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Update benchmarks #47

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Open
@apcamargo

Description

@apcamargo

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:

== Taxopydata: taxids.n100000.txtelapsed time: 8.591peak rss: 1090184b15e76dfe8cd3d7455bcf633909e3e97  taxids.n100000.txt.taxopy.lineage== Taxopydata: taxids.n10000.txtelapsed time: 5.119peak rss: 10902608debf4d37a7997c8ffdc13fd05e5d042  taxids.n10000.txt.taxopy.lineage== Taxopydata: taxids.n1000.txtelapsed time: 5.474peak rss: 10902364f47c764880ca614f9ac67c442f06144  taxids.n1000.txt.taxopy.lineage== Taxopydata: taxids.n100.txtelapsed time: 6.360peak rss: 10900244f7b7f23224e37658171a48780270d90  taxids.n100.txt.taxopy.lineage== Taxopydata: taxids.n10.txtelapsed time: 4.902peak rss: 1090316138e7cea6c35a595b6538a34c9d2b7b3  taxids.n10.txt.taxopy.lineage== Taxopydata: taxids.n1.txtelapsed time: 4.921peak rss: 1090000c1eda42e466916f0ef566c99c478907a  taxids.n1.txt.taxopy.lineage== Taxopydata: taxids.n20000.txtelapsed time: 5.966peak rss: 1090024b6ec2a1d717ddcd854c762bd555b03df  taxids.n20000.txt.taxopy.lineage== Taxopydata: taxids.n2000.txtelapsed time: 6.667peak rss: 10901123cf4c5b7d13f455ed645654d829fa484  taxids.n2000.txt.taxopy.lineage== Taxopydata: taxids.n40000.txtelapsed time: 6.467peak rss: 109030070ddd9aac0283a4c21800245b582c983  taxids.n40000.txt.taxopy.lineage== Taxopydata: taxids.n4000.txtelapsed time: 5.004peak rss: 109012009e46bef68ac2e532644e5356e7b9928  taxids.n4000.txt.taxopy.lineage== Taxopydata: taxids.n60000.txtelapsed time: 7.177peak rss: 109005226215e6e9a981800565b5de62eb48bda  taxids.n60000.txt.taxopy.lineage== Taxopydata: taxids.n6000.txtelapsed time: 5.240peak rss: 10902608da55d3d8e76f548b461dbb5322b1c77  taxids.n6000.txt.taxopy.lineage== Taxopydata: taxids.n80000.txtelapsed time: 7.685peak rss: 109022030d16a8b6ebef3c5ee20bee943981b39  taxids.n80000.txt.taxopy.lineage== Taxopydata: taxids.n8000.txtelapsed time: 5.125peak rss: 1090064cfecede52e185ee41336c6c1316e1a4e  taxids.n8000.txt.taxopy.lineage

After:

== Taxopydata: taxids.n100000.txtelapsed time: 6.760peak rss: 867460b15e76dfe8cd3d7455bcf633909e3e97  taxids.n100000.txt.taxopy.lineage== Taxopydata: taxids.n10000.txtelapsed time: 3.991peak rss: 8675328debf4d37a7997c8ffdc13fd05e5d042  taxids.n10000.txt.taxopy.lineage== Taxopydata: taxids.n1000.txtelapsed time: 4.102peak rss: 8676684f47c764880ca614f9ac67c442f06144  taxids.n1000.txt.taxopy.lineage== Taxopydata: taxids.n100.txtelapsed time: 3.995peak rss: 8653524f7b7f23224e37658171a48780270d90  taxids.n100.txt.taxopy.lineage== Taxopydata: taxids.n10.txtelapsed time: 3.898peak rss: 853752138e7cea6c35a595b6538a34c9d2b7b3  taxids.n10.txt.taxopy.lineage== Taxopydata: taxids.n1.txtelapsed time: 3.787peak rss: 862808c1eda42e466916f0ef566c99c478907a  taxids.n1.txt.taxopy.lineage== Taxopydata: taxids.n20000.txtelapsed time: 4.277peak rss: 867532b6ec2a1d717ddcd854c762bd555b03df  taxids.n20000.txt.taxopy.lineage== Taxopydata: taxids.n2000.txtelapsed time: 3.892peak rss: 8676243cf4c5b7d13f455ed645654d829fa484  taxids.n2000.txt.taxopy.lineage== Taxopydata: taxids.n40000.txtelapsed time: 4.914peak rss: 86756470ddd9aac0283a4c21800245b582c983  taxids.n40000.txt.taxopy.lineage== Taxopydata: taxids.n4000.txtelapsed time: 3.889peak rss: 86728009e46bef68ac2e532644e5356e7b9928  taxids.n4000.txt.taxopy.lineage== Taxopydata: taxids.n60000.txtelapsed time: 5.625peak rss: 86756426215e6e9a981800565b5de62eb48bda  taxids.n60000.txt.taxopy.lineage== Taxopydata: taxids.n6000.txtelapsed time: 3.785peak rss: 8674128da55d3d8e76f548b461dbb5322b1c77  taxids.n6000.txt.taxopy.lineage== Taxopydata: taxids.n80000.txtelapsed time: 6.216peak rss: 86737230d16a8b6ebef3c5ee20bee943981b39  taxids.n80000.txt.taxopy.lineage== Taxopydata: taxids.n8000.txtelapsed time: 3.883peak rss: 867676cfecede52e185ee41336c6c1316e1a4e  taxids.n8000.txt.taxopy.lineage

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