Will have their dashes replaced by underscores.Ĭreate datasets using the GenBankFASTA format. Interpreter assumed that part of the name was actually part of the sequence,įixed bug that produced FASTA sequences with underscores. Due to taxon names with whitespaces, the NEXUS Support lineages for genbank fasta files.Īvoid raising exception when translating sequence with dash.įixed creating dataset with 1st, 2nd or 3rd codon positions.įixed bug that did not replace all white spaces for underscores in taxon names To run the all tests run: tox Changelog 0.5.0 ()Īdded support for long taxon names in generated dataset filesįixed version of seqrecord expanded in setup.py. codon_positions = 'ALL', degenerate = 'S' ) > print ( dataset. 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 = '1st' ) > dataset = Dataset ( seq_records, format = 'NEXUS', partitioning = 'by gene'. codon_positions = 'ALL' ) > dataset = Dataset ( seq_records, format = 'NEXUS', partitioning = 'by gene'. codon_positions = 'ALL' ) > dataset = Dataset ( seq_records, format = 'PHYLIP', partitioning = '1st-2nd, 3rd'. taxonomy = ) > seq_records = > # codon positions can be 1st, 2nd, 3rd, 1st-2nd, ALL (default) > dataset = Dataset ( seq_records, format = 'TNT', partitioning = 'by codon position'. > from seqrecord_expanded import SeqRecord > from dataset_creator import Dataset > # `table` is the Translation Table code based on NCBI > seq_record1 = SeqRecord ( 'ACTACCTA', reading_frame = 2, gene_code = 'RpS5'. Then the list of SeqRecordExpanded objects should be sorted by gene_code first It can partition datasets by codon positions or by gene. FeaturesĬreates datasets in the following formats: FASTA, GenBankFASTA, NEXUS, TNT, MEGAĬan generate datasets of DNA and aminoacid sequences.Ĭan generate datasets of degenerated sequences. Such as MrBayes, TNT, BEAST, RAxML, MEGA, etc. Takes SeqRecordExpanded objects and creates datasets for phylogenetic software Dataset-Creator - easy way to creat phylogenetic datasets in many formats Documentation:
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |