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OBITools3
Last edited by Celine Mercier
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Updating and release notes

Current version: 3.0.1b26

You can check the version installed by running obi --version

How to update with pip:

From the OBITools3 virtual environment, run:

pip3 install --pre --upgrade OBITools3

How to update with git:

From the OBITools3 installation directory and virtual environment, run:

git pull
python3 setup.py install

Release notes:

  • 3.0.1b26:
    • obi export: columns are now in alphabetical order when exporting to tab format
    • Fixed stdout output
    • Taxonomy: fixed an issue related to StopIteration behaviour in new versions of python

  • 3.0.1b25:
    • obi import: fixed bug caused by new behaviour of StopIteration exceptions in Python>=3.7

  • 3.0.1b24:
    • ngsfilter and ecopcr: now check for primers too long for apat library to handle (31bp max)

  • 3.0.1b22:
    • obi rm: now removes column files and AVL files that are not used by other views, effectively freeing disk space.

  • 3.0.1b21:
    • New command: obi taxonomy to add local taxa
    • import: now automatically renames scientific_name tag to SCIENTIFIC_NAME, and suggests using --input-na-string when a sequence import fails
    • head: added output format options

  • 3.0.1b20:
    • alignpairedend and ngsfilter: ids of original sequences are now kept in the tags

  • 3.0.1b19:
    • import: made ngsfilter file parsing more resilient

  • 3.0.1b18:
    • import: added import of SINTAX format

  • 3.0.1b17:
    • import: added import of UNITE fasta format

  • 3.0.1b16:
    • annotate: fixed a bug where a column type could be wrongly guessed

  • 3.0.1b15:
    • split: new command

  • 3.0.1b14:
    • export: added options to export to metabaR compatible format
    • Various minor fixes and improvements

  • 3.0.1b13:
    • import: more lenient handling of white spaces for genbank files

  • 3.0.1b12:
    • ecopcr: now accepting taxonomy from a different DMS than the reference sequences
    • Various minor fixes and improvements

  • 3.0.1b11:
    • export: integer missing values now imported as '0' for tabular format ; header now printed by default for tabular format ; and added option to only export specific keys/columns
    • Various minor fixes and improvements

  • 3.0.1b10:
    • import: fixed a parsing issue with some GenBank files

  • 3.0.1b9:
    • import: now imports and adds NCBI taxids for SILVA and RDP training set fasta files
    • various minor fixes and improvements

  • 3.0.1b8:
    • ecotag: 'BEST_MATCH_TAXIDS' now dereplicated (no repeated taxids in the list)

  • 3.0.1b7:
    • alignpairedend: fixed bug that would cut out sequence ends when it should not have

  • 3.0.1b6:
    • Now handling large int values (import rewrites column in OBI_FLOAT if a value is > INT32_MAX)
    • Fixed a bug where some taxids could not be retrieved
    • import/export: fixed issue where the '\t' separator option was not read properly
    • stats: improved the tabular display to be properly read by R

  • 3.0.1b5:
    • obi rm: new command to delete any view (for now the user deleting a view accepts that there will be missing information when running obi history if other views descend from the deleted view)

  • 3.0.1b4:

    • ngsfilter: fixed critical bug where barcodes shorter than the forward primer would be missed
    • import: fixed the import of tabular files with no header

  • 3.0.1b3:

    • uniq: now OK to use -m option even if only one unique key in information to merge (e.g. one sample)

  • 3.0.1b2:
    • Made the OBITools3 more 'empty file friendly'

  • 3.0.1b1:
    • The OBITools3 now work on the Windows Subsystem for Linux

  • 3.0.0b43:
    • Dictionaries with one key are now handled

  • 3.0.0b42:

    • import: improved Genbank file parser

  • 3.0.0b41:

    • less: fixed an issue when trying to display 'tabular data' such as ngsfilter files

  • 3.0.0b40:

    • Fixed compilation issue with latest versions of gcc

  • 3.0.0b39:

    • export: fixed a bug where exporting to tab format with a header would not export the first line of data

  • 3.0.0b38:

    • grep: fixed --id-list option

  • 3.0.0b37:

    • import: can now import SILVA fasta files, and now handling sequences with Uracil (U) nucleotides (by converting them to Thymine (T) for now)

    • addtaxids: new command to annotate sequences with their NCBI taxid based on their taxon name

  • 3.0.0b36:

    • ls: reworked a bit (mostly just now done in C instead of Cython)

