Too meta?

Having just given a talk on reproducibility, I am in the midst of responding to reviewer comments about what we did (12 months ago!) and boy can I say every minute of putting [this notebook](https://github.com/che625/olson-ms-nb/blob/master/BiGo_dev.ipynb) was worth it. I even found [where we ran the entire notebook, so all result files are easily accessible](http://eagle.fish.washington.edu/cnidarian/index.php?dir=olson-ms-nb-master_12_1714%2Fwd%2F). Beyond praising Claire, I will document my follow up analysis here.

Essentially the want more quantitative information on differential methylation beyond ..

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/OlsonandRoberts2015_9_docx_1BC2FBAE.png" alt="OlsonandRoberts2015_9_docx_1BC2FBAE.png"/>

Makes sense.

Here is what was originally done.

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/olson-ms-nb_BiGo_dev_ipynb_at_master_·_che625_olson-ms-nb_1BC2FCC5.png" alt="olson-ms-nb_BiGo_dev_ipynb_at_master_·_che625_olson-ms-nb_1BC2FCC5.png"/>

For example the file named _linexon_ contained `16 exon_intersect_DML_lin_u.txt`. The 4 files were concatenated to produce `lintable` ....
       

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/eagle_fish_washington_edu_cnidarian_olson-ms-nb-master_12_1714_wd_lintable_1BC2FE30.png" alt="eagle_fish_washington_edu_cnidarian_olson-ms-nb-master_12_1714_wd_lintable_1BC2FE30.png"/>

and a little awk 

```
awk 'FNR==NR{sum+=$1;next}; {print $0,sum}' lintable{,} > lin_total
awk '{print $2, $1, $3, (($1/$3)*100)}' lin_total > lineage_DMLs
```

to create  `lineage_DMLs`...

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/eagle_fish_washington_edu_cnidarian_olson-ms-nb-master_12_1714_wd_lineage_DMLs_1BC2FE65.png" alt="eagle_fish_washington_edu_cnidarian_olson-ms-nb-master_12_1714_wd_lineage_DMLs_1BC2FE65.png"/>