file_io module

module which holds all functions relating to loading reference files

mavis.annotate.file_io.load_masking_regions(filepath)

reads a file of regions. The expect input format for the file is tab-delimited and the header should contain the following columns

• chr: the chromosome
• start: start of the region, 1-based inclusive
• end: end of the region, 1-based inclusive
• name: the name/label of the region

For example:

#chr    start   end     name
chr20   25600000        27500000        centromere

Parameters:filepath (str) – path to the input tab-delimited file Returns:a dictionary keyed by chromosome name with values of lists of regions on the chromosome Return type:dict of list of BioInterval by str

Example

>>> m = load_masking_regions('filename')
>>> m['1']
[BioInterval(), BioInterval(), ...]

mavis.annotate.file_io.load_reference_genes(filepath, verbose=True, REFERENCE_GENOME=None, filetype=None, best_transcripts_only=False)

loads gene models from an input file. Expects a tabbed or json file.

Parameters:

• filepath (str) – path to the input file
• verbose (bool) – output extra information to stdout
• REFERENCE_GENOME (dict of Bio.SeqRecord by str) – dict of reference sequence by template/chr name
• filetype (str) – json or tab/tsv. only required if the file type can’t be interpolated from the path extenstion

Returns:

lists of genes keyed by chromosome name

Return type:

dict of list of Gene by str

mavis.annotate.file_io.load_reference_genome(filename, low_mem=False)

Parameters:filename (str) – the path to the file containing the input fasta genome Returns:

a dictionary representing the sequences in the

fasta file

Return type:dict of Bio.SeqRecord by str

mavis.annotate.file_io.load_templates(filename)

primarily useful if template drawings are required and is not necessary otherwise assumes the input file is 0-indexed with [start,end) style. Columns are expected in the following order, tab-delimited. A header should not be given

1. name
2. start
3. end
4. band_name
5. giesma_stain

for example

chr1    0       2300000 p36.33  gneg
chr1    2300000 5400000 p36.32  gpos25

Parameters:filename (str) – the path to the file with the cytoband template information Returns:list of the templates loaded Return type:list of Template