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vbind

Small RNA mapping against circular and linear target RNAs

https://github.com/paviudes/vbind

Science Score: 10.0%

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    2 of 10 committers (20.0%) from academic institutions
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    Low similarity (10.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Small RNA mapping against circular and linear target RNAs

Basic Info
  • Host: GitHub
  • Owner: paviudes
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 15.8 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 7 years ago · Last pushed almost 5 years ago
Metadata Files
Readme License

README.md

vbind

Logo

vbind is a userfriedly tool for RNA sequencing. In particular, it can be used to compute and visualize the bindings between a pool of sRNA nuleotides and a genome sequence.

Usage

In what follows, we will describe the two parts of our software tool. The first part computes matchings between a gene and a nucleotide pool. Second, presents some tools to visualize the solution to the mapping problem.

Part one: Computing matchings between a gene and a nuleotide pool

  1. Key ingriedients: The gene and the pool.
    • gene: The gene sequence should be a string of characters from the alphabet {A, T, G, C}. We require the gene sequence to be specified in a text file without any line-breaks.
    • pool: The pool is a collection of several sRNA nucleotides, each represented as a string of characters from the alphabet {A, T, G, C}. Ideally, we require a text file, wherein each new line identifies a nucleotide sequence. However, since a pool is typically derived from a gene bank, we accomodate some other formats for specifying the pool. In particular, we accept a text file containing the nueotides of the pool, interleaved by other information that is irrelevant for sequencing. Hence, the pool should be specified by a text file, wherein every k-th line, for some k > 0.
  2. Other settings:
    • lines to skip: number of lines to skip (denoted above by k) in the text file describing the pool, before reading a valid nuleoide sequence.
    • tolerance: the maximum number of mismatches allowed
    • topology of the gene: an integer that takes the value 0 for linear matching and 1 for circular matching

A problem instance is specified as: <gene> <pool> <lines to skip> <tolerance> <topology> <cores>.

For example, gene.txt pool.txt 4 1 1 1 is a complete input specification, indicating that the problem of computing bindings, in the circular topology while allowing for at most one mismatch, between the sequence in gene.txt with those in the pool.txt. Furthermore, every fourth sequence in pool.txt is a valid sRNA nuleotide.

All such instances of the matching problem can be gathered in a text file, placed in vbind/data/input.

To solve the instances of the matching problem in a text file “example.txt”, we need to run the following command: ./vbind.sh example.txt and to solve only a particular instance, we can specify its line number: x, by ./vbind.sh example.txt x .

Part two: Postprocessing -- Visualize matching results

Matching results computed from part one can be visualized using plots in our software tool. In addition to plotting, we also offer the capability of normalizing to reads per million. The post processing steps can be executed from ./analyze.sh.

Installation

vbind is entriely developed and meant to be used with the Python 3 interpretter. The following packages are required for its seamless functioning.

| Package | Description | |-----------------|------------------------------------------------------------------------------| | numpy | Linear algebra | | scipy | Linear algebra | | tqdm | Progress bar | | multiprocessing | Parallel execution | | datetime | Date and Time |

License

This software is licensed under the BSD Clause 3 license.

Contact

Please contact the following developers for any additional help or requests for customization. * Pavithran Iyer: pavithran.iyer@uwaterloo.ca . * Charith Adkar: Charith.Adkar@USherbrooke.ca . * Jean-Pierre Perrault: Jean-Pierre.Perreault@USherbrooke.ca . * Teruo Sano: sano@hirosaki-u.ac.jp .

Owner

  • Name: Pavithran S Iyer
  • Login: paviudes
  • Kind: user
  • Location: Waterloo, Ontario
  • Company: @Xanadu

I'm a senior architecture scientist at Xanadu Quantum Technologies Inc.

GitHub Events

Total
Last Year

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 78
  • Total Committers: 10
  • Avg Commits per committer: 7.8
  • Development Distribution Score (DDS): 0.603
Top Committers
Name Email Commits
Pavi p****r@u****c 31
Pavithran S Iyer p****r@u****a 18
paviudes p****n@u****a 13
CharithRaj AdkarPurushothama c****h@i****m 6
pavithran iyer p****s 3
Charith Raj Adkar Purushothama c****h@i****m 2
Charith Raj Adkar Purushothama c****h@i****m 2
Charith Raj Adkar Purushothama c****h@i****m 1
Pavithran Iyer p****i@p****a 1
Charith Raj Adkar Purushothama c****h@i****m 1
Committer Domains (Top 20 + Academic)
ip20.m: 1 paviws.iqc.uwaterloo.ca: 1 ip16.m: 1 ip17.m: 1 ip18.m: 1 ip08.m: 1 usherbrooke.ca: 1 uwaterloo.ca: 1 uwaterloo.c: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 0
  • Total pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
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  • paviudes (1)
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 5 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 2
  • Total maintainers: 1
pypi.org: vbind

sRNA profiler

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 5 Last month
Rankings
Dependent packages count: 10.0%
Dependent repos count: 21.7%
Forks count: 29.8%
Average: 30.5%
Stargazers count: 38.8%
Downloads: 52.1%
Maintainers (1)
paviuw
Last synced: 10 months ago

Dependencies

setup.py pypi
  • datetime *
  • matplotlib *
  • numpy *
  • scipy *
  • tqdm *