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OBITools4
Release_4.2.0
Eric Coissac's avatar
Eric Coissac
@coissac
7fc5292a · Make obiconsensus using the count of the sequences · 
Release 4.2.0

April 2nd, 2024. Release 4.2.0

New feature

  • A new OBITools named obiscript allows to process each sequence according to a Lua script. This is an experimental tool. The --template option allows for generating an example script on the stdout.

API Changes

  • Two of the main class obiseq.SeqWorker and obiseq.SeqWorker have their declaration changed. Both now return two values a obiseq.BioSequenceSlice and an error. This allow a worker to return potentially several sequences as the result of the processing of a single sequence, or zero, which is equivalent to filter out the input sequence.

Enhancement

  • In obitag if the reference database contains sequences annotated by taxid not referenced in the taxonomy, the corresponding sequences are discarded from the reference database and a warning indicating the sequence id and the wrong taxid is emitted.
  • The bug corrected in the parsing of EMBL and Genbank files as implemented in version 4.1.2 of OBITools4, potentially induced some reduction in the performance of the parsing. This should have been now fixed.
  • In the same idea, parsing of genbank and EMBL files were reading and storing in memory not only the sequence but also the annotations (features table). Up to now none of the OBITools are using this information, but with large complete genomes, it is occupying a lot of memory. To reduce this impact, the new version of the parser doesn't any more store in memory the annotations by default.
  • Add a --taxonomic-path to obiannotate. The option adds a taxonomic_path tag to sequences describing the taxonomic classification of the sequence according to its taxid. The path is a string. Each level of the path is delimited by a | character. A level consists of three parts separated by a @. The first part is the taxid, the second the scientific name and the last the taxonomic rank. The first level described is always the root of the taxonomy. The latest corresponds to the taxid of the sequence. If a sequence is not annotated by a taxid, as usual the sequence is assumed having the taxid 1 (the root of the taxonomy).

Bug fixes

  • Fix a bug in the parsing of the JSON header of FASTA and FASTQ files occurring when a string includes a curly brace.
  • Fix a bug in the function looking for the closest match in obitag. This error led to some wrong taxonomic assignment.