- In `obimatrix` a **--transpose** option allows to transpose the produced matrix table in CSV format.
- In `obitpairing` and `obipcrtag` two new options **--exact-mode** and **--fast-absolute** to control the heuristic used in the alignment procedure. **--exact-mode** allows for disconnecting the heuristic and run the exact algorithm at the cost of a speed. **--fast-absolute** change the scoring schema of the heuristic.
- For efficiency purposes, now the `obiuniq` command run on disk by default. Consequently, the **--on-disk** option has been replaced by **--in-memory** to ask explicitly to use memory.
- In the OBITools language a new `gc` computes the GC fraction of a sequence.
- First version of the `obisummary` command. It produces summary statistics of the sequence file provided as input. The statistics includes, the number of reads, of variants, the total length of the DNA sequences (equivalent to `obicount`), some summaries about tags used in the sequence annotations and their frequencies of usage.
- First version of the `obimatrix` command. It allows producing OTU tables from sequence files in CSV format.
- The `obicsv` command has now a **--auto** option, that extract automatically the attributes present in a file for inspecting the beginning of the sequence file. Only attributes that do not correspond to map are reported. To extract information from map attributes, see the `obimatrix` command.
- 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". That's facilitates the writing of parsers for the sequence headers.
- 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).
- 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.
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.
- 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
- 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.
- 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.
- 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 :
- 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.
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.
- 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 :
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.
- 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`
- 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.
- 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.
- 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.
-*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`)
- 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
``` bash
export OBICPUMAX=4
```
- Adds a new option --out\|-o allowing to specify the name of an outpout file.
- 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 two function to the expression language related to sequence conposition : `composition` and `gcskew`. Both are taking a sequence as single argument.
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.
- 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.
- 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.
