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aevol post-treatment descriptions #5

Closed davisbk closed 5 years ago

davisbk commented 5 years ago

aevol post-treatment descriptions

1. aevol_misc_ancestor_mutagenesis

Generates and analyses mutants for the provided lineage. Specifically, this program generates evolvability, robustness, and antirobustness statistics for the mutants.

PREREQUISITES: Lineage file RESULTS: Output file (e.g. mutagenesis-n50-point-mutation.txt) which shows:

  1. Generation
  2. Fraction of positive mutants
  3. Fraction of neutral mutants (reproductive robustness)
  4. Faction of neutral mutants (mutational robustness)
  5. Fraction of negative mutants
  6. Cumulative delta-gaps of positive mutants
  7. Cumulative delta-gaps of negative mutants
  8. Delta-gap for the best mutants
  9. Delta-gap for the worst mutant
  10. Cumulative delta-fitness of positive mutants
  11. Cumulative delta-fitness of negative mutants
  12. Delta-fitness for the best mutants
  13. Delta-fitness for the worst mutants

    2. aevol_misc_ancestor_robustness

    Generates mutants for a given lineage and analyzes their robustness, providing several statistics:

  14. Generation
  15. Fraction of positive offspring
  16. Fraction of neutral offspring (aka reproductive robustness)
  17. Fraction of neutral mutants (aka mutational robustness)
  18. Fraction of negative offspring
  19. Cumulation of delta-gaps of positive offspring
  20. Cumulation of delta-gaps of negative offspring
  21. Delta-gap for the best offspring
  22. Delta-gap for the worst offspring
  23. Cumulation of delta-fitness of positive offspring
  24. Cumum of delta-fitness of negative offspring
  25. Delta-fitness for the best offspring
  26. Delta-fitness for the worst offspring

PREREQUISITES: Lineage file RESULTS: Output text file (e.g. robustness_summary.txt) that provides an overview of the robustness statistics.

3. aevol_misc_ancestor_stats

Analyzes a lineage and produces the following outputs:

  1. non-coding statistics (e.g. ancestor_stats_bp-b000000000-e000010000-i196-r1.out)
  2. mutation statistics (e.g. ancestor_stats_mutation-b000000000-e000010000-i196-r1.out)
  3. Each generation’s M W H (currently not working? – e.g. ancestor_stats_envir-b000000000-e000010000-i196-r1.out)
  4. Each generation’s genome size and termination number (e.g. ancestor_stats_nb_term-b000000000-e000010000-i196-r1.out)
  5. The lineage’s fitness statistics a. Generation b. Population size c. Fitness d. Genome size e. Metabolic error f. Parent’s metabolic error g. Metabolic fitness h. Secretion error i. Parent’s secretion error j. Secretion fitness k. Amount of compound present in the grid cell l. Int probe m. Double probe
  6. Statistics about the how many genes are in 20 RNA (e.g. ancestor_stats_operons-b000000000-e000010000-i196-r1.out)
  7. Individual gene statistics a. Generation b. Number of coding RNAs c. Number of non-coding RNAs d. Average size of coding RNAs e. Average size of non-coding RNAs f. Number of functional genes g. Number of non-functional genes h. Average size of functional genes i. Average size of non-functional genes
  8. Rearrangement statistics (e.g. ancestor_stats_rear-b000000000-e000010000-i196-r1.out) a. Generation b. Actual duplication rate c. Actual deletion rate d. Actual translocation rate e. Actual inversion rate f. Average alignment score

4. aevol_misc_coalescence

Prints coalescence statistics for a given lineage. PREREQUISITES: A lineage file. RESULTS: coalescence.csv , a CSV file which provides the coalescence calculation for certain generations.

5. aevol_misc_create_eps

Creates a directory, analysis-generation_XXXXX with several EPS files. I could only get it to run with no parameters, despite what the '--help` says. The EPS files are as follows:

  1. best_genome_with_CDS.eps
  2. best_genome_with_mRNAs.eps
  3. best_phenotype.eps
  4. best_pos_neg_profiles.eps
  5. best_triangles.eps

6. aevol_misc_extract

Extracts the genotype and/or data about the phenotype of individuals in the provided population and write them into text files for easy parsing by programs such as MATLAB. The program lets you specify whether you want the sequence, the triangle data, or both. By default (i.e. with no parameters) gives just the sequence, into a file called sequence”. PREREQUISITES: Backup file “exp_setup_constant.ae” OUTPUT: Triangle and/or sequence data in a text format.

7. aevol_misc_misc_lineage

Using the tree files, recreates the lineage of an individual. By default, this is done for the best individual, but another individual can be specified by ID number or rank ('-i` or '-r', respectively). PREREQUISITES: Tree files are generated (i.e. trees are requested in the parameter file). RESULTS: A file of the form lineage-b000000000-e000010000-i196-r1.ae is generated which contains all of the lineage information for the individual. The name of the file specifies the beginning generation, ending generation, the individual number, and their rank.

8. aevol_misc_mutagensis

This generates and analyzes mutations for an individual from a population backup (as opposed to a lineage file for ancestor_mutagenesis). One can specify point mutations, small indels, duplications, large deletion, translocations, or inversions.

PREREQUISITES: A population backup file for the specified generation (i.e. in the populations directory). RESULTS: A directory called “analysis-generation_XXXXXX” is created with the output files.

9. aevol_misc_protein_map

Creates a CSV file (e.g. protein_map_gen.csv) which analyzes the proteins generated by the specified lineage. The CSV file specifies:

  1. generation – Which generation is being described
  2. protein_id – An identifier for the protein.
  3. shine_dal – The Shine-Dalgarno location of the protein on the sequence
  4. length – The number of base pairs which encodes the protein.
  5. concentration – ???
  6. hamming_dist – ???
  7. dist_next_protein – The distance to the next protein?
  8. nb_proteins – The number of proteins?
  9. dna_length – The length of the DNA sequence

PREREQUISITES: A lineage file RESULTS: Outputs a CSV file (default “proteins_map_gen.csv”) with the above information.

10. aevol_misc_robustness

Calculates replication statistics for a given individual (specified by either ID or rank) at a given time. Specifically, the following information is saved in a new directory (analysis-generation_XXXXXXXXXX):

  1. Parent id – The identifier of this organism’s parent
  2. Parent metabolic error – The metabolic error rate of the parent
  3. Parent secretion – The secretion rate of the parent
  4. Mutant metabolic error – The metabolic error rate of the mutant
  5. Mutant secretion – The secretion rate of the mutant
  6. Mutant genome size – The genome size of the mutant
  7. Mutant number of functional genes – The number of functional genes in the mutant