improve efficiency drastically
ignore drugbank.xml backups
added verify_targets.py
Merge remote-tracking branch 'gberriz/master'
downloaded: lincs small_molecule.csv
fix downloaded small_molecule.csv

% python remove_embedded_nls.py small_molecule.130621F155906.csv > small_molecule.tsv
make input for scrape_kegg.py

% zsh extract_names.sh $(ls -1t small_molecule.*.tsv | head -1) > all_sm.$(ts).tsv

(ts is a shell function that returns a timestamp string)
update scraped data

% python -u scrape_kegg.py $(ls -1t all_sm.*.tsv | head -1) > scraped.$(ts).tsv
process drugs scraped from kegg

INPUT=$(ls -1t scraped.*.tsv | head -1)
python process_scraped_kegg.py $INPUT > hmsl_to_kegg.$(ts).tsv && \
 ( OUTPUT=$(ls -1t hmsl_to_kegg.*.tsv | head -1); \
   ( for k ( $(grep '^x' $OUTPUT | cutt 2 | nodup) ) \
       grep -P "\\b$k\\b" $OUTPUT ) > tocheck.$(ts).tsv )
10001 -> HMSL10001, etc.
hmsl_to_kegg* -> hmsl_to_kegg_unverified*
fix line endings
use namedtuples