Changes

0.3.1

This release adds several scripts and commands. Successive releases 0.3.x releases will be used to fix bugs and refine the APIs and CLI. Most importantly, since the publishing of the first paper using the framework, the releases will go torward the removal of as much deprecated code as possible. At the same time, a general review of the code to be able to run on Python3 (probably via the six package) will start. The general idea is to reach as a full removal of legacy code in 0.4.0, while full Python3 compatibility is the aim of 0.5.0, which also means dropping dependencies that are not compatible with Python3.

Added

• mgkit.graphs.from_kgml() to make a graph from a KGML file (allows for directionality)
• mgkit.graphs.add_module_compounds(): updates a graph with compounds information as needed
• mgkit.kegg.parse_reaction(): parses a reaction equation from Kegg
• added –no-frame option to hmmer2gff - Convert HMMER output to GFF, to use non translated protein sequences. Also changed the mgkit.io.gff.from_hmmer() function to enable this behaviour
• added options –num-gt and –num-lt to the values command of filter-gff - Filter GFF annotations to filter based on > and < inequality, in addition to >= and <=
• added uid as command in fasta-utils - Fasta Utilities to make unique fasta headers
• methods to make mgkit.db.mongo.GFFDB to behave like a dictionary (an annotation uid can be used as a key to retrieve it, instead of a query), this includes the possibility to iterate over it, but what is yielded are the values, not the keys (i.e. mgkit.io.gff.Annotation instances, not uid)
• added mgkit.counts.func.from_gff() to load count data stored inside a GFF, as is the case when the counts command of add-gff-info - Add informations to GFF annotations is used’
• added mgkit.kegg.KeggClientRest.conv() and mgkit.kegg.KeggClientRest.find() operations to mgkit.kegg.KeggClientRest
• mgkit.kegg.KeggClientRest now caches calls to several methods. The cache can be written to disk using mgkit.kegg.KeggClientRest.write_cache() or emptied via mgkit.kegg.KeggClientRest.empty_cache()
• added mgkit.utils.dictionary.merge_dictionaries() to merge multiple dictionaries where the keys contain different values
• added a Docker file to make a preconfigured mgkit/jupyter build
• added C functions (using Cython) for tetramer/kmer counting. The C functions are the default, with the pure python implementation having a _ appended to their names. This is because the Cython functions cannot have docstrings
• added mgkit.io.gff.annotation_coverage_sorted()
• added mgkit.io.gff.Annotation.to_dict()
• added mgkit.plots.utils.legend_patches() to create matplotlib patches, to be in legends
• added scripts download IDs to taxa tables from NCBI/Uniprot
• added mgkit.io.utils.group_tuples_by_key()
• added cov command to get-gff-info - Extract informations to GFF annotations and filter-gff - Filter GFF annotations
• added mgkit.io.fasta.load_fasta_prodigal(), to load the fasta file from prodigal for called genes (tested on aminoacids)
• added option to output a JSON file to the lca command in ref:taxon-utils and cov command in get-gff-info - Extract informations to GFF annotations
• added a bash script, sort-gff.sh to help sort a GFF
• added mgkit.taxon.UniprotTaxonomy.get_lineage() which simplifies the use of mgkit.taxon.get_lineage()
• added mgkit.io.fastq.load_fastq() as a simple parser for fastq files
• added a new script, sampling-utils - Resampling Utilities
• added mgkit.utils.common.union_ranges() and mgkit.utils.common.complement_ranges()
• added to_hdf command to taxon-utils - Taxonomy Utilities to create a HDF5 file to lookup taxa tables from NCBI/Uniprot
• added –hdf-table option to addtaxa command in add-gff-info - Add informations to GFF annotations
• mgkit.taxon.UniprotTaxonomy.add_taxon(), mgkit.taxon.UniprotTaxonomy.add_lineage() and mgkit.taxon.UniprotTaxonomy.drop_taxon()

