src.features.affymetrix

Created on Wed Jun 9 16:39:57 2021

@author: Paolo Cozzi <paolo.cozzi@ibba.cnr.it>

src.features.affymetrix.read_Manifest(path: Path, delimiter: str = ',') → namedtuple

Open an affymetrix manifest file and yields records as namedtuple. Add an additional column for manifacured date (when SNP is recorded in datafile)

Parameters

• path (Path) – The position of manifest file.

• delimiter (str, optional) – field delimiter. The default is “,”.

Yields

record (collections.namedtuple) – A single SNP record from manifest.

src.features.affymetrix.read_affymetrixRow(path: Path, delimiter='\t') → namedtuple

Open an affymetrix report file and yields namedtuple. Add two additional columns for the number of SNPs and samples in each returned record

Parameters

• path (Path) – The path of report file.

• delimiter (str, optional) – Fields delimiter. The default is ” “.

Yields

record (collections.namedtuple) – A single record (a SNP over all samples + affymetrix information)

src.features.affymetrix.search_manifactured_date(header: list) → Optional[datetime]

Grep manifactured date from affymetrix header

Parameters

header (list) – affymetrix header section

Returns

a datetime object

Return type

datetime.datetime

src.features.affymetrix.search_n_samples(header: list) → int

Grep number of samples in affymetrix reportfile

Parameters

header (list) – affymetrix header section

Returns

the number of samples in file

Return type

int

src.features.affymetrix.search_n_snps(header: list) → int

Grep number of SNPs in affymetrix reportfile

Parameters

header (list) – affymetrix header section

Returns

the number of SNPs in file

Return type

int