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Table of Contents

List of BBLab tools

A list of avaliable tools. Several tools exist in their own repos (and are included in the test branch as Git submodules). See Further Notes for more information.

Layout Generators

  • Sequencing layout designer
  • Guava layout designer

QC and data processing

  • Fasta Converter
  • Text to columns
  • False discovery rate q-value calculator

HIV sequence/function analyses

  • HXB2 Genome genome map
  • DNA translator
  • Quality Check Tool
  • Unique Sequence Finder (USF)
  • Variable Function Analysis: in house variable-function analyzer
  • Codon by codon in house analysis tool
  • Phylogenetic Dating : tracking cfe-lab/phylodating, missing some recent commits which update documentation
    • Blind Dating : old version of Pylogenetic Dating, also on Git at cfe-lab/blind-dating (tracking the web branch). Git structure is messy.

HLA interpretation and analyses

  • HLA class I sequence-based typing interpretation tool
  • PHAGE-I-expanded: should be tracking cfe-lab/PHAGE-I-expanded, needs some repo cleanup on the server.

TCR interpretation and analysis

  • TCR Distance : this tool uses the repo tcr-dist
  • TCR Visualizer

List of unavailable tools

These tools will not be hosted on the server. They exist in the BBLab-Wiki backup (MDF) but have not been ported to Python 3/Django. They are all under source control from deleted repos, dating from 2014-2017.

  • Best Probability (BPHI) - Get the best probabilities only from HLA Imputation
  • HAPC - HLA Associated Polymorphism Counter HAPC
  • HAPA - HLA Associated Polymorphism Analyzer HAPA
  • PHAGE-I - Proportion of HLA Associated Genomic Escape (individual)
  • PHAGE-P - Proportion of HLA Associated Genomic Escape (population) PHAGE-P
  • HAPLOID - HLA Associated PoLymOrphism IDentifier HAPLOID
  • CLEF - CTL Epitope Finder CLEF

Misc To-Do

  • Update Django from 2.2.0 to 2.2.26
  • (Longer term) Migrate to a newer Django version as 2.2 is losing support in April 2022.

Further Notes

Further explanation for some specific tools as needed.

Phylodating

  • This is tracking the Git repo cfe-lab/phylodating
  • There is also a version of this in alldata/bblab_site/tools/test/phylodating, which can probably be removed.

Blind Dating

  • An earlier version of Phylodating
  • This is not linked on the BBLab wiki page, however it is stored on the server. There is a tools/blind_dating/repo directory which is tracking the web branch of cfe-lab/blind-dating, though it is 7 commits behind.
  • There is another Git repo in the tools/blind_dating directory that is tracking a non-existent repository called cfe-lab/web_blind_dating.git. This one is integrated with Django and contains a Python script blind_dating.py which calls the R scripts located in repo/src.
    • (Note: the R scripts root_and_regress.R and plot_divergence_vs_time.R are also located in tools/phylodating, which is tracking cfe-lab/phylodating.)

PHAGE-I-expanded

The main directory is not under source control. But there is a tools/phage_i_expanded/repo folder which is the whole repo but still points to https://github.com/dmacmillan/PHAGE-I-expanded.git (now deleted). I suggest we remove tools/phage_i_expanded/repo and set page to track the copy hosted at cfe-lab/PHAGE-I-expanded.

HLA Class

This tool is not part of the Django framework, as it's written in Ruby and PHP and wasn't ported. It is aliased in the Apache config file (httpd/conf/httpd.conf (385-392)). Porting to Python seems possible but non-trivial -- hla-easy.rb is 500+ lines and relies on at least one method from BioRuby (Bio::FlatFile.auto)

Web Links

Under the Other useful resources section of the Wiki