_view_generation.1 aevol_misc_create_eps.1
dist_man1_MANS += aevol_misc_extract.1 aevol_misc_fixed_mutations.1
dist_man1_MANS += aevol_misc_gene_families.1
# How to build the devel doc
doxygen: ../src/*.cpp ../src/libaevol/*.h ../src/libaevol/*.cpp ../src/post_treatments/*.cpp
doxygen aevol.conf ; echo "document generated\n" > doxygen
# Cleaning rules
CLEANFILES = index.html
clean-local:
rm -rf html doxygen
# Extra files to include in releases (dist)
EXTRA_DIST = README.txt aevol.conf
The documentation being quite heavy, it is not included in basic distributions.
Please visit www.aevol.fr
This diff is collapsed.
./"test with man -l <file>
.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
.SH NAME
aevol \- an in silico experimental evolution platform
.SH SYNOPSIS
.B aevol_create \-h
or
.B \-\-help
.br
.B aevol_create \-V
or
.B \-\-version
.br
.B aevol_create \fR[\fB\-v\fR] \fR[\fB\-f\fI PARAM_FILE\fR] \fR[\fB\-o\fI OUTDIR\fR] \fR[\fB\-c\fI CFILE\fR] \fR[\fB\-p\fI PFILE\fR]
.SH DESCRIPTION
.B Aevol
is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
.TP
.B aevol_create
create an experiment with setup as specified in
.I param_file
.SH OPTIONS
.TP
.B \-h, \-\-help
print help, then exit
.TP
.B \-V, \-\-version
print version number, then exit
.HP
.B \-f, \-\-file
.I PARAM_FILE
.br
specify parameter file (default: param.in)
.HP
.B \-o, \-\-out
.I OUTDIR
.br
specify output directory (default "./")
.HP
.B \-c, \-\-chromosome
.I CFILE
.br
load chromosome from given text file instead of generating it
.HP
.B \-p, \-\-plasmid
.I PFILE
.br
load plasmid from given text file instead of generating it (params must allow plasmids)
.SH "SEE ALSO"
.B aevol_run, aevol_modify, aevol_propagate
./"test with man -l <file>
.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
.SH NAME
aevol \- an in silico experimental evolution platform
.SH SYNOPSIS
.B aevol_misc_ancstats \-h
|
.B \-\-help
.br
.B aevol_misc_ancstats \-V
|
.B \-\-version
.br
.B aevol_misc_ancstats \fB\-f\fI LINEAGE_FILE
.SH DESCRIPTION
.B Aevol
is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
.TP
.B aevol_misc_ancstats
issues statistics for the line of descent of a given individual.
.SH OPTIONS
.TP
.B \-h, \-\-help
print help, then exit
.TP
.B \-V, \-\-version
print version number, then exit
.HP
.B \-f, \-\-file
.I LINEAGE_FILE
.br
specify which lineage file to use. Lineage files are created by the ae_misc_lineage tool
.SH "SEE ALSO"
.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run
./"test with man -l <file>
.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
.SH NAME
aevol \- an in silico experimental evolution platform
.SH SYNOPSIS
.B aevol_misc_compute_pop_stats \-h
|
.B \-\-help
.br
.B aevol_misc_compute_pop_stats \-V
|
.B \-\-version
.br
.B aevol_misc_compute_pop_stats \fR[\fB\-i\fI INDEX\fR | \fB\-r\fI RANK\fR] \fR[\fB\-b\fI GENER1\fR] \fB\-e\fI GENER2
.SH DESCRIPTION
.B Aevol
is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
.TP
.B aevol_misc_compute_pop_stats
issues population and replication statistics for each available backup from GENER1 to GENER2. These statistics are written in files global_pop_stats.out and stats/pop_stats/*.
