• added TransDecoder full-pipeline wrapper as the primary entrypoint for transcript FASTA and genome+GTF workflows
• phase-specific executables are now provided under util/TransDecoder.LongOrfs and util/TransDecoder.Predict
• wrapper now supports automated protein homology searches using NCBI BLAST or DIAMOND via --blast_search_pep
• wrapper now supports integrated Pfam searching via --pfam-search-db

Minor updates to better support Docker-based execution.

Output directory (via --output_dir | -O) can be set by user, but the working directory name will be fixed within the output directory and based on the name of the target transcriptome.

• compatible with hmmsearch or hmmscan output
• cleaner organization of outputs and checkpoints
• TransDecoder.LongOrfs includes option for --complete_orfs_only (as requested)
• GFF3 files no longer have the uri-encoding so easier to directly read.
• misc bugfixes - corrected length in fasta header for start-refined orfs

(and earlier updates from 5.6.0 that apparently never officially released)

• genome propagation of orfs resets orientation for unspliced transcripts with opposite strand orfs.
• speed update from Yanick Paco Hagemeijer
• added option --output_dir | -O to both TransDecoder.LongOrfs and TransDecoder.Predict, as per request, so users can point to specific output directories rather than relying on the default ( basename(target.fasta) + ".transdecoder_dir/").
• removing track name from bed output
• if select single best orf, do selection before removing overlapping preds
• updated get_longest_ORF_per_transcript.pl to match current header formatting
• really retain all blast hits, ignoring overlaps to prev selected entries, unless single_best_orf indicated
• updated genetic code options in help menu

v5.5.0

added option --output_dir | -O to both TransDecoder.LongOrfs and TransDecoder.Predict, as per request, so users can point to specific output directories rather than relying on the default ( basename(target.fasta) + ".transdecoder_dir/").

v5.4.0, Oct 17, 2018

bugfix - earlier version was inadvertently reporting a single best orf per transcript when --single_best_orf was not invoked. Now fixed and behaves as advertised.
Also, less verbose.
Added tests for runmode validation.
Other minor updates

removed the DB_File requirement.

Allow to rerun w/ blast and pfam results and to just reexecute the steps needed to take those data into account.
The test runner now includes a small pfam and blast on-the-fly execution step as well.

Better support for different genetic codes as described here:
https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

Also, shouldn't report UTR records for cases where the coding region starts at a partial codon.

-protein identifiers are more manageable (ex. ${transcript_acc}.p1, .p2, ..., .pn)
-added example for use w/ supertranscripts

the start-adjustment can now cope with sequences containing non-{GATC} characters.