obitools4/Release-notes.md

OBITools release notes

Latest changes

New feature

• In the OBITools language a new gc computes the GC fraction of a sequence.

Enhancement

• A new completely rewritten GO version of the fastq and fasta parser is now used instead of the original C version.
• A new file format guesser is now implemented. This is a first step towards allowing new formats to be managed by OBITools.
• New way of handling header definitions of fasta and fastq formats with JSON headers. The sequence definition is now printed in new files as an attribute of the JSON header named "definition".
• The -D (--delta) option has been added to obipcr. It allows extracting flanking sequences of the barcode.
  • If -D is not set, the output sequence is the barcode itself without the priming sites.
  • If -D is set to 0, the output sequence is the barcode with the priming sites.
  • When -D is set to ### (where ### is an integer), the output sequence is the barcode with the priming sites,
    and ### base pairs of flanking sequences.
• A new output format in JSON is proposed using the --json-output. The sequence file is printed as a JSON vector, where each element is a map corresponding to a sequence. The map has at most four elements:
  • "id" : which is the only mandatory element (string)
  • "sequence" : if sequence data is present in the record (string)
  • "qualities" : if quality data is associated to the record (string)
  • "annotations" : annotations is associated to the record (a map of annotations).

Bugs

• in the obitools language, the composition function now returns a map indexed by lowercase string "a", "c", "g", "t" and "o" for other instead of being indexed by the ASCII codes of the corresponding letters.
• Correction of the reverse-complement operation. Every reverse complement of the DNA sequence follow now the following rules :
  • Nucleotide codes are complemented to their lower complementary base
  • . and - characters are returned without change
  • [ is complemented to ] and oppositely
  • all other characters are complemented as n
• Correction of a bug is the Subsequence method of the BioSequence class, duplicating the quality values. This made obimultiplex to produce fastq files with sequences having quality values duplicated.

Becareful

GO 1.21.0 is out, and it includes new functionalities which are used in the OBITools4 code. If you use the recommanded method for compiling OBITools on your computer, their is no problem, as the script always load the latest GO version. If you rely on you personnal GO install, please think to update.

August 29th, 2023. Release 4.0.5

Bugs

• Patch a bug in the obiseq.BioSequence constructor leading to a error on almost every obitools. The error message indicates : fatal error: sync: unlock of unlocked mutex This bug was introduced in the release 4.0.4

August 27th, 2023. Release 4.0.4

Bugs

• Patch a bug in the install-script for correctly follow download redirection.
• Patch a bug in obitagpcr to consider the renaming of the forward_mismatch and reverse_mismatch tags to forward_error and reverse_error.

Enhancement

• Comparison algorithms in obitag and obirefidx take more advantage of the data structure to limit the number of alignments actually computed. This increase a bit the speed of both the software. obirefidx is nevertheless still too slow compared to my expectation.
• Switch to a parallel version of the gzip library, allowing for high speed compress and decompress operation on files.

New feature

• In every OBITools, writing an empty sequence (sequence of length equal to zero) through an error and stops the execution of the tool, except if the --skip-empty option is set. In that case, the empty sequence is ignored and not printed to the output. When output involved paired sequence the --skip-empty option is ignored.
• In obiannotate adds the --set-identifier option to edit the sequence identifier
• In obitag adds the --save-db option allowing at the end of the run of obitag to save a modified version of the reference database containing the computed index. This allows next time using this partially indexed reference library to accelerate the taxonomic annotations.
• Adding of the function gsub to the expression language for substituting string pattern.

May 2nd, 2023. Release 4.0.3

New features

• Adding of the function contains to the expression language for testing if a map contains a key. It can be used from obibrep to select only sequences occurring in a given sample :

  obigrep -p 'contains(annotations.merged_sample,"15a_F730814")' wolf_new_tag.fasta
  

• Adding of a new command obipcrtag. It tags raw Illumina reads with the identifier of their corresponding sample. The tags added are the same as those added by obimultiplex. The produced forward and reverse files can then be split into different files using the obidistribute command.

  obitagpcr -F library_R1.fastq \
            -R library_R2.fastq \
            -t sample_ngsfilter.txt \
            --out tagged_library.fastq \
            --unidentified not_assigned.fastq
  

  the command produced four files : tagged_library_R1.fastq and tagged_library_R2.fastq containing the assigned reads and not_assigned_R1.fastq and not_assigned_R2.fastq containing the unassignable reads.

  the tagged library files can then be split using obidistribute:

  mkdir pcr_reads
  obidistribute --pattern "pcr_reads/sample_%s_R1.fastq" -c sample tagged_library_R1.fastq
  obidistribute --pattern "pcr_reads/sample_%s_R2.fastq" -c sample tagged_library_R2.fastq
  

