12. Whats' new, what has changedΒΆ

Revision 0.4.3

24 Aug 2019

  • Fix version in the setup which did not match the releas

  • Remove deprecated warning

  • Fix syntax error in embl.py module

Revision 0.4.2

21 Aug 2019

Revision 0.4.1

12th Aug 2019

  • BUG FIXES:

    • nexus2fasta fix bug #235

Revisin 0.4.0

(Aug 2019)

  • NEW:
    • 1-to-many and many-to-1 converters are now part of the API (Sulyvan Dollin)

    • Complete documentation with formats and bibliography

    • Validation of all currently implemented converters

    • New layout for the output graph

  • NEW converters:
    • cram2fasta

    • fasta2faa

  • CHANGES:
    • cram2sam, bam2cram and related cram files have now a --reference option.

    • removed fastq2bam and fasta2bed (no clear output format)

  • BUG FXIES:
    • closed all bugs not related to new converters implementation (up to #234)

Revision 0.3.1

(May/June 2019)

  • NEW converters:
    • bigbed2bed based on pyBigWig

    • abi2qual

  • NEW methods:
    • new method in bigwig2bedgraph based on pyBigWig

    • new method in twobit2fasta based on py2bit

  • NEW features:
    • new module io/sniffer.py

  • NEW bioconvert behaviour:
    • bioconvert --threads option added

    • bioconvert --extra-arguments option added

  • CHANGES:
    • rename the ggf3gff2 converter correctly into gff32gff2 and add test

    • fastq2fasta: (i) remove quality-file option to export qual (ii) remove method python_external (issues #215)

    • bam2bedgraph changes: now also reports 0-coverage bases.

    • bioconvert has now a --level option (same as --verbosity)

    • bioconvert -c/--methods is now set to -m/--methods and

  • OTHERS:
    • update setup.py to include all scripts in ./misc package (#214)

    • More features in bioconvert_stats standalone

    • update the singularity recipes for v 0.3.0

    • update bioconda recipes (on bioconda-recipes)

    • Fix https://github.com/bioconvert/bioconvert/issues/204

    • add pytest-env plugin in the developer requirements

    • mv utils/ modules into new directory ./io

  • BUG FIXES:
Revision 0.3.0

April/May 2019

  • refactoring of the core including the implementation of an implicit conversion. So, we can use bioconvert without specifying the conversion when there is no ambiguity (based on the extensions provided).

  • New working version for pypi.

  • new converters: wig2bed

  • new methods in various converters related to phylogeny

  • Fixing the goalign and gotree scripts

  • Fixing all tests on Travis

Revision 0.2.0

7 Aug 2018

  • remove pandoc from requirements. The version installed is the one from conda. However, conda version is a standalone only, not the code source so, using it in the requirements causes trouble on bioconda when building bioconvert. We do not use pandoc in the code for now, so let us remove it.

  • added tests for gff22gff3; moved test data sets related to GFF2 and GFF3.

Revision 0.1.3

2nd Aug 2018

  • add abi2fastq

  • add abi2fasta

  • add script called bioconvert_stats

  • refactorise scf2fasta and sc2fastq putting common code in utils.scf

  • update go version in requirements + update of modules using go

Revision 0.1.1
  • add phylip2xmfa and xmfa2phylip,

  • add bedgraph2bed

  • Fixed #132 (bedgraph2bigwig can now have chrom sizes as input)

  • add bam2wiggle, bed2wiggle, bcf2wiggle, vcf2wiggle etc

Revision 0.1.0

3 April 2018

Major refactoring to allow sub commands to be used:

bioconvert fastq2fasta test.fastq test.fasta

instead of:

bioconvert test.fastq test.fasta

as well as transitive conversion: if a conversion is not implemented but a path exists, then conversion can be performed using -a option:

bioconvert A2C test.A test.C -a
  • new converters: maf2sam, ods2csv, xls2csv, xlsx2csv

Revision 0.0.12
  • new converters: embl2fasta, embl2genbank, fasta2twobit, twobit2fasta fasta2fasta, sra2fastq

  • refactoring of the extensions framework to simplify the code

Revision 0.0.11
  • add abiliy to use go executables (add go to the requirements)

  • added converters: fasta2nexux, newick2nexus, newick2phyloxml, nexus2fasta, nexus2newick, nexus2phylip, nexus2phyloxml, phylip2nexus, phyloxml2newick, phyloxml2nexus, genbank2embl, genbank2fasta, stockholm2clustal and clustal2phylip

Revision 0.0.10
  • added samlint validator

Revision 0.0.9
  • added sam2paf

Revision 0.0.8
  • added compressor decorator

  • update bioconvert main script with several options

  • new converters: dsrc2gz, bam2bigwig draft

  • provided squizz on bioconda and added as dependencies

  • added paflint validator

Revision 0.0.7
  • added converters: bam2cram and cram2bam, vcf2bed

  • new class: Bioconvert that could be used for all converters !

  • new modules: core/shell, core/converter

  • add singularity to provide dot executable in the documentation and remove the pygraphviz dependency.

Revision 0.0.6

added converters: bcf2vcf; vcf2bcf; bam2json; gz2bz2, bz22gz, gz2dsrc, .... benchmarking implemented.

Revision 0.0.5

added bioconvert_init standalone to help developers. added gz2bz2 converter. switch default of bam2fasta with sambamba

Revision 0.0.4

update requirements and MANIFEST; added fastq2fasta, gfa2fasta

Revision 0.0.3

benchmark in place; added fastq2fasta, scf2fastq, scf2fastq

Revision 0.0.2

setup travis, RTD, tests; added bam2sam

Revision 0.0.1

add bioconvert tree structure; added bam2bed, json2yaml...