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biomedicalinformaticsgroup / Sargasso

Sargasso disambiguates mixed-species high-throughput sequencing data.
http://biomedicalinformaticsgroup.github.io/Sargasso/
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Check code speed vs latest release. #87

Closed lweasel closed 5 years ago

hxin commented 5 years ago

I tested the speed of the current master verson 76f536f7d23d4b369d167bde0111a62d0aabe63a against the dev version f79200f996f65be41bff0b94f535bc0a3cb36426, to make sure the refactoring of the dna-seq is not slowing down the code.

The test data is: 'rna_mouse_11|rnaseq|mouse|/srv/data/ghardingham/activity_dependence_nora|_1.sanfastq.gz|_2.sanfastq.gz|AM1,AM2'

The result shows that filter_sample_reads took almost the same time between the versions, suggesting that the refactoring is at least not slowing down the code, which is as expected.

  Data.Name Sargasso.Strategy difference(days) original
1 rna_mouse_11 best -0.0006481 dev=00:43:09,master=00:42:13
2 rna_mouse_11 conservative -0.0001505 dev=00:38:22,master=00:38:09
3 rna_mouse_11 permissive -0.0003935 dev=00:44:59,master=00:44:25
4 rna_mouse_11 recall -0.0005671 dev=00:44:44,master=00:43:55