Changed

• changed domain to superkingdom as for NCBI taxonomy in mgkit.taxon.UniprotTaxonomy.read_from_gtdb_taxonomy()
• updated scripts documentation to include installed but non advertised scripts (like translate_seq - Translate Nucleotides to Aminoacids (Deprecated))
• mgkit.kegg.KeggReaction was reworked to only store the equation information
• some commands in fastq-utils - Fastq Utilities did not support standard in/out, also added the script usage to the script details
• translate_seq - Translate Nucleotides to Aminoacids (Deprecated) now supports standard in/out
• added haplotypes parameter to mgkit.snps.funcs.combine_sample_snps()
• an annotation from mgkit.db.mongo.GFFDB now doesn’t include the lineage, because it conflicts with the string used in a GFF file
• an mgkit.io.gff.Annotation.coverage() now returns a float instead od a int
• moved code from package mgkit.io to mgkit.io.utils
• changed behaviour of mgkit.utils.common.union_range()
• removed mgkit.utills.common.range_substract_()
• added progressbar2 as installation requirement
• changed how mgkit.taxon.UniprotTaxonomy.find_by_name()

Fixed

Besides smaller fixes:

• mgkit.plots.abund.draw_circles() behaviour when sizescale doesn’t have the same shape as order
• parser is now correct for taxon-utils - Taxonomy Utilities, to include the Krona options
• ondition when a blast output is empty, hence lineno is not initialised when a message is logged

Deprecated

• translate_seq - Translate Nucleotides to Aminoacids (Deprecated) will be removed in version 0.4.0, instead use the similar command in fasta-utils - Fasta Utilities

0.3.0

A lot of bugs were fixed in this release, especially for reading NCBI taxonomy and using the msgpack format to save a UniprotTaxonomy instance. Also added a tutorial for profiling a microbial community using MGKit and BLAST (Profile a Community with BLAST)

Added

• mgkit.align.read_samtools_depth() to read the samtools depth format iteratively (returns a generator)
• mgkit.align.SamtoolsDepth, used to cache the samtools depth format, while requesting region coverage
• mgkit.kegg.KeggModule.find_submodules(), mgkit.kegg.KeggModule.parse_entry2()
• mgkit.mappings.enzyme.get_mapping_level()
• mgkit.utils.dictionary.cache_dict_file() to cache a large dictionary file (tab separated file with 2 columns), an example of its usage is in the documentation
• mgkit.taxon.UniprotTaxonomy.read_from_gtdb_taxonomy() to read a custom taxonomy from a tab separated file. The taxon_id are not guaranteed to be stable between runs
• added cov_samtools to add-gff-info script
• added mgkit.workflow.fasta_utils and correspondent script fasta-utils
• added options -k and -kt to taxon_utils, which outputs a file that can be used with Krona ktImportText (needs to use -q with this script)

Changed

• added no_zero parameter to mgkit.io.blast.parse_accession_taxa_table()
• changed behaviour of mgkit.kegg.KeggModule and some of its methods.
• added with_last parameter to mgkit.taxon.get_lineage()
• added –split option to add-gff-info exp_syn and get-gff-info sequence scripts, to emulate BLAST behaviour in parsing sequence headers
• added -c option to add-gff-info addtaxa

0.2.5

Changed

• added the only_ranked argument to mgkit.taxon.get_lineage()
• add-gff-info addtaxa (add-gff-info - Add informations to GFF annotations) doesn’t preload the GFF file if a dictionary is used instead of the taxa table
• blast2gff blastdb ((blast2gff - Convert BLAST output to GFF) offers more options to control the format of the header in the DB used
• added the sequence command to filter-gff (filter-gff - Filter GFF annotations), to filter all annotations on a per-sequence base, based on mean bitscore or other comparisons

Added

• added mgkit.counts.func.load_counts_from_gff()
• added mgkit.io.blast.parse_accession_taxa_table()
• added mgkit.plots.abund.draw_axis_internal_triangle()
• added representation of mgkit.taxon.UniprotTaxonomy, it show the number of taxa in the instance
• added mgkit.taxon.last_common_ancestor_multiple()
• added taxon_utils (taxon-utils - Taxonomy Utilities) to filter GFF based on their taxonomy and find the last common ancestor for a reference sequence based on either GFF annotations or a list of taxon_ids (in a text file)

0.2.4

Changed

• mgkit.utils.sequence.get_contigs_info() now accepts a dictionary name->seq or a list of sequences, besides a file name (r536)
• add-gff-info counts command now removes trailing commas from the samples list
• the axes are turned off after the dendrogram is plo

Fixed

• the snp_parser script requirements were set wrong in setup.py (r540)
• uncommented lines to download sample data to build documentation (r533)
• add-gff-info uniprot command now writes the lineage attribute correctly (r538)

0.2.3

The installation dependencies are more flexible, with only numpy as being required. To install every needed packages, you can use:

$ pip install mgkit[full]

