You can find some sample commands at examples and some sample data files at examples/data.
Run the commands inside a file:
run PATH_TO_FILE
Add a new object to the workspace:
add genome -id ID -rna RNA_STRAND -dna FIRST_STRAND SECOND_STRAND
add chromosome -to [cell/animal] -id PARENT_ID -dna FIRST_STRAND SECOND_STRAND
add cell -id ID -number NUMBER_OF_CHROMOSOMES
add animal -id ID -number NUMBER_OF_CHROMOSOMES
add virus -id ID -rna RNA_STRAND
Parse a FastA file and add its records to the workspace:
load genomes -from PATH_TO_FILE
load cells -from PATH_TO_FILE
load animals -from PATH_TO_FILE
load viruses -from PATH_TO_FILE
Note: The header of each record in a FastA file must follow a specific pattern. Please take a look at examples/data to find out how to feed records into the program.
Delete an object from the workspace:
delete genome -id ID
delete chromosome -from [cell/animal] -id PARENT_ID -index INDEX
delete cell -id ID
delete animal -id ID
delete virus -id ID
Show an existing object:
show genome -id ID
show chromosome -from [cell/animal] -id ID -index INDEX
show cell -id ID
show animal -id ID
show virus -id ID
List all existing objects:
list genomes
list cells
list animals
list viruses
Transform RNA to DNA:
genomes transform -id ID
Perform different kinds of mutation:
genomes mutate rna small -id ID -from SOURCE_NUCLEOTIDE -to DESTINATION_NUCLEOTIDE -number NUMBER_OF_MUTATIONS
genomes mutate rna large -id ID -from SOURCE_CHUNK -to DESTINATION_CHUNK
genomes mutate rna inversely -id ID -on TARGET_CHUNK
genomes mutate dna small -id ID -from SOURCE_NUCLEOTIDE -to DESTINATION_NUCLEOTIDE -number NUMBER_OF_MUTATIONS
genomes mutate dna large -id ID -from SOURCE_CHUNK -to DESTINATION_CHUNK
genomes mutate dna inversely -id ID -on TARGET_CHUNK
Perform different kinds of mutation:
cells mutate small -id ID -chromosome INDEX -from SOURCE_NUCLEOTIDE -to DESTINATION_NUCLEOTIDE -number NUMBER_OF_MUTATIONS
cells mutate large -id ID -from SOURCE_INDEX SOURCE_CHUNK -to DESTINATION_INDEX DESTINATION_CHUNK
cells mutate inversely -id ID -on INDEX TARGET_CHUNK
List all complementary palindromes within all chromosomes of the cell:
cells palindromes -id ID
Kill the cell if it has abnormal chromosomes:
cells die -id ID
Perform different kinds of mutation:
animals mutate small -id ID -chromosome INDEX -from SOURCE_NUCLEOTIDE -to DESTINATION_NUCLEOTIDE -number NUMBER_OF_MUTATIONS
animals mutate large -id ID -from SOURCE_INDEX SOURCE_CHUNK -to DESTINATION_INDEX DESTINATION_CHUNK
animals mutate inversely -id ID -on INDEX TARGET_CHUNK
List all complementary palindromes within all chromosomes of the animal:
animals palindromes -id ID
Compute the similarity score between two animals:
animals similarity FIRST_ANIMAL_ID SECOND_ANIMAL_ID
Check if two animals are of the same species:
animals equality FIRST_ANIMAL_ID SECOND_ANIMAL_ID
Perform asexual reproduction:
animals reproduce ANIMAL_ID -id CHILD_ID
Perform sexual reproduction:
animals reproduce FIRST_ANIMAL_ID SECOND_ANIMAL_ID -id CHILD_ID
Kill abnormal chromosomes:
animals kill chromosomes -id ID
Kill the cell if it has abnormal chromosomes:
animals die -id ID
Perform different kinds of mutation:
viruses mutate small -id ID -from SOURCE_NUCLEOTIDE -to DESTINATION_NUCLEOTIDE -number NUMBER_OF_MUTATIONS
viruses mutate large -id ID -from SOURCE_CHUNK -to DESTINATION_CHUNK
viruses mutate inversely -id ID -on TARGET_CHUNK
Check if a virus is pathogenic for an animal:
viruses pathogenicity -id VIRUS_ID -for ANIMAL_ID
Clear the screen:
clear
See the help:
help
See the about:
about
Exit the program:
exit