### denovo discovery and analysis practical 2015


## copy files
mkdir denovo
cp -r /faculty/dan/practical_2015/* denovo
less denovo-example.fam
less -S denovo-example.vcf


## view program and ESP counts
less -S de_novo_finder_3.py
less -S all_ESP_counts_5.28.13.txt


## run de_novo_finder_3.py
python de_novo_finder_3.py \
denovo-example.vcf \
denovo-example.fam \
all_ESP_counts_5.28.13.txt -q > example.denovo.txt


## view output
less -S example.denovo.txt
column -t example.denovo.txt | less -S


## view gene modeled mutation probabilities
less -S fixed_mut_prob_fs_adjdepdiv.txt


## collapse multi-hit genes
Neale_2012_denovo.txt > Neale_2012_genes.txt


## run single gene analysis
python overlap2mutprobs_1.2.py \
Neale_2012_genes.txt \
fixed_mut_prob_fs_adjdepdiv.txt \
175 > Neale_2012_gene_results.txt


## view single gene results
perl -pe 's{, }{:}g' Neale_2012_gene_results.txt \
| column -t | less -S


## run gene-set analysis
python list_crusher3_5.py \
fixed_mut_prob_fs_adjdepdiv.txt \
Neale_2012_denovo.txt \
JOINT_CONSTRAINT_829.set -p