Added

• new option to pass the query sequences to blast2gff, this allows to add the correct frame of the annotation in the GFF
• added the attributes evalue, subject_start and subject_end to the output of blast2gff. The subject start and end position allow to understand on which frame of the subject sequence the match was found
• added the options to annotate the heatmap with the numbers. Also updated the relative example notebook
• Added the option to reads the taxonomy from NCBI dump files, using mgkit.taxon.UniprotTaxonomy.read_from_ncbi_dump(). This make it faster to get the taxonomy file
• added argument to return information from mgkit.net.embl.datawarehouse_search(), in the form of tab separated data. The argument fields can be used when display is set to report. An example on how to use it is in the function documentation
• added a bash script download-taxonomy.sh that download the taxonomy
• added script venv-docs.sh to build the documentation in HTML under a virtual environment. matplotlib on MacOS X raises a RuntimeError, because of a bug in virtualenv, the documentation can be first build with this, after the script create-apidoc.sh is create the API documentation. The rest of the documentation (e.g. the PDF) can be created with make as usual, afterwards
• added mgkit.net.pfam, with only one function at the moment, that returns the descriptions of the families.
• added pfam command to add-gff-info, using the mentioned function, it adds the description of the Pfam families in the GFF file
• added a new exception, used internally when an additional dependency is needed

Changed

• using the NCBI taxonomy dump has two side effects:

  • the scientific/common names are kept as is, not lower cased as was before
  • a merged file is provided for taxon_id that changed. While the old taxon_id is kept in the taxonomy, this point to the new taxon, to keep backward compatibility

• renamed the add-gff-info gitaxa command to addtaxa. It now accepts more data sources (dictionaries) and is more general

• changed mgkit.net.embl.datawarehouse_search() to automatically set the limit at 100,000 records

• the taxonomy can now be saved using msgpack, making it faster to read/write it. It’s also more compact and better compression ratio

• the mgkit.plots.heatmap.grouped_spine() now accept the rotation of the labels as option

• added option to use another attribute for the gene_id in the get-gff-info script gtf command

• added a function to compare the version of MGKit used, throwing a warning, when it’s different (mgkit.check_version())

• removed test for old SNPs structures and added the same tests for the new one

• mgkit.snps.classes.GeneSNP now caches the number of synonymous and non-synonymous SNPs for better speed

• mgkit.io.gff.GenomicRange.__contains__() now also accepts a tuple (start, end) or another GenomicRange instance

Fixed

• a bug in the gitaxa (now addtaxa) command: when a taxon_id was not found in the table, the wrong taxon_name and lineage was inserted
• bug in mgkit.snps.classes.GeneSNP that prevented the correct addition of values
• fixed bug in mgkit.snps.funcs.flat_sample_snps() with the new class
• mgkit.io.gff.parse_gff() now correctly handles comment lines and stops parsing if the fasta file at the end of a GFF is found

0.2.2

Added

• new commands for the add-gff-info script (add-gff-info - Add informations to GFF annotations):

  • eggnog to add information from eggNOG HMMs (at the moment the 4.5 Viral)
  • counts and fpkms to add count data (correctly exported to mongodb)
  • gitaxa to add taxonomy information directly from GI identifiers from NCBI

• added blastdb command to blast2gff script (blast2gff - Convert BLAST output to GFF)

• updated MGKit GFF Specifications

• added gtf command to get-gff-info script (get-gff-info - Extract informations to GFF annotations) to convert a GFF to GTF, that is accepted by featureCounts, in conjunction with the counts command of add-gff-info

• added method to mgkit.snps.classes.RatioMixIn.calc_ratio_flag to calculate special cases of pN/pS

Changed

• added argument in functions of the mgkit.snps.conv_func to bypass the default filters
• added use_uid argument to mgkit.snps.funcs.combine_sample_snps() to use the uid instead of the gene_id when calculating pN/pS
• added flag_values argument to mgkit.snps.funcs.combine_sample_snps() to use mgkit.snps.classes.RatioMixIn.calc_ratio_flag instead of mgkit.snps.classes.RatioMixIn.calc_ratio

