Metadata-Version: 2.1
Name: biopython.convert
Version: 1.0.4
Summary: Interconvert various file formats supported by biopython. Supports querying records with JMESPath.
Home-page: https://github.com/brinkmanlab/biopython-convert
Author: Nolan Woods
Author-email: nolan_w@sfu.ca
License: MIT Amended
Description: .. image:: https://zenodo.org/badge/195302632.svg
            :target: https://zenodo.org/badge/latestdoi/195302632
        
        ==================
        BioPython-Convert
        ==================
        
        Interconvert various file formats supported by BioPython.
        
        Supports querying records with JMESPath.
        
        Installation
        ------------
        ::
        
            pip install biopython-convert
        
        or::
        
            conda install biopython-convert
        
        or::
        
            git clone https://github.com/brinkmanlab/BioPython-Convert.git
            cd BioPython-Convert
            ./setup.py install
        
        Use
        ---
        ::
        
            biopython.convert [-s] [-v] [-i] [-q JMESPath] input_file input_type output_file output_type
                -s Split records into seperate files
                -q JMESPath to select records. Must return list of SeqIO records or mappings. Root is list of input SeqIO records.
                -i Print out details of records during conversion
                -v Print version and exit
        
        Supported formats
            abi, abi-trim, ace, cif-atom, cif-seqres, clustal, embl, fasta, fasta-2line, fastq-sanger, fastq,
            fastq-solexa, fastq-illumina, genbank, gb, ig, imgt, nexus, pdb-seqres, pdb-atom, phd, phylip, pir, seqxml,
            sff, sff-trim, stockholm, swiss, tab, qual, uniprot-xml, gff3
        
        JMESPath_
        ---------
        The root node for a query is a list of SeqRecord_ objects. The query can return a list with a subset of these or
        a mapping, keying to the `constructor parameters`_ of a SeqRecord object.
        
        
        Examples:
            Append a new record::
        
                [@, [{`seq`: `AAAA`, `name`: `my_new_record`}]] | []
        
            Filter out any plasmids::
        
                [?!(features[?type==`source`].qualifiers.plasmid)]
        
            Keep only the first record::
        
                [0]
        
        
        See CONTRIBUTING.rst_ for information on contributing to this repo.
        
        .. _CONTRIBUTING.rst: CONTRIBUTING.rst
        .. _JMESPath: http://jmespath.org/
        .. _SeqRecord: https://biopython.org/DIST/docs/api/Bio.SeqRecord.SeqRecord-class.html
        .. _constructor parameters: https://biopython.org/DIST/docs/api/Bio.SeqRecord.SeqRecord-class.html#__init__
        
        
Keywords: convert,biopython,bioinformatics,gff,genbank,embl,filter,fasta,fastq
Platform: UNKNOWN
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/x-rst; charset=UTF-8
