diff --git a/src/post_treatments/aevol_post_extract.cpp b/src/post_treatments/aevol_post_extract.cpp index a5d3286368a3365ade7a7f766409ec48e0e16aa1..402e41cd80c5581fb6bd6ef418afb1b7f07ebb6f 100644 --- a/src/post_treatments/aevol_post_extract.cpp +++ b/src/post_treatments/aevol_post_extract.cpp @@ -332,46 +332,48 @@ void print_help(char* prog_path) { printf("\n\ -This program extracts some data about the individuals and write\n\ -them into text files easy to parse with e.g. matlab.\n\ +This program extracts some data about the individuals at a given generation\n\ +and write them into text files that are easy to parse with e.g. matlab.\n\ \n\ -Two kinds of data can be extracted :\n\ +Two kinds of data can be extracted:\n\ \n\ - * data about the phenotype (option -t) : write information about\n\ - the proteins in a text file. A space delimits two proteins, a\n\ - new line delimits two individuals. For each protein, the output\n\ - is \"m_h_w_c_r_s_f_l_z_g\" where :\n\ - * m, h, w and c are the mean, height, width and concentration of the protein\n\ - * r is an identifier of the rna it belongs (useful to\n\ - know if several proteins are on the same rna)\n\ - * s indicates the strand (LEADING/LAGGING)\n\ - * f and l are the first and last translated base\n\ - * z indicates the feature (at the center of the protein)\n\ + * data about the phenotype (option -T or --triangles):\n\ + write information about the proteins in a text file.\n\ + A space delimits two proteins, a new line delimits two individuals.\n\ + For each protein, the output is \"m_h_w_c_r_s_f_l_z_g\" where:\n\ + * m, h, w and c are the mean, height, width and concentration of the protein\n\ + * r is an identifier of the rna it belongs (useful to\n\ + know if several proteins are on the same rna)\n\ + * s indicates the strand (LEADING/LAGGING)\n\ + * f and l are the first and last translated bases\n\ + * z indicates the feature (at the center of the protein)\n\ \n\ - * sequences of the individuals (option -s) : write the sequences\n\ + * sequences of the individuals (option -S or --sequence): write the sequences\n\ in a text file. A new line delimits two individuals. In case\n\ - there are several GU, they are separated by whitespaces.\n\ + there are several genetic units (GUs), they are separated by whitespaces.\n\ \n\ -With option -b, only the best individual is treated.\n\ +By default, only the best individual is treated. You may use one of the\n\ +following options to modify this behaviour: + * With option -a, all the individuals in the population are treated.\n\ + * With option -i, only the individual with the provided ID is treated.\n\ + * With options -x and -y, only the individual at the provided position on\n\ + the grid is treated.\n\ \n\ -The input can be either a generation number, in which case we\n\ -will attempt to load a full backup tree, or a population file,\n\ -in which case features of the proteins won't be outputed as we\n\ -need to know the environment to infer them.\n\ +Use option -t (or --timestep) to specify timestep of the individual(s) of\n\ +interest. A full backup tree must exist for the provided timestep.\n\ \n\ Examples :\n\ \n\ -For generation 20000, write infos about the phenotypes of all the\n\ +For generation 20000, write info about the phenotypes of all the\n\ individuals in phe_020000 and the sequences of all the\n\ individuals in seq_020000 :\n\ \n\ - extract -r 20000 -t phe_020000 -s seq_020000\n\ + extract --timestep 20000 --all --triangles phe_020000 --sequence seq_020000\n\ \n\ For generation 20000, write the best individual's sequence in\n\ seq_020000_best :\n\ \n\ - extract -b -r 20000 -s seq_020000_best\n\ -or extract -b -p populations/pop_020000.ae -s seq_020000_best\n"); + extract --timestep 20000 --sequence seq_020000_best\n"); } void interpret_cmd_line_options(int argc, char* argv[]) {