Removed

• deprecated code from the snps package

0.2.1

Added

• added mgkit.db.mongo
• added mgkit.db.dbm
• added mgkit.io.gff.Annotation.get_mappings()
• added mgkit.io.gff.Annotation.to_json()
• added mgkit.io.gff.Annotation.to_mongodb()
• added mgkit.io.gff.from_json()
• added mgkit.io.gff.from_mongodb()
• added mgkit.taxon.get_lineage()
• added mgkit.utils.sequence.get_contigs_info()
• added mongodb and dbm commands to script get-gff-info
• added kegg command to add-gff-info script, caching results and -d option to uniprot command
• added -ft option to blast2gff script
• added -ko option to download_profiles
• added new HMMER tutorial
• added another notebook to the plot examples, for misc. tips
• added a script that downloads from figshare the tutorial data]
• added function to get an enzyme full name (mgkit.mappings.enzyme.get_enzyme_full_name())
• added example notebook for using GFF annotations and the mgkit.db.dbm, mgkit.db.mongo modules

Changed

• mgkit.io.blast.parse_uniprot_blast()
• mgkit.io.gff.Annotation
• mgkit.io.gff.GenomicRange
• mgkit.io.gff.from_hmmer()
• mgkit.taxon.UniprotTaxonomy.read_taxonomy()
• mgkit.taxon.parse_uniprot_taxon()
• changed behaviour of hmmer2gff script
• changed tutorial notebook to specify the directory where the data is

Deprecated

• mgkit.filter.taxon.filter_taxonomy_by_lineage()
• mgkit.filter.taxon.filter_taxonomy_by_rank()

Removed

• removed old filter_gff script

0.2.0

• added creation of wheel distribution
• changes to ensure compatibility with alter pandas versions
• mgkit.io.gff.Annotation.get_ec() now returns a set, reflected changes in tests
• added a –cite option to scripts
• fixes to tutorial
• updated documentation for sphinx 1.3
• changes to diagrams
• added decoration to raise warnings for deprecated functions
• added possibility for mgkit.counts.func.load_sample_counts() info_dict to be a function instead of a dictionary
• consolidation of some eggNOG structures
• added more spine options in mgkit.plots.heatmap.grouped_spine()
• added a length property to mgkit.io.gff.Annotation
• changed filter-gff script to customise the filtering function, from the default one, also updated the relative documentation
• fixed a few plot functions

0.1.16

• changed default parameter for mgkit.plots.boxplot.add_values_to_boxplot()
• Added include_only filter option to the default snp filters mgkit.consts.DEFAULT_SNP_FILTER
• the default filter for SNPs now use an include only option, by default including only protozoa, archaea, fungi and bacteria in the matrix
• added widths parameter to def mgkit.plots.boxplot.boxplot_dataframe() function, added function mgkit.plots.boxplot.add_significance_to_boxplot() and updated example boxplot notebook for new function example
• use_dist and dist_func parameters to the mgkit.plots.heatmap.dendrogram() function
• added a few constants and functions to calculate the distance matrices of taxa: mgkit.taxon.taxa_distance_matrix(), mgkit.taxon.distance_taxa_ancestor() and mgkit.taxon.distance_two_taxa()
• mgkit.kegg.KeggClientRest.link_ids() now accept a dictionary as list of ids
• if the conversion of an Annotation attribute (first 8 columns) raises a ValueError in mgkit.io.gff.from_gff(), by default the parser keeps the string version (cases for phase, where is ‘.’ instead of a number)
• treat cases where an attribute is set with no value in mgkit.io.gff.from_gff()
• added mgkit.plots.colors.palette_float_to_hex() to convert floating value palettes to string
• forces vertical alignment of tick labels in heatmaps
• added parameter to get a consensus sequence for an AA alignment, by adding the nucl parameter to mgkit.utils.sequence.Alignment.get_consensus()
• added mgkit.utils.sequence.get_variant_sequence() to get variants of a sequence, essentially changing the sequence according to the SNPs passed
• added method to get an aminoacid sequence from Annotation in mgkit.io.gff.Annotation.get_aa_seq() and added the possibility to pass a SNP to get the variant sequence of an Annotation in mgkit.io.gff.Annotation.get_nuc_seq().
• added exp_syn command to add-gff-info script
• changed GTF file conversion
• changed behaviour of mgkit.taxon.is_ancestor(): if a taxon_id raises a KeyError, False is now returned. In other words, if the taxon_id is not found in the taxonomy, it’s not an ancestor
• added mgkit.io.gff.GenomicRange.__contains__(). It tests if a position is inside the range
• added mgkit.io.gff.GenomicRange.get_relative_pos(). It returns a position relative to the GenomicRange start
• fixed documentation and bugs (Annotation.get_nuc_seq)
• added mgkit.io.gff.Annotation.is_syn(). It returns True if a SNP is synonymous and False if non-synonymous
• added to_nuc parameter to mgkit.io.gff.from_nuc_blast() function. It to_nuc is False, it is assumed that the hit was against an amino acidic DB, in which case the phase should always set to 0
• reworked internal of snp_parser script. It doesn’t use SNPDat anymore
• updated tutorial
• added ipython notebook as an example to explore data from the tutorial
• cleaned deprecated code, fixed imports, added tests and documentation

