biopython.convert 1.2.0

Interconvert various file formats supported by biopython. Supports querying records with JMESPath.

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, txt, json, yaml

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.

If the formats are txt, json, or yaml, then the JMESPath resulting object will simply be dumped in those formats.

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]

Output taxonomy of each record (txt output):

[*].annotations.taxonomy

Output json object containing id and molecule type:

[*].{id: id, type: annotations.molecule_type}

See CONTRIBUTING.rst for information on contributing to this repo.