  • 3.0.0b35:

    • ecotag: added separate threshold for minimum circle identity (sequence is assigned to the LCA of all sequences within a similarity circle of the best matches; the threshold for this circle is the highest value between the chosen minimum circle identity and the best assignment score found for the query sequence)

  • 3.0.0b34:

    • cat: fixed open file descriptor leak

  • 3.0.0b33:

    • cat: fixed a bug introduced in 3.0.0b28 (KeyError: 'noprogressbar')

  • 3.0.0b32:

    • export: now automatically sorts dictionary keys alphabetically for tab/csv output
    • various small bug fixes and improvements

  • 3.0.0b31:

    • export: fixed a bug introduced in version v3.0.0b28
    • ls: added more information about view creation date and OBITools3 version

  • 3.0.0b30: alignpairedend: fixed division by 0 error introduced in version v3.0.0b28

  • 3.0.0b29:

    • import: added --space-priority option to prioritize saving space over time when importing a view with a line selection associated
    • fixed and improved the associated column system

  • 3.0.0b28:

    • all commands: now handle output to standard output (use - as output URI)
    • ngsfilter: unidentified sequences are now kept untrimmed
    • alignpairedend: improved/fixed the output tags for the alignment score and lengths
    • grep: now prints the number of entries grepped

  • 3.0.0b27:

    • uniq: fixed a bug where some sequences were not properly dereplicated
    • clean: fixed the behaviour when no or bad sample information is given

  • 3.0.0b26:

    • export: dictionaries are now formatted as they were in the original OBITools, and fixed tuple formatting
    • ngsfilter: reversed tag is now set to 'False' instead of 'None' when false.

  • 3.0.0b25:

    • ls: fixed an issue with big DMS
    • ngsfilter: made one of the tag error messages more accurate ('No tags found' changed to 'No sample with that tag combination')
    • grep and uniq now output empty views when the input is an empty view

  • 3.0.0b24:

    • Improved ecotag output with list of taxids of best matches
    • Improved uniq progress bar
    • Fixed bash history display for views
    • Fixed bugs with the output of sequences unaligned ('joined') by alignpairedend
    • Fixed a bug where tuple columns would 'lose' their indexer in some cases

  • 3.0.0b23: Fixed installation on Ubuntu without pip (problem introduced in 3.0.0b20).

  • 3.0.0b22: Fixed a bug when skipping unreadable sequences in obi import.

  • 3.0.0b21: Improved import of Genbank seq files.

  • 3.0.0b20: Reworked the installation (and version formatting) to work with pip, and made obi import work with seq Genbank extension (+ other minor import fixes).

  • 3.0.0-beta17: Fixed a bug in obi import stopping the program when the last line of a fasta file contained a single nucleotide.

  • 3.0.0-beta16: Fixed the import and dereplication of old obitools files containing premerged informations, and other minor improvements.

  • 3.0.0-beta15: Various fixes and improvements, including notable bugs in ecotag and build_ref_db that made ecotag less specific than it should have been.

  • 3.0.0-beta14:

    • Fixed a memory bug when importing a taxdump and building the list of merged taxids
    • Improved disk space management when filling columns

  • 3.0.0-beta13:

    • obi import: fixed a critical bug where the last entry of embl and genbank files was not imported.

    • ecopcr now prints a warning instead of stopping when not finding a taxid.

    • Various other small bug fixes, and improvements in documentation, error messages and checks.

  • 3.0.0-beta11: Fixed a bug in obi cat when concatenating views with columns having different key sets, and a bug in obi ecotag generating badly formatted column comments.

  • 3.0.0-beta10: obi import: new option --preread to do a first readthrough of the dataset if it contains huge dictionaries for a much faster import.

  • 3.0.0-beta9: Better disk space management when importing files (rewritten columns are deleted).

  • 3.0.0-beta8: Fixed a bug when importing a file where the first entry would contain a dictionary with a single key.

  • 3.0.0-beta7: Added the 'obi' prefix in the bash history commands, and fixed a compilation issue with some versions of gcc.

  • 3.0.0-beta6: New command: obi cat to concatenate views, and various inconsequential fixes.

  • 3.0.0-beta5: Fixed a bug in ngsfilter when there is only one tag.

  • 3.0.0-beta4: Fixed and improved the options to keep nucleotides around the amplicon in ecopcr.

  • 3.0.0-beta3: Fixed bugs in ngsfilter when cutting sequences, and a few minor bugs.