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mirvestigator-rust - Implementation of the miRvestigator algorithm in Rust

Description

This is an implementation of miRvestigator in Rust. It is designed as a standalone tool improve a few properties of the original version:

  • miRvestigator has generally been used within a larger context, either FIRM or SYGNAL or the miRvestigator website, but it makes sense to maintain it as a separate tool that can be called separately from various different contexts
  • Running data sets with a larger number of PSSMs leads to very long run times, sometimes a few days for a few thousand PSSMs, this is largely to 2 aspects: 1. the computationally heavy parts are done in pure Python 2. even though the nature of the data lends itself naturally to running computations concurrently there is a no parallelization

By choosing Rust a native implementation was realized that can be easily maintained and enhanced if necessary. The port was relatively straightforward.

Building

Development builds:

$ cargo build

Release builds:

$ cargo build --release

The difference in performance is pretty dramatic between development and release version, so for production always compile for release

Running

$ mirvestigator <SEQS> <PSSMS> <MIRBASE>

The parameters are as follows

  • seqs.txt file:

    a file that contains one DNA sequence per row, this will be used to optimize internal filtering

  • PSSM JSON file:

    A list of PSSM objects, the only required fields are

    • "name": the name of the PSSM
    • "matrix" the PSSM, which is a list of lists, n rows of 4 columns, assuming the alphabet A, C, G, T
  • mature.fa.gz file: a file downloaded from mirbase.org containing the miRNAs

The tool will write a list of entries to stdout in the format

<PSSM name>,<mirnas>,<match type>

mirnas is a list of micro RNAs that is separated with underscores. The output format is compatible with the output format of the original miRvestigator.

So one could run the tool and redirect its output into a file

$ mirvestigator <SEQS> <PSSMS> <MIRBASE> > results.csv

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Standalone implementation of miRvestigator in Rust

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