funannotate v1.8.17

Bug fix release.

• fix FASTA splitter in iprscan local 83ceee5
• pin docker and pip installs to biopython<1.80; so we try to avoid any of the other deprecated or breaking code
• update to support EVM v1 or v2; back-port training data from funannotate2 (for testing)
• run signalp6 if in PATH
• fix pandas compatibility >v2
• add config-window parameter to protein2genome script

funannotate v1.8.15

Bug fix release

• Trying hard to support augustus v3.5
• fix sorting by length #896
• update dbCAN Cazyme filtering #890
• fixes for parsing eggnog mapper #868 #892
• signalp6 fixes #822
• and many others

funannotate v1.8.13

Bug fix release

• fix to internal BUSCO code to support Augustus v3.4 #742 @IanDMedeiros
• several fixes to funannotate update #727 #740
• several patches to Docker build

funannotate v1.8.11

Bug fix release

• support for signalp v6 parsing #650 #716
• improve protein2genome performance #652 #654
• add --tmpdir options to most scripts (defaults to /tmp), ie use if have access to SSD to improve speed
• upgrade eggnog-mapper to newer version, use in memory if enough is available to improve speed
• fix version check #655
• fix for abnormal contig identifiers #672
• fix for EVM contig memory parsing #646
• add -m,--mito-pass-thru to funannotate annotate to add back mitochondrial genome, mitochondrial contigs should be removed prior to running funannotate as uses different genetic code
• antismash6 support #692
• update download urls to https from ftp
• fix for EVM if last line of GFF3 is blank #709
• simplify runSuprocess functions #707 #710 @mglubber
• move temporary files for check for soft masking to output folder #722
• conda augustus is apparently broken, fix in docker#722 #724, so need to install augustus a different way (ie apt-get on Debian)
• add missing help menu options #714
• fix for funannotate update compare annotations function #727
• add --ml_model to funannotate compare to control ML model selection in iqtree, default is to run modelfinder which is very slow.

funannotate v1.8.9

• fix for EvidenceModeler partitioning -- on rare cases genes/contigs were not getting partitioned correctly
• fix logic for PASA training of glimmer/snap #591
• fix logic for pre-trained datasets in funannotate predict #597
• re-organize tbl2asn and provide single threaded backup if failure #599 and fix log error #621
• remove perl script generating AGP file --> now python. which removes bioperl as dependency #617
• fix cds-transcripts coordinates (not used for any other processing) but on partial transcripts they were incorrect #614
• fix bug in EVM filtering if no genes to remove #620
• update eggnog parser to support versions >2.1.2 #566
• fix tmpdir error in funannotate clean #594
• python2 is no longer supported.

funannotate v1.8.7

Bug fix release

• bug fix for eggnog mapper v2 parsing, occasionally some records have more than 1 OG in the "best_OG" field -- this is probably a bug in emapper.py, but funannotate will now ignore those entries as there is no way to tell which is actually the best OG.
• make fasta2agp accept more IUPAC characters #532
• fix for diamond >v2.0.8 (yet another change in the database info format resulted in error).
• remove support for python 2

funannotate v1.8.5

Bug fix release, recommended for all users.

• use uuid unique identifier for tmp file names (previous uses process id)
• fix diamond command in mapping proteins to genome #529
• add some contig name checking for inputs to predict -- some users erroneously pass GFF3 files that reference transcripts or some other assembly, warn user #528
• add support for antiSMASH v6 #531 #539
• check genome for IUPAC errors #532
• re-write long reads mapping to trinity transcripts #539
• allow for fewer busco models for training #556
• expose some EVM parameters to predict #558
• modify EVM partitioning -- some gene models close to partition were not being called correctly #558.
• support newly released eggnog-mapper >= v2.0.5 #566, note that v2.x - 2.0.4 will not be supported as the output is broken in the sense that it is impossible to parse the proper EggNog reference ID. If you are using any eggnog results from this code, strongly advised to re-run with new release.
• add _pasa to PASA database names #398. Note -- this change could potentially cause pre-existing databases run with older funannotate code to not be recognized properly after v1.8.5.

funannotate v1.8.3

Bug fix release

• remove auto fix for RNA-seq data if it does not have Trinity compatible headers -- warn user to fix instead #485
• fix antiSMASH v5 parsing #490, update secmet GBK format of clusters
• add funannotate util gff-rename script
• use natsort for sorting contigs/names so gene names are correctly auto incremented #501
• fix for signalp v5 #494
• support fasta headers with spaces for clean #504
• rstrip(*) from proteins if GFF/FASTA passed; #508
• expose --p2g_prefilter to use tblastn for mapping protein evidence #495
• add --anysymbol to mafft calls #514
• use frameshift diamond if >2.0.5 #503
• improve glimmerhmm parsing error report #519
• add --no-progress option to clean up terminal output (ie log files from cluster)
• use sorted bedtools intersection to reduce memory usage #522
• add --trnascan option to predict #523

funannotate v1.8.1

• highly recommend all users upgrade
• Code now python 2/3 compatible (only 9 months late....)
• EVM now uses interlap for slicing input files, significant speed increase for larger genomes
• if --organism other is passed, codingquarry is now disabled by default -- you can turn it on by specifying a valid weight, ie --weights codingquarry:2
• support for signalp version 5
• move resources to JSON download via GitHub, will allow for updating/changing resources without re-installing a new version of funannotate
• several fixes for more robust GFF3 parsing
• fix for cazyme assignments where results were duplicated; also upgraded to database version 8
• fix bug where PASA results not properly passed to EVM if funannotate predict was re-run
• many other bug fixes

funannotate v1.7.4

Okay, so apparently I lied about bug fixes before py3 release. Here are some quick ones.

Also -- some users have said that conda recipe fails to find a solution, with the help of @reslp this is perhaps caused by ete3 package as a dependency. Since ete3 is only used in funannotate for the dN/dS calculation in funannotate compare, I'm going to remove it from conda recipe as a dependency. Users that would like to continue using the dN/dS function in compare will need to manually install ete3 (ie conda could work on your system or pip, etc).

• update the log file copy/remove in funannotate annotate which causes a problem in singularity container
• encoding bug fixes for some PFAM results
• fix for funannotate iprscan which was not correctly combining XML files with newer versions of Interproscan.