• Adding of two options --add-lca-in and --lca-error to obiannotate. These options aim to help during construction of reference database using obipcr. On obipcr output, it is commonly run obiuniq. To merge identical sequences annotated with different taxids, it is now possible to use the following strategie :

  obiuniq -m taxid myrefdb.obipcr.fasta \
  | obiannotate -t taxdump --lca-error 0.05 --add-lca-in taxid \
  > myrefdb.obipcr.unique.fasta
  

  The obiuniq call merge identical sequences keeping track of the diversity of the taxonomic annotations in the merged_taxid slot, while obiannotate loads a NCBI taxdump and computes the lowest common ancestor of the taxids represented in merged_taxid. By specifying --lca-error 0.05, we indicate that we allow for at most 5% of the taxids disagreeing with the computed LCA. The computed LCA is stored in the slot specified as a parameter of the option --add-lca-in. Scientific name and actual error rate corresponding to the estimated LCA are also stored in the sequence annotation.

Enhancement

• Rename the forward_mismatches and reverse_mismatches from instanced by obimutiplex into forward_error and reverse_error to be coherent with the tags instanced by obipcr

Corrected bugs

• Correction of a bug in memory management and Slice recycling.
• Correction of the --fragmented option help and logging information
• Correction of a bug in obiconsensus leading into the deletion of a base close to the beginning of the consensus sequence.

March 31th, 2023. Release 4.0.2

Compiler change

OBItools4 requires now GO 1.20 to compile.

New features

• Add the possibility for looking pattern with indels. This has been added to obimultiplex through the --with-indels option.
• Every obitools command has a --pprof option making the command publishing a profiling web site available at the address : http://localhost:8080/debug/pprof/
• A new obiconsensus command has been added. It is a prototype. It aims to build a consensus sequence from a set of reads. The consensus is estimated for all the sequences contained in the input file. If several input files, or a directory name are provided the result contains a consensus per file. The id of the sequence is the name of the input file depleted of its directory name and of all its extensions.
• In obipcr an experimental option --fragmented allows for spliting very long query sequences into shorter fragments with an overlap between the two contiguous fragment insuring that no amplicons are missed despite the split. As a site effect some amplicon can be identified twice.
• In obipcr the -L option is now mandatory.

Enhancement

• Add support for IUPAC DNA code into the DNA sequence LCS computation and an end free gap mode. This impact obitag and obimultiplex in the --with-indels mode.
• Print the synopsis of the command when an error is done by the user at typing the command
• Reduced the memory copy and allocation during the sequence creation.

Corrected bugs

• Better management of non-existing files. The produced error message is not yet perfectly clear.
• Patch a bug leading with some programs to crash because of : "empty batch pushed on the channel"
• Patch a bug when directory names are used as input data name preventing the system to actually analyze the collected files.
• Make the --help or -h options working when mandatory options are declared
• In obimultiplex correct a bug leading to a wrong report of the count of reverse mismatch for sequences in reverse direction.
• In obimultiplex correct a bug when not enough space exist between the extremities of the sequence and the primer matches to fit the sample identification tag
• In obipcr correction of bug leading to miss some amplicons when several amplicons are present on the same large sequence.

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.

February 18th, 2023. Release 4.0.0

It is the first version of the OBITools version 4. I decided to tag then following two weeks of intensive data analysis with them allowing to discover many small bugs present in the previous non-official version. Obviously other bugs are certainly persent in the code, and you are welcome to use the git ticket system to mention them. But they seems to produce now reliable results.

Corrected bugs

• On some computers the end of the output file was lost, leading to the loose of sequences and to the production of incorrect file because of the last sequence record, sometime truncated in its middle. This was only occurring when more than a single CPU was used. It was affecting every obitools.
• The obiparing software had a bug in the right aligment procedure. This led to the non alignment of very sort barcode during the paring of the forward and reverse reads.
• The obipairing tools had a non deterministic comportment when aligning a paor very low quality reads. This induced that the result of the same low quality read pair was not the same from run to run.

New features

• Adding of a --compress|-Z option to every obitools allowing to produce gz compressed output. OBITools were already able to deal with gziped input files transparently. They can now produce their results in the same format.
• Adding of a --append|-A option to the obidistribute tool. It allows to append the result of an obidistribute execution to preexisting files.
• Adding of a --directory|-d option to the obidistribute tool. It allows to declare a secondary classification key over the one defined by the '--category|-c` option. This extra key leads to produce directories in which files produced according to the primary criterion are stored.
• Adding of the functions subspc, printf, int, numeric, and bool to the expression language.