DNA PROJECT

Description

This project stands for creating and manipulating DNA sequences, using special command lines.

Usage

run the main function in the main file and then use one or more of the following commands:

• Create a DNA sequence ATC named first (if no @name will be sent, a default name will be generated):

new ATC @first

• Duplicate a sequence with id number 1:

dup #1

• Load sequence from some_file.rawdna and name it third:

load some_file.rawdna @third

• 1. Count the amount of times that subsequence A appears in the sequence named third
  2. Count the amount of times that subsequence named first appears in the sequence named third

1. count @third A
2. count @second @first

• Find the first index of:
  1. Explicit subsequence in an existing sequence
  2. Existing sequence in an existing sequence (using @name or #id)

1. find @third A 
   find #3 A
2. find @second @first

• Find all indexes of explicit subsequence in an existing sequence

findall @third A 
findall #3 A

• Return the length of a sequence by @name or by #id:

len @third 
len #3

• Delete a sequence by @name or by #id:

del @third 
del #3

• Save a sequence by @name or by #id to a file with .rawdna suffix with a given filename or a default one:

#this will create a file named newfile.rawdna:
save @second newfile.rawdna
#this will create a file named second.rawdna (default name):
save #2 

• Replace the letter in the (0-based) index of @seq_name/#seq_id by <new_letter>. if the command ends with : @@ or : @new_name the replaced sequence will get default / new_name name

#this will create a sequence named new_name:
replace @first 0 T : @new_name
#this will create a sequence named first_r1 (default name):
replace @first 0 T : @@
#this will change the @name sequence itself:
replace @first 0 T

• Create sequence @seq_name/#seq_id with its pair sequence, that is, each T is replaced by an A (and vice versa), and each C is replaced by a G (and vice versa). if the command ends with : @@ or : @new_name the replaced sequence will get default / new_name name

#this will create a sequence named new_name:
pair @first : @new_name
#this will create a sequence named first_r1 (default name):
pair @first : @@
#this will change the @name sequence itself:
pair @first

• Get into batch mode - every command that is entered in batch mode wil be saved in the batch and will run by running the batch:

batch batch_name

• Finish batch mode:

end

• Get the list of existing batches:

batchlist

• Get the content of batch_name batch:

batchshow @batch_name

• Save batch_name batch in file_name.dnabatch:

batchsave @batch_name file_name.dnabatch

• Load file_name.dnabatch into batch_name batch if given, otherwise batch name will be file_name:

#this will create a batch called batch_name
batchload file_name.dnabatch : @batch_name
#this will create a batch called file_name
batchload file_name.dnabatch

• Run batch_name batch:

run @batchname