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PERF

Introduction

PERF is a Python package developed for fast and accurate identification of microsatellites from DNA sequences. Microsatellites or Simple Sequence Repeats (SSRs) are short tandem repeats of 1-6nt motifs. They are present in all genomes, and have a wide range of uses and functional roles. The existing tools for SSR identification have one or more caveats in terms of speed, comprehensiveness, accuracy, ease-of-use, flexibility and memory usage. PERF was designed to address all these problems.

PERF is a recursive acronym that stands for “PERF is an Exhaustive Repeat Finder”. It is compatible with both Python 2 (tested on Python 2.7) and 3 (tested on Python 3.5). Its key features are:

  • Fast run time, despite being a single-threaded application. As an example, identification of all SSRs from the entire human genome takes less than 7 minutes. The speed can be further improved ~3 to 4 fold using (human genome finishes in less than 2 minutes using PyPy v5.8.0)
  • Linear time and space complexity (O(n))
  • Identifies perfect SSRs
  • 100% accurate and comprehensive
  • Does not miss any repeats or does not pick any incorrect ones
  • Easy to use
  • The only required argument is the input DNA sequence in FASTA format
  • Flexible
  • Most of the parameters are customizable by the user at runtime
  • Repeat cutoffs can be specified either in terms of the total repeat length or in terms of number of repeating units
  • TSV output and HTML report

The default output is an easily parseable and exportable tab-separated format. Optionally, PERF also generates an interactive HTML report that depicts trends in repeat data as concise charts and tables.

Installation

PERF can be directly installed using pip with the package name perf_ssr.

$ pip install perf_ssr

This name was chosen for the package so as not to clash with the existing perf package.

Alternatively, it can also be installed from the source code:

# Download the git repo
$ git clone https://github.com/RKMlab/perf.git

# Install
$ cd perf
$ python setup.py install

Both of the methods add a console command PERF, which can be executed from any directory. It can also be used without installation by running the core.py file in the PERF subfolder:

$ git clone https://github.com/RKMlab/perf.git
$ cd perf/PERF
$ python core.py -h # Print the help message of PERF (see below)

Usage

The help message and available options can be accessed using

$ PERF -h # Short option
$ PERF --help # Long option

which gives the following output

usage: PERF [-h] -i <FILE> [-o <FILE>] [-a] [-l <INT> | -u INT or FILE]
            [-rep <FILE>] [-m <INT>] [-M <INT>] [--version]

Required arguments:
  -i <FILE>, --input <FILE>
                        Input file in FASTA format

Optional arguments:
  -o <FILE>, --output <FILE>
                        Output file name. Default: Input file name + _perf.tsv
  -a, --analyse         Generate a summary HTML report.
  -l <INT>, --min-length <INT>
                        Minimum length cutoff of repeat
  -u INT or FILE, --min-units INT or FILE
                        Minimum number of repeating units to be considered.
                        Can be an integer or a file specifying cutoffs for
                        different motif sizes.
  -rep <FILE>, --repeats <FILE>
                        File with list of repeats (Not allowed with -m and/or
                        -M)
  -m <INT>, --min-motif-size <INT>
                        Minimum size of a repeat motif in bp (Not allowed with
                        -rep)
  -M <INT>, --max-motif-size <INT>
                        Maximum size of a repeat motif in bp (Not allowed with
                        -rep)
  --version             show program's version number and exit