Closed AndreaGuarracino closed 1 year ago
By default, we emit similarity measures:
odgi similarity -i MHC.og -D '#' -p 2 | column -t | head -n 5
group.a group.b group.a.length group.b.length intersection jaccard.similarity cosine.similarity dice.similarity tanimoto.similarity estimated.identity
chm13#1 chm13#1 3316253 3316253 3316253 1 1 1 1 1
mSymSyn1#2 GRC38#1 3087908 3366997 1743857 0.370163 0.540826 0.54032 0.370163 0.54032
mPonPyg2#2 GRC38#1 3780557 3366997 2296869 0.473514 0.643779 0.642701 0.473514 0.642701
mPonAbe1#2 GRC38#1 3669057 3366997 2322227 0.492642 0.660703 0.660094 0.492642 0.660094
With -d/--distances
, we emit dissimilarity measures plus Euclidean and Manhattan distances:
odgi similarity -i MHC.og -D '#' -p 2 --distances | column -t | head -n 5
group.a group.b group.a.length group.b.length intersection jaccard.distance cosine.distance dice.distance tanimoto.distance estimated.difference.rate euclidean.distance manhattan.distance
chm13#1 chm13#1 3316253 3316253 3316253 0 0 0 0 0 0 0
mSymSyn1#2 GRC38#1 3087908 3366997 1743857 0.629837 0.459174 0.45968 0.629837 0.45968 1722.55 2967191
mPonPyg2#2 GRC38#1 3780557 3366997 2296869 0.526486 0.356221 0.357299 0.526486 0.357299 1598.07 2553816
mPonAbe1#2 GRC38#1 3669057 3366997 2322227 0.507358 0.339297 0.339906 0.507358 0.339906 1546.48 2391600
We move part of the
odgi paths
functionalities in a dedicated command,odgi similarity
.