This repo is meant to be used as a refactoring training repo. Study the code and refactor it to be
- more efficient
- better OO design
- easier to read/understand
- more extendable
This may involve
- changing names
- changing logic
- extracting variables, methods, classes, enums, interfaces
- reorganizing code
- applying design patterns
- externalizing data
- improving the Readme "GffQuery Usage" section (!)
Although this is not exactly in the spirit of refactoring, changing some functionality for the better is also allowed (but not the purpose of this assignment).
Maybe you can even whip up some test cases?
This is my repo for the gff query, only raw code will be submitted here along with gradle files to build a jar.
The data folder contains example files for testing the script. Info on the gff format can be found here
After the jar is built, you can run it.
Usage; usage: java -jar GffQuery-Jar-1.1-SNAPSHOT.jar [-f <arg>] [-fc <arg>] [-fr <arg>] [-ft <arg>] [-fw <arg>] [-h] -i <arg> [-s]
For further explanation, use the help defined below;
-f,--filter <arg> miscellaneous filters, defined like so:
"source|score|orientation|maximum_length|min
imum_length"
-fc,--fetch_children <arg> input which Parent group attributes to sort
on, e.g. "PGSC0003DMT400039136".
-fr,--fetch_region <arg> fetches region in between start..end, e.g.
"250000..260000"
-ft,--fetch_type <arg> fetches type, e.g. "CDS"
-fw,--find_wildcard <arg> input which wildcard, e.g. "[dD]efesin" to
match on. (gff3 name attribute)
-h,--help Gives program help.
-i,--infile <arg> input gff3 file, e.g. "gff3_sample.gff3"
-s,--summary makes a summary of the gff3 file.
for gffFilePath, both windows and linux paths work. When specifying a relative
gffFilePath from the currect working directory however, watch out that you DO NOT
prepend you gffFilePath with a "/". e.g.: NOT /data/gene_sample.gff3 but
data/gene_sample.gff3
When specifying the filter argument, it has to in the following format;
source|score|orientation|maximum_length|minimum_length", where suppression
of an individual filter is indicated using an asterisk (*).
SOURCE should filter on source attribute
SCORE should filter on score attribute
ORIENTATION should be defined using a "+", "-" or "." character
MINIMUM LENGTH should be defined using an integer
MAXIMUM LENGTH should be defined using an integer