DRAM v1.3

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