refactor: outputs to file in ./plots, updated cli and tests

.gitignore

plots/reads_plot_220106_1.svg

requirements.txt

requirements_dev.txt

src/cli_plot_read_counts.py

src/plot_read_counts.py

tests/resources/Transcript4.csv

tests/resources/Transcript5.csv

tests/resources/Transcript6.csv

tests/resources/Transcript7negctrl.csv

tests/resources/Transcript_read_counts_invalid.csv

tests/resources/Transcript_read_counts_missing-gene7.csv

tests/resources/Transcript_read_counts_valid.csv

tests/resources/Transcript_read_counts_valid2.csv

tests/test_plot_read_counts.py