funannotate v0.5.5

• typo fixes for log file names
• typo fix for fuNOG annotations in secondary metabolism module, this was now fixed to use the proper --eggnog_dboption
• test for dN/dS ratio test to assert that the tree that was drawn by Phyml has the correct number of proteins
• new feature for BUSCO models if --ploidy is greater than 1 in funannotate predict that duplicated BUSCO models are also parsed, the one that is picked has the highest score
• Support for bypassing RepeatModeler/RepeatMasker, you can now enter --masked_genome and --repeatmasker_gff3 options to skip that step. Note that both options are required.

funannotate v0.5.4

• update to tblastn/exonerate protein mapping for better speed and more thorough searches
• added --ploidy option to funannotate predict which controls the max number of hits for tblastn filter to pass to exonerate, which is set at 2 x ploidy. You should likely only increase this if your assembly is more than haploid - so perhaps newer assemblies with nanopore/pacbio may be able to resolve diploid chromosomes. It shouldn't have negative consequences in increase --ploidy, but will increase run time for protein mapping.
• happy holidays...

funannotate v0.5.3

• re-organize output so that temporary folders are created in the "final" resting place and not in the current directory
• modification of the multiprocessing function to include a simple progress percentage output
• bug fixes in funannotate compare and the orthology dN/dS output hanging when the dN/dS calculation failed
• modification to the logging to capture STDERR/STDOUT from many external tools into the log file, hopefully this will result in catching more errors than piping them to os.devnull
• bug fix in funannotate annotate where output folders not being created if the input was GFF, proteins, and fasta.
• made it a requirement to pass --species argument to funannotate annotate if you do not pass in a GenBank file. This is to prevent downstream problems in funannotate compare with how the scripts name the genome/isolates.
• made a FAQ section in the docs that includes how to manually adjust gene models using the included tools
• all internal tests passed, however guaranteed there are more bugs. please let me know when you find them.

funannotate v0.5.2

• update to dN/dS function to have two options: 1) --run_dnds estimate (which runs the M0 model only), and 2) --run_dnds full (which runs M0, M1, M2, M7, M8 and calculates the LTR of M1/M2 and M7/M8).
• update to the multiprocessing progress function - a simple progress meter is used on most multiprocessing functions to let user know how many processes have finished
• bug fix where transcripts and proteins were getting written to same file in funannotate predict
• minor bug fix in funannotate clean where input number of scaffolds was not printed out correctly
• change the default location of DB as per requested by some users, now defaults to $HOME/funannotate. Note you can set this to whatever directory you want.

funannotate 0.5.1

• bug fixes for funannotate compare
• bug fix for funannotate predict during gene model filtering of large genomes occasional parent:child features would get missed
• added feature of calculating dN/dS ratios in funannotate compare

funannotate v0.4.0

• integration of BUSCO2 script and models. Can see the BUSCO2 distribution here, funannotate uses a slightly modified version to be compatible with the BUSCO->EVM workflow.
• BUSCO2 models have changed a bit, there are now a lot more options for various taxonomic groups. Something to keep in mind though is that the model names for dikarya are not the same as pezizomycotina so if you use an --outgroup option be sure that the outgroup was generated with same BUSCO DB
• The funannotate setup script will remove previous BUSCO DB models and download the new ones because of the extensive change in the BUSCO2 structure.
• addition of funannotate outgroups to help you mange the outgroups available to funannotate compare
• the scripts will download and format any of the available BUSCO2 eukaryote models, to see a list in a taxonomic tree format you can type funannotate outgroups --show_buscos

funannotate v0.3.14

• funannotate annotate will now support a single XML file for InterProScan5, you either pass a folder of single XML files 1 per protein, or a single XML file containing all of the annotations to the --iprscan option
• fix in funannotate annotate that did alert user that --email is required if using remote IPR5 search; this is default setting

funannotate v0.3.12

• bug fix for path issue when running EVM; discovered on new install on Mac - not sure why it wasn't found earlier, but resulted in failed EVM run
• some improved logging for EVM module

funannotate v0.3.11

• bug fix for funannotate compare where the genome stats was not printing for all genomes
• goatools changed their headers on the output of the GO enrichment (again), so re-wrote how the data is parsed, hopefully this fix applies to all versions.

funannotate v0.3.10

• explicitly run rmblast/ncbi engine for RepeatMasker to avoid problems if user has default setup as something else, i.e. DFAM. Note you still need to install RepBase Libraries, e.g.

        wget --user name --password pass http://www.girinst.org/server/RepBase/protected/repeatmaskerlibraries/repeatmaskerlibraries-20150807.tar.gz
        tar zxvf repeatmaskerlibraries-20150807.tar.gz -C #{HOMEBREW_PREFIX}/opt/repeatmasker/libexec

        cd #{HOMEBREW_PREFIX}/opt/repeatmasker/libexec
        ./configure <config.txt