.SH OPTIONS
.TP
.B \-h, \-\-help
print help, then exit
.TP
.B \-V, \-\-version
print version number, then exit
.HP
.B \-i, \-\-index
.I INDEX
.br
specify the index (ID in current generation) of the individual whose replication statistics should be outputted
.HP
.B \-r, \-\-rank
.I RANK
.br
specify the rank of the individual whose replication statistics should be outputted
.HP
.B \-b, \-\-begin
.I GENER
.br
specify the first generation for which the statistics should be computed
.HP
.B \-e, \-\-end
.I GENER
.br
specify the last generation for which the statistics should be computed
.SH "SEE ALSO"
.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run
./"test with man -l <file>
.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
.SH NAME
aevol \- an in silico experimental evolution platform
.SH SYNOPSIS
.B aevol_misc_create_eps \-h
|
.B \-\-help
.br
.B aevol_misc_create_eps \-V
|
.B \-\-version
.br
.B aevol_misc_create_eps \fR[\fB\-i\fI INDEX\fR | \fB\-r\fI RANK\fR] \fB\-g\fI GENER
.SH DESCRIPTION
.B Aevol
is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
.TP
.B aevol_misc_create_eps
produces several eps files describing an individual of this population
.SH OPTIONS
.TP
.B \-h, \-\-help
print help, then exit
.TP
.B \-V, \-\-version
print version number, then exit
.HP
.B \-i, \-\-index
.I INDEX
.br
specify the index (ID in current generation) of the individual
.HP
.B \-r, \-\-rank
.I RANK
.br
specify the rank of the individual
.HP
.B \-g, \-\-gener
.I GENER
.br
specify the generation of the individual
.SH "SEE ALSO"
.B aevol_create, aevol_modify, aevol_propagate, aevol_run
./"test with man -l <file>
.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
.SH NAME
aevol \- an in silico experimental evolution platform
.SH SYNOPSIS
.B aevol_misc_extract \-h
|
.B \-\-help
.br
.B aevol_misc_extract \-V
|
.B \-\-version
.br
.B aevol_misc_extract \fR[\fB\-r\fI GENER\fR | \fB\-p\fI POP_FILE\fR] \fR[\fB\-t\fI PHEN_FILE\fR] \fR[\fB\-s\fI SEQ_FILE\fR] \fR[\fB\-g\fI NUM_GU\fR] \fR[\fB\-b\fR]
.SH DESCRIPTION
.B Aevol
is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
.TP
.B aevol_misc_extract
extracts the genotype and/or data about the phenotype of individuals in the provided population and write them into text files easy to parse with e.g. matlab.
.SH OPTIONS
.TP
.B \-h, \-\-help
print help, then exit
.TP
.B \-V, \-\-version
print version number, then exit
.HP
.B \-r
.I GENER
.br
read generation GENER from a full aevol backup
.HP
.B \-p
.I POP_FILE
.br
read the population saved in population file POP_FILE
.HP
.B \-t
.I PHEN_FILE
.br
extract and save some infos about the phenotypes of the individuals to file PHEN_FILE
.HP
.B \-s
.I SEQ_FILE
.br
extract and save the sequences of the individuals to file SEQ_FILE
.HP
.B \-g
.I num_gu
.br
only treat this genetic unit (by default: treat all genetic units)
.HP
.B \-b
.br
only treat the best individual
.SH "SEE ALSO"
.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run
./"test with man -l <file>
.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
.SH NAME
aevol \- an in silico experimental evolution platform
.SH SYNOPSIS
.B aevol_misc_fixed_mutations \-h
|
.B \-\-help
.br
.B aevol_misc_fixed_mutations \-V
|
.B \-\-version
.br
.B aevol_misc_fixed_mutations \fB\-f\fI LINEAGE_FILE
.SH DESCRIPTION
.B Aevol
is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
.TP
.B aevol_misc_fixed_mutations
issues the detailed list of mutations that occurred in the lineage of a given individual
.SH OPTIONS
.TP
.B \-h, \-\-help
print help, then exit
.TP
.B \-V, \-\-version
print version number, then exit
.HP
.B \-f, \-\-file
.I LINEAGE_FILE
.br
specify which lineage file to use. Lineage files are created by the ae_misc_lineage tool
.SH "SEE ALSO"
.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run
./"test with man -l <file>
.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
.SH NAME
aevol \- an in silico experimental evolution platform
.SH SYNOPSIS
.B aevol_misc_gene_families \-h
|
.B \-\-help
.br
.B aevol_misc_gene_families \-V
|
.B \-\-version
.br
.B aevol_misc_gene_families \fB\-f\fI LINEAGE_FILE
.SH DESCRIPTION
.B Aevol
is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
.TP
.B aevol_misc_gene_families
issues the detailed history of each gene family on the lineage of a given individual
.SH OPTIONS
.TP
.B \-h, \-\-help
print help, then exit
.TP
.B \-V, \-\-version
print version number, then exit
.HP
.B \-f, \-\-file
.I LINEAGE_FILE
.br
specify which lineage file to use. Lineage files are created by the ae_misc_lineage tool
.SH "SEE ALSO"
.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run
./"test with man -l <file>
.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
.SH NAME
aevol \- an in silico experimental evolution platform
.SH SYNOPSIS
.B aevol_misc_lineage \-h
|
.B \-\-help
.br
.B aevol_misc_lineage \-V
|
.B \-\-version
.br
.B aevol_misc_lineage \fR[\fB\-i\fI INDEX\fR | \fB\-r\fI RANK\fR] \fR[\fB\-b\fI GENER1\fR] \fB\-e\fI GENER2
.SH DESCRIPTION
.B Aevol
is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
.TP
.B aevol_misc_lineage
allows for the reconstruction of the lineage of a given individual. Requires the tree to have been recorded during evolution.
