echo "WeightingRegularizer /projects/compbio/lib/recode3.20comp" > tmp.script echo "SequenceWeight EntropyWeight 0.5 10.0" >> tmp.script echo "ReadA2M T0098.t2k.a2m.gz" >> tmp.script echo "SavingsRegularizer /projects/compbio/lib/recode3.20comp" >> tmp.script echo "PrintSavings T0098.t2k.saves" >> tmp.script echo "exit" >> tmp.script estimate-dist < tmp.script # command:Weighting regularizer set to recode3.20comp # command:Sequence weighting on input set to EntropyWeight(0.5, 10) # command:Reading A2M format from T0098.t2k.a2m.gz % using regularizer recode3.20comp % T0098.t2k.a2m.gz with 36 sequences, total weight= 1.33298 avg weight= 0.0370271 After reading T0098.t2k.a2m.gz, have 121 columns, totalling 132.511 Using SequenceWeight EntropyWeight(0.5, 10) Using regularizer recode3.20compfor sequence weight regularizer. # command:Savings regularizer set to recode3.20comp # command:% Computing savings using regularizer recode3.20comp Printed 121 columns to T0098.t2k.saves # command:rm tmp.script if test -e T0098.t2k-logo.labels ;\ then makelogo -b 60 -t T0098.t2k -o T0098.t2k-logo.eps -l T0098.t2k-logo.labels T0098.t2k.saves ;\ else makelogo -b 60 -t T0098.t2k -o T0098.t2k-logo.eps -lf T0098.t2k.2d.seq T0098.t2k.saves ;\ fi rm T0098.t2k.saves