rotifer.genome.io.parse#

rotifer.genome.io.parse(handle, informat, *args, assembly=<function GenbankAssemblyFromFilename>, **kwargs)[source]#

Load genomic data from sequence file(s). This method crates an iterator capable of return SeqRecords.

Arguments:

  • handle : one or more file handles or filenames

  • informat : either gff or a Bio.SeqIO supported format

  • assemblyrule for setting genome assembly accession ID

    Assembly identifiers are not part of the INSDC (http://www.insdc.org/) standard but can be found in some NCBI entries under the DBLINK tag, such as in many RefSeq entries:

    DBLINK BioProject: PRJNA224116

    BioSample: SAMEA3138382 Assembly: GCF_000210855.2 <– here!

    This parameter allows the user to automate the definition of genome identifiers. You can use either a string or a lambda function that takes two arguments: file path and sequence record object.

    See GenbankAssemblyFromFilename and SequenceNameToAssembly for examples of functions compatible with this parameter.

  • retvalue : object(s) type to return. Supported objects are

Other arguments depend on the parser (see methods below)