pycallingcards.preprocessing.clean_qbed#

pycallingcards.preprocessing.clean_qbed(qbed, chrom=['chr1', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr2', 'chr20', 'chr21', 'chr22', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chrX', 'chrY', 'chrI', 'chrII', 'chrIII', 'chrIV', 'chrV', 'chrVI', 'chrVII', 'chrVIII', 'chrIX', 'chrX', 'chrXI', 'chrXII', 'chrXIII', 'chrXIV', 'chrXV', 'chrXVI'])[source]#

Clean qbed with some extra chromosomes. Only preserve insertions in chrom.

Parameters:

qbed (DataFrame) – qbed file.
chrom (list (default: ['chr1', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr2', 'chr20', 'chr21', 'chr22', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chrX', 'chrY', 'chrI', 'chrII', 'chrIII', 'chrIV', 'chrV', 'chrVI', 'chrVII', 'chrVIII', 'chrIX', 'chrX', 'chrXI', 'chrXII', 'chrXIII', 'chrXIV', 'chrXV', 'chrXVI'])) – list of valid chromosomes.

Returns:

pd.DataFrame for the cleaned qbed file.

Return type:

DataFrame

Example:

>>> import pycallingcards as cc
>>> qbed = cc.rd.read_qbed("https://github.com/The-Mitra-Lab/pycallingcards_data/releases/download/data/SP1_P10.txt")
>>> qbed = cc.pp.clean_qbed(qbed)