This week I finished writing and debugging my first script. The script is called ChrBuild2 and is a major extension of an existing script. ChrBuild2 was originally capable of generating an AGP file (contains summary of scaffolds in a chromosome) and a FASTA file (contains a chromosome DNA sequence) after inputting a row of scaffolds in the command line terminal.
The new version of the script has expanded from 100 lines of code to about 400 lines. The new features of the script allow the following:
For input:
- Input in the form of an input synteny file (contains scaffolds of all chromosomes of an organism).
- Input in the form of command line input (= original script).
For processing:
The script can process both the scaffolds of a single chromosome (= original script) and the scaffolds of all chromosomes, depending on what is requested by the user.
For output (with the option of choosing which output files you desire, instead of always generating all the outputs types):
- Output a FASTA file (with custom name option)
- Output an AGP file (with custom name option)
- Output a summary file (contains the sequence length of the chromosome and the amount of scaffolds, once again with custom name option).
It is clear that the capabilities of the script have largely expanded. Next week I shall receive a new task to create the largest script of my project. I’m looking forward to this assignment, because I like writing scripts in the Python language.