nebseq Basic Biological Sequence Manipulations
Download

nebseq Ranking & Summary

nebseq Tags

Python library handler sequence biological biological sequence sequence manipulations

nebseq Description

Basic Biological Sequence Manipulations nebseq is a Python module for basic biological sequence manipulations.Import as usual >>> import nebseqReverse complementsThe only note here is that revcomp does not check the input sequence to see if it looks like DNA or RNA. >>> nebseq.revcomp('ACGT') 'ACGT' >>> nebseq.revcomp('TTACC') 'GGTAA'And if we give it garbage it just gives us garbage back. >>> nebseq.revcomp('ZQ') 'QZ'TranslationThe translation function should allow for full support of sequence translation. This includes things like trimming the first couple bases and using alternate translation tables. There is also support for the more esoteric post translational modifications that can be found in some Genbank files as well as translating partial peptides (for things like fuzzy coordinates).Basic translation: >>> nebseq.translate('TTGGCCAAGGAACGA', table=11) 'MAKER'Showing the effects of a partial peptide translation. By default the first codon should be a start codon according to the selected translation table, if not then its converted to an 'X' >>> nebseq.translate('GCCAAG') 'XK' >>> nebseq.translate('GCCAAG', partial=True) 'AK'Or we can remove the first couple of bases for fuzzy coordinates. >>> nebseq.translate('TTGCCAAG', start=2, partial=True) 'AK'Modifications are specified as an (index, amino_acid) two-tuple. Notice that modification indexes are specified as one-based indexes into the amino acid sequence. >>> nebseq.translate('ATGAAGGAA', modifications=) 'MUE'ExtractionSequence extraction is for when you want to slice out part of a larger sequence. This is useful if you use the nebgb module and its definition of locations parsed from strings like join(1..5,9..100). >>> location = {'type': 'span', 'from': 4, 'to': 10} >>> nebseq.extract('ACCGTACCATAGTT', location) ('GTACCAT', (False, False)) >>> location = { ... "type": "complement", ... "segment": { ... "type": "join", ... "segments": ... } ... } >>> nebseq.extract('ACCGTATTTCGGGGACAT', location) ('CCCCGAATACG', (False, False)) Requirements: · Python

nebseq Related Software