.SH OPTIONS
.TP
.B \-h, \-\-help
print help, then exit
.TP
.B \-V, \-\-version
print version number, then exit
.HP
.B \-i, \-\-index
.I INDEX
.br
specify the index (ID in current generation) of the individual whose lineage is to be reconstructed
.HP
.B \-r, \-\-rank
.I RANK
.br
specify the rank of the individual whose lineage is to be reconstructed
.HP
.B \-b, \-\-begin
.I GENER
.br
specify the generation up to which the lineage is to be reconstructed
.HP
.B \-e, \-\-end
.I GENER
.br
specify the generation of the individual whose lineage is to be reconstructed
.SH "SEE ALSO"
.B aevol_create, aevol_modify, aevol_propagate, aevol_run
./"test with man -l <file>
.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
.SH NAME
aevol \- an in silico experimental evolution platform
.SH SYNOPSIS
.B aevol_misc_mutagenesis \-h
|
.B \-\-help
.br
.B aevol_misc_mutagenesis \-V
|
.B \-\-version
.br
.B aevol_misc_mutagenesis \fR\fB\-g\fI GENER \fR[\fB\-i\fI INDEX\fR | \fB\-r\fI RANK\fR] \fR [\fB\-m\fI MUTATIONTYPE] \fR [\fB\-n\fI NBMUTANTS]
.SH DESCRIPTION
.B Aevol
is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
.TP
.B aevol_misc_mutagenesis
creates and evaluates single mutants of an individual saved in a backup, by default the best of its generation. Use option \-g to specify the generation number contanining the individual of interest. There must have been a backup of the population at this generation. For example, if the program is called with the option \-g 4000, there must be a file called pop_004000.ae in the populations directory.
Use either the \-r or the \-i option to select another individual than the best one: with \-i, you have to provide the ID of the individual, and with \-r the rank (1 for the individual with the lowest fitness, N for the fittest one).
The type of mutations to perform must be specified with the \-m option. Choose 0 to create mutants with a point mutation, 1 for a small insertion, 2 for a small deletion, 3 for a duplication, 4 for a large deletion, 5 for a translocation or 6 for an inversion.
For the point mutations, all single mutants will be created and evaluated. For the other mutation types, an exhaustive mutagenesis would take too much time, hence only a sample of mutants (1000 by default) will be generated. Use option \-n to specify another sample size.
The output file will be placed in a subdirectory called analysis-generationNUMGENER.
