funannotate v1.4.1

• bug fix for funannotate predict during parsing the soft masked genome -- for large genomes this was slow and used too much memory. it is now multithreaded and has lower memory footprint. #197
• bug fix for ncRNA models are now listed as full length, should no longer cause NCBI errors #195
• support multiple inputs to --other_gff #191
• make augustus use --softmasking=1 option
• default value for --soft_mask is now set to 2 kb 2000
• output fasta files are now wrapped at 80 characters
• tbl2asn is now multithreaded on large genomes or those with more than 10000 contigs
• several updates to parsing of GenBank files to deal with unexpected formatting #196

funannotate v1.4.0

• support for long-read RNA-seq data: funannotate train and funannotate update can take PacBio isoSeq (--pacbio_isoseq), Nanopore cDNA reads (--nanopore_cdna), and Nanopore direct mRNA (--nanopore_mrna).
• fix for important bug in transcript alignments in funannotate predict -- bug in previous versions related to multi-exon crick alignments not getting correctly parsed into GFF3 alignments
• soft masking is now decoupled from funannotate predict, this is now done with funannotate mask. Reason for this switch is to allow more flexibility in how the assembly is soft masked -- this can be done externally with another program. This change will allow users that don't have access to RepBase to use an alternative from RepeatMasker/RepeatModeler. One alternative is RED -- I wrote a wrapper for called RedMask
• funannotate predict can now run without GeneMark being installed -- again to accommodate users that may be unable to use GeneMark due to licensing. Note you can pass gene predictions from any external program to --other_gff and they will be handed off to Evidence Modeler.
• spaces in either strain or isolate name will be stripped #180
• default program for funannotate clean changed to minimap2 #176
• fix errors in partial gene models derived from using EVM script to generate proteins, this is now done internally using exact coordinates #184
• added --soft_mask option to funannotate predict which will control the option with same name in GeneMark, i.e. default is --soft_mask 5000 which means that repeat regions less than 5 kb will be ignored for GeneMark prediction, those greater than 5 kb will be fed to Genemark. #185
• bug fixes for tbl file generation. all tRNA models will be partial #184
• improvement to how data from funannotate train is used in prediction steps
• Slight changes for clarity to funannotate predict flags for evidence alignments:

--protein_evidence       Proteins to map to genome (prot1.fa prot2.fa uniprot.fa). Default: uniprot.fa
--protein_alignments     Pre-computed exonerate protein alignments (see docs for format)
--transcript_evidence    mRNA/ESTs to align to genome (trans1.fa ests.fa trinity.fa). Default: none
--transcript_alignments  Pre-computed transcript alignments in GFF3 format

• added funannotate util bam2gff3 script to convert coordsorted RNA-seq BAM alignments to GFF3 compatible alignment file.
• fix bug for input of files+weight in funannotate predict -- script would get hung up if you passed --other_gff snap_alignemnts.gff3:5 #191
• allow for non-standard LocusTags - will now split on last underscore #191

funannotate v1.3.4

• bug fixes for sec met cluster output files and corresponding MiBIG cluster mapping
• add tRNAscan-SE to funannotate check and predict
• update menu with some params that were missing

funannotate v1.3.3

• bug fix for funannotate compare where GO enrichment not being run in parallel from last update
• use diamond blastp search for ortholog detection --> speed increased.
• don't run seqclean if file present
• update docker release to newest version of funannotate as well as newest version of Trinity, PASA

funannotate v1.3.2

• added several utility scripts --> accessible by funannotate util submenu. This includes funannotate util compare which will compare multiple annotations to a reference.

$ funannotate util

Usage:       funannotate util <arguments>
version:     1.3.2
    
Commands:    compare        Compare annotations to reference (GFF3 or GBK annotations)
             tbl2gbk        Convert TBL format to GenBank format
             gbk2parts      Convert GBK file to individual components
             gff2proteins   Convert GFF3 + FASTA files to protein FASTA
             gff2tbl        Convert GFF3 format to NCBI annotation table (tbl) 

• bug fix for funannotate remote moving logfile
• bug fix for mapping proteins to genome where tmp folder wasn't being properly removed
• run GO enrichment in parallel in funannotate compare
• update colors in some graphs from funannotate compare to 24-pack Crayola colors
• add option to use iqtree to draw ML phylogeny in funannotate compare
• bug fix for funannotate database command where it was not displaying table correctly.

funannotate v1.3.1

• bug fix for funannotate setup added missing shutil library import

funannotate v1.3.0

• bug fix for weights being set for Augustus HiQ models in funannotate predict
• bug fix for download_buscos function
• bug fix for funannotate annotate where tbl file was occasionally not being parsed correctly --> re-write of parsing function
• fix bug in antiSMASH/MiBIG parsing
• add method to try to recover from failed GeneMark run
• several bug fixes for funannotate update related to UTRs and multiple transcripts per locus.
• added missing dependencies to funannotate check
• updated code to work with PASA > v2.3 - this is important PASA update that allows SQLite usage instead of MySQL
• improved terminal log output to tell user which files (with locations) are being re-used if they are found.

funannotate v1.2.0

• v1.2.0 now supports multiple transcripts per gene locus. The funannotate pipeline will only generate multiple transcripts per locus if given evidence in the form of RNA-seq data, this is done in the funannotate update command. It should also now support input with multiple transcripts as well.
• move installation of busco models to funannotate setup
• added annotation edit distance (AED) to funannotate update to record the changes in annotation. As well the PASA annotation update text file is changed to incorporate these changes as well
• accessory script util/compare2annotations.py can compare multiple annotations in either GFF3 or GBK format to a reference, generating summary stats as well as individual gene stats (AED per mRNA and CDS)
• added a --drop option to funannotate fix that you can remove unwanted gene model annotations, to use pass a file containing locus_tag (1 per line) to the --drop parameter
• fix bug in finding high-quality Augustus predictions (HiQ) models in funannotate predict
• funannotate predict will now detect if a training folder exists in output directory, if it does it will find the correct PASA, BAM, and Trinity output and use automatically during the prediction step.

funannotate v1.1.1

• fix for braker to work on docker. For some reason (I don't know why) the symlinks that braker tries to create cause an error when run on docker. The error references too many levels of symlinks essentially. To circumvent this, I modified braker.pl code to copy instead of symlink. Also fixed the braker.pl --version option which was broke in most recent release.
• Note for a "normal" system, v1.1.0 should work fine. The updated braker code was run on both docker and Mac native and runs fine on those, hopefully also working well on linux.

funannotate v1.1.0

• bumping version to 1.1.0 to highlight that v1.0.X versions have a bug in the tbl annotation file and will not pass GenBank specs. This was derived from dropping GAG from funannotate I had the tbl spec wrong for adding transcript_id and protein_id to both CDS and mRNA features.
• fixes for funannotate update and properly filtering overlapping genes
• fix for funannotate annotate that was switching the 5' and 3' partial gene designations on crick orientated gene models, causing them to look correct after predict step and then become errors after annotate step
• added Braker 2.0.3 to funannotate.... this was necessary as braker.pl --version doesn't display the version number so I can't enforce a version requirement. The larger issue has to do with how the different versions of braker save the output data, there are at least 3 different behaviors in the last 4 or 5 versions which makes impossible for funannotate to determine where output will be.