0.1.15

• changed name of mgkit.taxon.lowest_common_ancestor() to mgkit.taxon.last_common_ancestor(), the old function name points to the new one
• added mgkit.counts.func.map_counts_to_category() to remap counts from one ID to another
• added get-gff-info script to extract information from GFF files
• script download_data can now download only taxonomy data
• added more script documentation
• added examples on gene prediction
• added function mgkit.io.gff.from_hmmer() to parse HMMER results and return mgkit.io.gff.Annotation instances
• added mgkit.io.gff.Annotation.to_gtf() to return a GTF line, mgkit.io.gff.Annotation.add_gc_content() and mgkit.io.gff.Annotation.add_gc_ratio() to calculate GC content and ratio respectively
• added mgkit.io.gff.parse_gff_files() to parse multiple GFF files
• added uid_used parameter to several functions in mgkit.counts.func
• added mgkit.plots.abund to plot abundance plots
• added example notebooks for plots
• HTSeq is now required only by the scripts that uses it, snp_parser and fastq_utils
• added function to convert numbers when reading from htseq count files
• changed behavior of -b option in add-gff-info taxonomy command
• added mgkit.io.gff.get_annotation_map()

0.1.14

• added ipthon notebooks to the documentation. As of this version the included ones (in docs/source/examples) are for two plot modules. Also added a bash script to convert them into rst files to be included with the documentation. The .rst are not versioned, and they must be rebuild, meaning that one of the requirements for building the docs is to have IPython installed with the notebook extension
• now importing some packages automatically import the subpackages as well
• refactored mgkit.plots into a package, with most of the original functions imported into it, for backward compatibility
• added mgkit.graphs.build_weighted_graph()
• added box_vert parameter in mgkit.plots.boxplot.add_values_to_boxplot(), the default will be changed in a later version (kept for compatibility with older scripts/notebooks)
• added an heatmap module to the plots package. Examples are in the notebook
• added mgkit.align.covered_annotation_bp() to find the number of bp covered by reads in annotations (as opposed to using the annotation length)
• added documentation to mgkit.mappings.eggnog.NOGInfo and an additional method
• added mgkit.net.uniprot.get_uniprot_ec_mappings() as it was used in a few scripts already
• added mgkit.mappings.enzyme.change_mapping_level() and other to deal with EC numbers. Also improved documentation with some examples
• added mgkit.counts.func.load_sample_counts_to_genes() and mgkit.counts.func.load_sample_counts_to_taxon(), for mapping counts to only genes or taxa. Also added index parameter in mgkit.counts.func.map_counts() to accomodate the changes
• added mgkit.net.uniprot.get_ko_to_eggnog_mappings() to get mappings of KO identifiers to eggNOG
• added mgkit.io.gff.split_gff_file() to split a gff into several ones, assuring that all annotations for a sequence is in the same file; useful to split massive GFF files before filtering
• added mgkit.counts.func.load_deseq2_results() to load DESeq2 results in CSV format
• added mgkit.counts.scaling.scale_rpkm() for scale with rpkm a count table
• added caching options to mgkit.counts.func.load_sample_counts() and others
• fixes and improvements to documentation