.SH OPTIONS
.TP
.B \-h, \-\-help
print help, then exit
.TP
.B \-V, \-\-version
print version number, then exit
.HP
.B \-g, \-\-gener
.I NUMGENER
.br
generation of the backup containing the individual of interest
.HP
.B \-i, \-\-index
.I INDEX
.br
index of individual of interest
.HP
.B \-r, \-\-rank
.I RANK
.br
rank of individual of interest. Default = size of the population (fittest individual)
.HP
.B \-m, \-\-mutation\-type
.I MUTATIONTYPE
.br
integer type of the mutation carried by each mutant: 0 for a point mutation, 1 for a small insertion, 2 for small deletions, 3 for a duplication, 4 for a large deletion, 5 for a translocation or 6 for an inversion
.HP
.B \-n, \-\-nb\-mutants
.I NBMUTANTS
.br
number of single mutants to create and evaluate. Default = 1000. Note that this option is ignored in the case of point mutations, where all single mutants are created (exhaustive mutagenesis)
.SH "SEE ALSO"
.B aevol_create, aevol_modify, aevol_propagate, aevol_run, aevol_misc_view_generation, aevol_misc_create_eps, aevol_misc_robustness
./"test with man -l <file>
.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
.SH NAME
aevol \- an in silico experimental evolution platform
.SH SYNOPSIS
.B aevol_misc_robustness \-h
|
.B \-\-help
.br
.B aevol_misc_robustness \-V
|
.B \-\-version
.br
.B aevol_misc_robustness \fR\fB\-g\fI GENER\fR [\fB\-n\fI NBCHILDREN] \fR[\fB\-i\fI INDEX\fR | \fB\-r\fI RANK\fR]
.SH DESCRIPTION
.B Aevol
is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
.TP
.B aevol_misc_robustness
computes the replication statistics of all the individuals of a given generation, like the proportion of neutral, beneficial, deleterious offsprings. This is done by simulating NBCHILDREN replications for each individual (1000 replications by default), with its mutation, rearrangement and transfer rates. Depending on those rates and genome size, there can be several mutations per replication. Those global statistics are written in stat/robustness_GENER.out, with one line per individual in the specified generation. The program also outputs detailed statistics for one of the individuals (the best one by default). The detailed statistics for this individual are written in stats/replication_GENER.out, with one line per simulated child of this particular individual.
.SH OPTIONS
.TP
.B \-h, \-\-help
print help, then exit
.TP
.B \-V, \-\-version
print version number, then exit
.HP
.B \-g, \-\-gener
.I GENER
.br
specify the generation number for which the robustness statistics are desired
.HP
.B \-n, \-\-nb\-children
.I NBCHILDREN
.br
specify the number of reproductions to simulate for each individual
.HP
.B \-i, \-\-index
.I INDEX
.br
specify the index (ID in current generation) of the individual for whom detailed reproduction statistics are desired
.HP
.B \-r, \-\-rank
.I RANK
.br
specify the rank of the individual for whom detailed reproduction statistics are desired
.SH "SEE ALSO"
.B aevol_create, aevol_modify, aevol_propagate, aevol_run, aevol_misc_view_generation, aevol_misc_create_eps
./"test with man -l <file>
.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
.SH NAME
aevol \- an in silico experimental evolution platform
.SH SYNOPSIS
.B aevol_misc_view_generation \-h
|
.B \-\-help
.br
.B aevol_misc_view_generation \-V
|
.B \-\-version
.br
.B aevol_misc_view_generation \fB\-g\fI GENER
.SH DESCRIPTION
.B Aevol
is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
.TP
.B aevol_misc_view_generation
allows one to visualize a generation using the exact same graphical outputs used in aevol_run.
.SH OPTIONS
.TP
.B \-h, \-\-help
print help, then exit
.TP
.B \-V, \-\-version
print version number, then exit
.HP
.B \-g, \-\-gener
.I GENER
.br
specify generation to visualize (default 0)
.SH "SEE ALSO"
.B aevol_create, aevol_modify, aevol_propagate, aevol_run
./"test with man -l <file>
.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
.SH NAME
aevol \- an in silico experimental evolution platform
.SH SYNOPSIS
.B aevol_modify \-h
or
.B \-\-help
.br
.B aevol_modify \-V
or
.B \-\-version
.br
.B aevol_modify \-g\fI GENER \fR[\fB\-f\fI param_file\fR]
.SH DESCRIPTION
.B Aevol
is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
.TP
.B aevol_modify
modify an experiment as specified in
.I param_file
.SH OPTIONS
.TP
.B \-h, \-\-help
print help, then exit
.TP
.B \-V, \-\-version
print version number, then exit
.HP
.B \-g, \-\-gener
.I GENER
.br
specify generation number
.HP
.B \-f, \-\-file
.I param_file
.br
specify parameter file (default: param.in)
.SH "SEE ALSO"
.B aevol_create, aevol_run, aevol_propagate
\"test with man -l <file>
.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
.SH NAME
aevol \- an in silico experimental evolution platform
.SH SYNOPSIS