Flair 2.0

This release accompanies the Flair 2.0 paper https://www.biorxiv.org/content/10.1101/2023.06.09.544396v1

• Fixes tickets (#261 #234)
• Moves or links some scripts to /bin so users have access
• Adds FAQ; updates documentation
• Removes sam flag name extension from bed files because users have trouble getting it to parse their own IDs properly.
• Adds --nvrna tag to flair quantify to allow for strand-aware alignment, like used in flair align
• Adds quoting to handle wildcard characters in filenames
• Removes obsolete fusion_dist option from collapse

Flair 1.7

• adding user tests
  

• added cannot_verify output file to ssCorrect to avoid flair correct silently removing reads for which the chromosome cannot be found in the input annotation
  

• removed psl from main Flair to simplify code and inputs. Conversion tools remain in bin directory. Programs in src directory still take psl but are renamed to avoid confusion
  

• removed file path inputs to flair module parameters to simplify code and input. With conda or docker install these are never necessary
  

• full usage statements for each flair module in documentation
  

• info on testing local installation in documentation
  

• removed salmon option
  

• standardized es output with other diffSplice output (added gene ID) and removed strand from ir output
  

Changes to diffExp, diffSplice output and error/warning messages

• Reorganized diffSplice and diffExp outputs; added human readable p-adj filtered tables
• Improved diffSplice error and warning notifications
• flake 8 code cleanup
• Fixed wiggleWindow bug (was not getting passed on from flair to ssPrep) and set default to 15
• Reorganized usage statements
• Added sanity checks and warnings

Fixed reliance on specific bedtools version

This version no longer specifically needs bedtools v2.25
There is also a new docker container on dockerhub: brookslab/flair:1.6.3

changes to flair collapse isoforms output

• changed filter_collapsed_isoforms (which is called by flair collapse) to include subset isoforms only if it is more abundant than the most expressed superset isoform instead of an average
• added input file sanity checks
• fixed openblas issue that occurs on some servers when running docker
• added more commandline programs to pip install

Pip installable version

• Bug fix for flair correct, see issue #207

Pip installable version - slight changes to run commands

This release can be pip installed using

pip install flair-brookslab

Please note that this does not install non-python dependencies (like samtools and bedtools)

• Removed Python-2 support
• Reorganized code into bin (scripts; removed extensions) and src (modules)
• Added readthedocs documentation; updated code calls
• Created files for pip installation

Note: Commands have changed from e.g. python flair.py align to flair align
See readthedocs for details

v1.5.1

State of FLAIR before major code organization reformatting. This version does include the annotation_reliant option to the collapse step that will be the major difference between v1.5 and v2.0.

v1.5

The flair-correct module now requires an additional argument, the genome sequence, to check splice site motifs to determine strand for ambiguous splice junctions. Scripts for plotting differential isoform usage and have also been included. There is also a new module for calling the 4 main alternative splicing event types (A3'SS, A5'SS, IR, SE). We have also worked through various bugs with the help of users.

v1.4

The --stringent collapse option has been added. Temporary files between concurrent runs no longer clash and we have made other bug fixes and improvements.