0.1.13

• added counts package, including functions to load HTSeq-counts results and scaling
• added mgkit.filter.taxon.filter_by_ancestor(), as a convenience function
• deprecated functions in mgkit.io.blast module, added more to parse blast outputs (some specific)
• mgkit.io.fasta.load_fasta() returns uppercase sequences, added a function (mgkit.io.fasta.split_fasta_file()) to split fasta files
• added more methods to mgkit.io.gff.Annotation to complete API from old annotations
• fixed mgkit.io.gff.Annotation.dbq property to return an int (bug in filtering with filter-gff)
• added function to extract the sequences covered by annotations, using the mgkit.io.gff.Annotation.get_nuc_seq() method
• added mgkit.io.gff.correct_old_annotations() to update old annotated GFF to new conventions
• added mgkit.io.gff.group_annotations_by_ancestor() and mgkit.io.gff.group_annotations_sorted()
• moved deprecated GFF classes/modules in mgkit.io.gff_old
• added mgkit.io.uniprot module to read/write Uniprot files
• added mgkit.kegg.KeggClientRest.get_ids_names() to remove old methods to get specific class names used to retrieve (they are deprecated at the moment)
• added mgkit.kegg.KeggModule to parse a Kegg module entry
• added mgkit.net.embl.datawarehouse_search() to search EMBL resources
• made mgkit.net.uniprot.query_uniprot() more flexible
• added/changed plot function in mgkit.plots
• added enum34 as a dependency for Python versions below 3.4
• changed classes to hold SNPs data: deprecated mgkit.snps.classes.GeneSyn, replaced by mgkit.snps.classes.GeneSNP which the enum module for mgkit.snps.classes.SNPType
• added mgkit.taxon.NoLcaFound
• fixed behaviour of mgkit.taxon.UniprotTaxonomy.get_ranked_taxon() for newer taxonomies
• change behaviour of mgkit.taxon.UniprotTaxonomy.is_ancestor() to use module mgkit.taxon.is_ancestor() and accept multiple taxon IDs to test
• mgkit.taxon.UniprotTaxonomy.load_data() now accept compressed data and file handles
• added mgkit.taxon.lowest_common_ancestor() to find the lowest common ancestor of two taxon IDs
• changed behaviour of mgkit.taxon.parse_uniprot_taxon()
• added functions to get GC content, ratio of a sequence and it composition to mgkit.utils.sequence
• added more options to blast2gff script
• added coverage, taxonomy and unipfile to add-gff-info
• refactored snp_parser to use new classes
• added possibility to use sorted GFF files as input for filter-gff to use less memory (the examples show how to use sort in Unix)

0.1.12

• added functions to elongate annotations, measure the coverage of them and diff GFF files in mgkit.io.gff
• added ranges_length and union_ranges to mgkit.utils.common
• added script filter-gff, filter_gff will be deprecated
• added script blast2gff to convert blast output to a GFF
• removed unneeded dependencies to build docs
• added script add-gff-info to add more annotations to GFF files
• added mgkit.io.blast.parse_blast_tab() to parse BLAST tabular format
• added mgkit.io.blast.parse_uniprot_blast() to return annotations from a BLAST tabular file
• added mgkit.graph module
• added classes mgkit.io.gff.Annotation and mgkit.io.gff.GenomicRange and deprecated old classes to handle GFF annotations (API not stable)
• added mgkit.io.gff.DuplicateKeyError raised in parsing GFF files
• added functions used to return annotations from several sources
• added option gff_type in mgkit.io.gff.load_gff()
• added mgkit.net.embl.dbfetch()
• added mgkit.net.uniprot.get_gene_info() and mgkit.net.uniprot.query_uniprot() mgkit.net.uniprot.parse_uniprot_response()
• added apply_func_to_values to mgkit.utils.dictionary
• added mgkit.snps.conv_func.get_full_dataframe(), mgkit.snps.conv_func.get_gene_taxon_dataframe()
• added more tests

0.1.11

• removed rst2pdf for generating a PDF for documentation. Latex is preferred
• corrections to documentation and example script
• removed need for joblib library in translate_seq script: used only if available (for using multiple processors)
• deprecated mgkit.snps.funcs.combine_snps_in_dataframe() and mgkit.snps.funcs.combine_snps_in_dataframe(): mgkit.snps.funcs.combine_sample_snps() should be used
• refactored some tests and added more
• added docs_req.txt to help build the documentation ont readthedocs.org
• renamed mgkit.snps.classes.GeneSyn gid and taxon attributes to gene_id and taxon_id. The old names are still available for use (via properties), but the will be taken out in later versions. Old pickle data should be loaded and saved again before in this release
• added a few convenience functions to ease the use of combine_sample_snps()
• added function mgkit.snps.funcs.significance_test() to test the distributions of genes share between two taxa.
• fixed an issue with deinterleaving sequence data from khmer
• added mgkit.snps.funcs.flat_sample_snps()
• Added method to mgkit.kegg.KeggClientRest to get names for all ids of a certain type (more generic than the various get_*_names)
• added first implementation of mgkit.kegg.KeggModule class to parse a Kegg module entry
• mgkit.snps.conv_func.get_rank_dataframe(), mgkit.snps.conv_func.get_gene_map_dataframe()