GitLab

March 7th, 2023. Release 4.0.1

Corrected bugs

• Makes progress bar updating at most 10 times per second.
• Makes the command exiting on error if undefined options are used.

Enhancement

• OBITools are automatically processing all the sequences files contained in a directory and its sub-directory
  recursively if its name is provided as input. To process easily Genbank files, the corresponding filename extensions have been added. Today the following extensions are recognized as sequence files : .fasta, .fastq, .seq, .gb, .dat, and .ecopcr. The corresponding gziped version are also recognized (e.g. .fasta.gz)

New features

• Takes into account the OBIMAXCPU environmental variable to limit the number of CPU cores used by OBITools in bash the below command will limit to 4 cores the usage of OBITools

  export OBICPUMAX=4

• Adds a new option --out|-o allowing to specify the name of an outpout file.

  obiconvert -o xyz.fasta xxx.fastq

  is thus equivalent to

  obiconvert  xxx.fastq > xyz.fasta

  That option is actually mainly useful for dealing with paired reads sequence files.

• Some OBITools (now obigrep and obiconvert) are capable of using paired read files. Options have been added for this (--paired-with FILENAME, and --paired-mode forward|reverse|and|andnot|xor). This, in combination with the --out option shown above, ensures that the two matched files remain consistent when processed.

• Adding of the function ifelse to the expression language for computing conditionnal values.

• Adding two function to the expression language related to sequence conposition : composition and gcskew. Both are taking a sequence as single argument.