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Release v2.0.5
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@Cantalapiedra Cantalapiedra released this 02 Feb 18:30
· 390 commits to master since this release
2.0.5
ca6fc0e

This is the first release for the merge of the refactor version into master.

  • All code migrated to Python 3. Therefore, python3 is now required to run eggnog-mapper scripts.
  • HMMER search capabilities moved to new scripts: '''''hmm_search.py''''', '''''hmm_server.py''''', '''''hmm_worker.py'''''.
  • Changes in output format, specially the "annotations" output file.
  • Changes in available parameters and behaviour of existing ones.
  • Added some integration and unit tests
  • New ''--tax_scope'' modes.
  • Added eggNOG DB version to ''-v, --version'' options.
  • New eggnog DB version 5.0.1 including PFAM annotations and PFAM HMMs.
  • Added expected eggNOG DB version, and warning if found version is different than expected one.
  • Added PFAM annotations, which are directly transferred from orthologs.
  • Added ''--pfam transfer'' option to ''emapper.py''.
  • Gene prediction step using Prodigal.
  • Search and annotation of ORFs using diamond blastx or MMseqs2. This can be used to annotate ORFs of contigs without using Prodigal.
  • MMseqs2 support for the search step of eggNOG-mapper.
  • Parameters to allow users to control sensitivity of diamond/MMseqs2 searches.
  • Improved report of orthologs.
  • NCBITaxa support is now included in eggNOG-mapper without relying on ete3.
  • ''--md5'' option, which can be used to add the md5 hash of the query as a new column in the annotations output file.
  • ''-m cache'' mode and ''-c FILE'' options, to annotate using an annotations file with md5 hashes as cached results. A fasta file with unannotated sequences is output also, which can be used in a subsequent conventional emapper annotation run.
  • "Bottom-top" orthology search if no proper orthologs are retrieved from a priori chosen best OG.
  • ''--go_evidence all'' option to report all GO terms.
  • ''--dbmem'' option to pre-load the ''eggnog.db'' sqlite3 DB into memory.
  • if --translate option is used (along with --itype CDS), input sequences will be translated to proteins before searching with either diamond "blastp", mmseqs "blastp" or hmmer. If --itype CDS is used without --translate, it will raise error for hmmer, but it will run diamond or mmseqs in "blastx" modes.
  • Bug fix when running hmmer with only-numerical identifiers in input sequences
  • Other minor changes
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