<commit_before>

test: test_edgeR test_DESeq2 test_voom #test_ROTS

test_edgeR:
	../../Analysis/DifferentialExpression/run_DE_analysis.pl  -m Trinity_trans.counts.matrix --method edgeR -s samples.txt -o edgeR_outdir
	cd edgeR_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl  --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt

test_DESeq2:
	../../Analysis/DifferentialExpression/run_DE_analysis.pl  -m Trinity_trans.counts.matrix --method DESeq2 -s samples.txt -o DESeq2_outdir
	cd DESeq2_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl  --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt 
<commit_msg>turned ROTS test back on<commit_after>

test: test_edgeR test_DESeq2 test_voom test_ROTS

test_edgeR:
	../../Analysis/DifferentialExpression/run_DE_analysis.pl  -m Trinity_trans.counts.matrix --method edgeR -s samples.txt -o edgeR_outdir
	cd edgeR_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl  --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt

test_DESeq2:
	../../Analysis/DifferentialExpression/run_DE_analysis.pl  -m Trinity_trans.counts.matrix --method DESeq2 -s samples.txt -o DESeq2_outdir
	cd DESeq2_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl  --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt 

{'fraction_non_alphanumeric': 0.14046579330422126, 'fraction_numerical': 0.00727802037845706, 'mean_word_length': 3.824561403508772, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '509310', 'n_tokens_mistral': 491, 'n_tokens_neox': 466, 'n_words': 84}