taxonkit
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Published
20 hours ago •
shenwei356
shenwei356
Update benchmarks
I just released version 0.6.0 of taxopy where the only change is that taxids are now encoded as integers instead of strings. The code is now faster and uses less memory.
Before:
== Taxopy
data: taxids.n100000.txt
elapsed time: 8.591
peak rss: 1090184
b15e76dfe8cd3d7455bcf633909e3e97 taxids.n100000.txt.taxopy.lineage
== Taxopy
data: taxids.n10000.txt
elapsed time: 5.119
peak rss: 1090260
8debf4d37a7997c8ffdc13fd05e5d042 taxids.n10000.txt.taxopy.lineage
== Taxopy
data: taxids.n1000.txt
elapsed time: 5.474
peak rss: 1090236
4f47c764880ca614f9ac67c442f06144 taxids.n1000.txt.taxopy.lineage
== Taxopy
data: taxids.n100.txt
elapsed time: 6.360
peak rss: 1090024
4f7b7f23224e37658171a48780270d90 taxids.n100.txt.taxopy.lineage
== Taxopy
data: taxids.n10.txt
elapsed time: 4.902
peak rss: 1090316
138e7cea6c35a595b6538a34c9d2b7b3 taxids.n10.txt.taxopy.lineage
== Taxopy
data: taxids.n1.txt
elapsed time: 4.921
peak rss: 1090000
c1eda42e466916f0ef566c99c478907a taxids.n1.txt.taxopy.lineage
== Taxopy
data: taxids.n20000.txt
elapsed time: 5.966
peak rss: 1090024
b6ec2a1d717ddcd854c762bd555b03df taxids.n20000.txt.taxopy.lineage
== Taxopy
data: taxids.n2000.txt
elapsed time: 6.667
peak rss: 1090112
3cf4c5b7d13f455ed645654d829fa484 taxids.n2000.txt.taxopy.lineage
== Taxopy
data: taxids.n40000.txt
elapsed time: 6.467
peak rss: 1090300
70ddd9aac0283a4c21800245b582c983 taxids.n40000.txt.taxopy.lineage
== Taxopy
data: taxids.n4000.txt
elapsed time: 5.004
peak rss: 1090120
09e46bef68ac2e532644e5356e7b9928 taxids.n4000.txt.taxopy.lineage
== Taxopy
data: taxids.n60000.txt
elapsed time: 7.177
peak rss: 1090052
26215e6e9a981800565b5de62eb48bda taxids.n60000.txt.taxopy.lineage
== Taxopy
data: taxids.n6000.txt
elapsed time: 5.240
peak rss: 1090260
8da55d3d8e76f548b461dbb5322b1c77 taxids.n6000.txt.taxopy.lineage
== Taxopy
data: taxids.n80000.txt
elapsed time: 7.685
peak rss: 1090220
30d16a8b6ebef3c5ee20bee943981b39 taxids.n80000.txt.taxopy.lineage
== Taxopy
data: taxids.n8000.txt
elapsed time: 5.125
peak rss: 1090064
cfecede52e185ee41336c6c1316e1a4e taxids.n8000.txt.taxopy.lineage
After:
== Taxopy
data: taxids.n100000.txt
elapsed time: 6.760
peak rss: 867460
b15e76dfe8cd3d7455bcf633909e3e97 taxids.n100000.txt.taxopy.lineage
== Taxopy
data: taxids.n10000.txt
elapsed time: 3.991
peak rss: 867532
8debf4d37a7997c8ffdc13fd05e5d042 taxids.n10000.txt.taxopy.lineage
== Taxopy
data: taxids.n1000.txt
elapsed time: 4.102
peak rss: 867668
4f47c764880ca614f9ac67c442f06144 taxids.n1000.txt.taxopy.lineage
== Taxopy
data: taxids.n100.txt
elapsed time: 3.995
peak rss: 865352
4f7b7f23224e37658171a48780270d90 taxids.n100.txt.taxopy.lineage
== Taxopy
data: taxids.n10.txt
elapsed time: 3.898
peak rss: 853752
138e7cea6c35a595b6538a34c9d2b7b3 taxids.n10.txt.taxopy.lineage
== Taxopy
data: taxids.n1.txt
elapsed time: 3.787
peak rss: 862808
c1eda42e466916f0ef566c99c478907a taxids.n1.txt.taxopy.lineage
== Taxopy
data: taxids.n20000.txt
elapsed time: 4.277
peak rss: 867532
b6ec2a1d717ddcd854c762bd555b03df taxids.n20000.txt.taxopy.lineage
== Taxopy
data: taxids.n2000.txt
elapsed time: 3.892
peak rss: 867624
3cf4c5b7d13f455ed645654d829fa484 taxids.n2000.txt.taxopy.lineage
== Taxopy
data: taxids.n40000.txt
elapsed time: 4.914
peak rss: 867564
70ddd9aac0283a4c21800245b582c983 taxids.n40000.txt.taxopy.lineage
== Taxopy
data: taxids.n4000.txt
elapsed time: 3.889
peak rss: 867280
09e46bef68ac2e532644e5356e7b9928 taxids.n4000.txt.taxopy.lineage
== Taxopy
data: taxids.n60000.txt
elapsed time: 5.625
peak rss: 867564
26215e6e9a981800565b5de62eb48bda taxids.n60000.txt.taxopy.lineage
== Taxopy
data: taxids.n6000.txt
elapsed time: 3.785
peak rss: 867412
8da55d3d8e76f548b461dbb5322b1c77 taxids.n6000.txt.taxopy.lineage
== Taxopy
data: taxids.n80000.txt
elapsed time: 6.216
peak rss: 867372
30d16a8b6ebef3c5ee20bee943981b39 taxids.n80000.txt.taxopy.lineage
== Taxopy
data: taxids.n8000.txt
elapsed time: 3.883
peak rss: 867676
cfecede52e185ee41336c6c1316e1a4e taxids.n8000.txt.taxopy.lineage
