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DRAM v1.3

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@shafferm shafferm released this 06 Jan 22:11
· 217 commits to master since this release

DRAM v1.3 change log

  • Add --amg_database_loc parameter that was missing in DRAM-setup.py
  • Shift DRAM download of UniRef from FTP to HTTP address to address firewall issues
  • Rename of headers in annotations.tsv files to be more uniform across databases
  • By default DRAM.py annotate now does not annotated with VOGDB by default, flag added to use VOGDB
  • By default don't split DRAM-v.py annotate input contigs into separate files because HMMER doesn't care for E-values
  • Users can now pass multiple --input_fasta arguments to DRAM.py annotate and DRAM-v.py annotate
  • Now DRAM makes sure bin names (pulled from file names) are unique and not full paths
  • Update pandas methods to get rid of warnings and increase speed
  • When annotating with KEGG Genes the KEGG Genes IDs are stored in the annotations.tsv in addition to the KO IDs
  • Complete rewrite of how HMM annotation is handled inside DRAM to reduce redundancy and allow...
  • Users can now annotate using custom HMM sets which may include custom bitScore cutoffs
  • Complete rewrite of database handling from setup through annotation, in the future this will allow more flexible configuration
  • Change CI to CircleCI from travis
  • DRAM strainer and gene neighborhood pulling can now both use custom distillate information