Package: dataset-creator
Dataset creator for phylogenetic softwaretestspackageDataset-Creator - easy way to creat phylogenetic datasets in many formatsDocumentation:dataset-creator.readthedocs.orgTakes SeqRecordExpanded objects and creates datasets for phylogenetic software
such as MrBayes, TNT, BEAST, RAxML, MEGA, etc.FeaturesCreates datasets in the following formats: FASTA, GenBankFASTA, NEXUS, TNT, MEGA
and Phylip.Can generate datasets of DNA and aminoacid sequences.Can generate datasets of degenerated sequences.It can partition datasets by codon positions or by gene.Quick startFirst:pip install dataset_creatorThen the list of SeqRecordExpanded objects should be sorted by gene_code first
then by voucher_code.>>>fromseqrecord_expandedimportSeqRecord>>>fromdataset_creatorimportDataset>>>>>># `table` is the Translation Table code based on NCBI>>>seq_record1=SeqRecord('ACTACCTA',reading_frame=2,gene_code='RpS5',...table=1,voucher_code='CP100-10',...taxonomy={'genus':'Aus','species':'bus'})>>>>>>seq_record2=SeqRecord('ACTACCTA',reading_frame=2,gene_code='RpS5',...table=1,voucher_code='CP100-10',...taxonomy={'genus':'Aus','species':'bus'})>>>>>>seq_record3=SeqRecord('ACTACCTA',reading_frame=2,gene_code='wingless',...table=1,voucher_code='CP100-10',...taxonomy={'genus':'Aus','species':'bus'})>>>>>>seq_record4=SeqRecord('ACTACCTA',reading_frame=2,gene_code='winglesss',...table=1,voucher_code='CP100-10',...taxonomy={'genus':'Aus','species':'bus'})>>>>>>seq_records=[...seq_record1,seq_record2,seq_record3,seq_record4,...]>>># codon positions can be 1st, 2nd, 3rd, 1st-2nd, ALL (default)>>>dataset=Dataset(seq_records,format='TNT',partitioning='by codon position',...codon_positions='ALL')>>>dataset=Dataset(seq_records,format='PHYLIP',partitioning='1st-2nd, 3rd',...codon_positions='ALL')>>>dataset=Dataset(seq_records,format='NEXUS',partitioning='by gene',...codon_positions='1st')>>>dataset=Dataset(seq_records,format='NEXUS',partitioning='by gene',...codon_positions='ALL',aminoacids=True)>>># Produce a dataset of degenerated sequences using the 'S' method:>>>dataset=Dataset(seq_records,format='NEXUS',partitioning='by gene',...codon_positions='ALL',degenerate='S')>>>print(dataset.dataset_str)#NEXUSblahblah...Further documentation can be found atdataset-creator.readthedocs.orgDevelopmentTo run the all tests run:toxChangelog0.5.0 (2021-03-20)added support for bankit format0.4.0 (2020-06-28)dropped support for python 2added support for long taxon names in generated dataset files0.3.20 (2018-01-07)Updated seq record expanded.0.3.19 (2018-01-06)Fixed version of seqrecord expanded in setup.py.0.3.18 (2018-01-06)Support lineages for genbank fasta files.0.3.17 (2018-01-06)Avoid raising exception when translating sequence with dash.0.3.16 (2017-10-01)Fixed creating dataset with 1st, 2nd or 3rd codon positions.0.3.14 (2016-09-11)upgradeseqrecord-expanded.0.3.13 (2016-08-27)Fixed bug that did not replace all white spaces for underscores in taxon names
when building datasets. Due to taxon names with whitespaces, the NEXUS
interpreter assumed that part of the name was actually part of the sequence,
rendering the sequence invalid.Added some dependencies to requirements.0.3.11 (2016-06-25)Upgraded seqrecord-expanded requirement.0.3.10 (2015-12-01)Fixed bug that produced FASTA sequences with underscores. Now all voucher codes
will have their dashes replaced by underscores.0.3.9 (2015-11-06)Create datasets using the GenBankFASTA format. This format has the following
extra info in the description of sequences:
>Aus_aus_CP100-10 [org=Aus aus] [Specimen-voucher=CP100-10] [note=ArgKin gene, partial cds.] [Lineage=]0.3.8 (2015-10-30)Fixed making dataset as aminoacid seqs for MEGA format.Fixed making dataset as degenerated seqs for MEGA format.Fixed making dataset as degenerated seqs for TNT format.Fixed making dataset as aa seqs with specified outgroup for TNT format.Raise ValueError when asked to degenerate seqs that will go to partitioning
based on codon positions.Dataset creator returns warnings if translated sequences have stop codons ‘*’.Cannot generate MEGA datasets with partitioning.0.3.7 (2015-10-30)Fixed 2nd, 3rd codon positions bug that returned empty FASTA datasets.0.3.6 (2015-10-30)Fixed 3rd codon positions bug that returned FASTA datasets with 3rd codon
positions even if they were not needed.0.3.5 (2015-10-29)If user provides outgroup, then TNT datasets will place its sequences in first
position in the dataset blocks.0.3.4 (2015-10-02)Fixed bug that did not show DATATYPE=PROTEIN in Nexus files when aminoacid
sequences were requested by user.0.3.3 (2015-10-02)Fixed bug that raised an exception when SeqExpandedRecords did not have data
in thetaxonomyfield.0.3.2 (2015-10-01)Fixed bug that raised an exception when user wanted partitioned dataset as
1st-2nd and 3rd codon positions of only one codon.0.3.1 (2015-10-01)Fixed bug that raised an exception when user wanted partitioned dataset by
codon positions of only one codon.0.3.0 (2015-10-01)Accepts voucher code as string that will be used to generate the outgroup
string needed for NEXUS and TNT files.0.2.0 (2015-09-30)Creates datasets as degenerated sequences using the method by Zwick et al.0.1.1 (2015-09-30)It will issue errors if reading frames are not specified unless they
are strictly necessary to build the dataset (datasets need to be divided by
codon positions).Added documentation using sphinx-docCreates datasets as aminoacid sequences.0.1.0 (2015-09-23)Creates Nexus, Tnt, Fasta, Phylip and Mega dataset formats.0.0.1 (2015-06-10)First release on PyPI.