ViralSeq

A Ruby Gem containing bioinformatics tools for processing viral NGS data.

Specifically for Primer-ID sequencing and HIV drug resistance analysis.

Install

    $ gem install viral_seq

Usage

Excutables

Use executable locator to get the coordinates of the sequences on HIV/SIV reference genome from a FASTA file through a terminal

    $ locator -i sequence.fasta -o sequence.fasta.csv

Use executable tcs pipeline to process Primer ID MiSeq sequencing data.

    $ tcs -p params.json # run TCS pipeline with params.json
    $ tcs -j # CLI to generate params.json
    $ tcs -h # print out the help

Some Examples

Load all ViralSeq classes by requiring 'viral_seq.rb' in your Ruby scripts.

#!/usr/bin/env ruby
require 'viral_seq'

Load nucleotide sequences from a FASTA format sequence file

my_seqhash = ViralSeq::SeqHash.fa('my_seq_file.fasta')

Make an alignment (using MUSCLE)

aligned_seqhash = my_seqhash.align

Filter nucleotide sequences with the reference coordinates (HIV Protease)

qc_seqhash = aligned_seqhash.hiv_seq_qc(2253, 2549, false, :HXB2)

Further filter out sequences with Apobec3g/f hypermutations

qc_seqhash = qc_seqhash.a3g

Calculate nucleotide diveristy π

qc_seqhash.pi

Calculate cut-off for minority variants based on Poisson model

cut_off = qc_seqhash.pm

Examine for drug resistance mutations for HIV PR region

qc_seqhash.sdrm_hiv_pr(cut_off)

Known issues

  1. ~~have a conflict with rails.~~
  2. ~~Update on 03032021. Still have conflict. But in rails gem file, can just use requires: false globally and only require "viral_seq" when the module is needed in controller.~~
  3. The conflict seems to be resovled. It was from a combination of using ! as a function for factorial and the gem name viral_seq. @_@

Updates

Version 1.1.3-03032021

  1. Fixed the conflict with rails.

Version 1.1.2-03032021

  1. Fixed an issue that may cause conflicts with ActiveRecord.

Version 1.1.1-03022021

  1. Fixed an issue when calculating Poisson cutoff for minority mutations ViralSeq::SeqHash.pm.
  2. fixed an issue loading class 'OptionParser'in some ruby environments.

Version 1.1.0-11112020:

  1. Modularize TCS pipeline. Move key functions into /viral_seq/tcs_core.rb
  2. tcs_json_generator is removed. This CLI is delivered within the tcs pipeline, by running tcs -j. The scripts are included in the /viral_seq/tcs_json.rb
  3. consensus model now includes a true simple majority model, where no nt needs to be over 50% to be called.
  4. a few optimizations.
  5. TCS 2.1.0 delivered.
  6. Tried parallel processing. Cannot achieve the goal because parallel gem by default can't pool data from memory of child processors and in_threads does not help with the speed.

Version 1.0.9-07182020:

  1. Change ViralSeq::SeqHash#stop_codon and ViralSeq::SeqHash#a3g_hypermut return value to hash object.

  2. TCS pipeline updated to version 2.0.1. Add optional export_raw: TRUE/FALSE in json params. If export_raw is TRUE, raw sequence reads (have to pass quality filters) will be exported, along with TCS reads.

Version 1.0.8-02282020:

  1. TCS pipeline (version 2.0.0) added as executable. tcs - main TCS pipeline script. tcs_json_generator - step-by-step script to generate json file for tcs pipeline.

  2. Methods added: ViralSeq::SeqHash#trim

  3. Bug fix for several methods.

Version 1.0.7-01282020:

  1. Several methods added, including ViralSeq::SeqHash#error_table ViralSeq::SeqHash#random_select
  2. Improved performance for several functions.

Version 1.0.6-07232019:

  1. Several methods added to ViralSeq::SeqHash, including ViralSeq::SeqHash#size ViralSeq::SeqHash#+ ViralSeq::SeqHash#write_nt_fa ViralSeq::SeqHash#mutation
  2. Update documentations and rspec samples.

Version 1.0.5-07112019:

  1. Update ViralSeq::SeqHash#sequence_locator. Program will try to determine the direction (+ or - of the query sequence)
  2. update executable locator to have a column of direction in output .csv file

Version 1.0.4-07102019:

  1. Use home directory (Dir.home) instead of the directory of the script file for temp MUSCLE file.
  2. Fix bugs in bin locator

Version 1.0.3-07102019:

  1. Bug fix.

Version 1.0.2-07102019:

  1. Fixed a gem loading issue.

Version 1.0.1-07102019:

  1. Add keyword argument :model to ViralSeq::SeqHashPair#join2.
  2. Add method ViralSeq::SeqHash#sequence_locator (also: #loc), a function to locate sequences on HIV/SIV reference genomes, as HIV Sequence Locator from LANL.
  3. Add executable 'locator'. An HIV/SIV sequence locator tool similar to LANL Sequence Locator.
  4. update documentations

Version 1.0.0-07092019:

  1. Rewrote the whole ViralSeq gem, grouping methods into modules and classes under main Module::ViralSeq

Development

Bug reports and pull requests are welcome on GitHub at https://github.com/ViralSeq/viral_seq. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the Contributor Covenant code of conduct.

License

The gem is available as open source under the terms of the MIT License.

Code of Conduct

Everyone interacting in the viral_seq project’s codebases, issue trackers, chat rooms and mailing lists is expected to follow the code of conduct.