API Reference

A python module for using rust to access data from fiberseq BAM files.

class pyft.Fiberbam(bam_file, threads=8)

Bases: object

Open a fiberseq bam file. Must have an index.

center(chrom, start, end, strand='+'): Returns an iterator over Fiberdata objects; however, the data is centered around the region that has been fetched (should work the same as ft center).

fetch(chrom, start=None, end=None): Returns an iterator over Fiberdata objects for the selected region. Arguments for the region to fetch can be provided in multiple ways, e.g.:

fiberdata.fetch(“chr1”, 100, 200)

fiberdata.fetch(“chr1”, start=100, end=200)

fiberdata.fetch(“chr1:100-200”)

fiberdata.fetch(“chr1”)

class pyft.Fiberdata

Bases: object

Class for fiberseq data. This class corresponds to a single record in the bam file.

aligned_block_pairs: Aligned block pairs from the bam record

chrom: Chromosome

cpg: cpg Basemods object

ec: Number of c_s

end: Chromosome end

get_seq_length(): return the length of the sequence

hp: Haplotype tag

lift_query_positions(positions): liftover query (fiber) positions to the reference

lift_reference_positions(positions): liftover reference positions to the query (fiber)

m6a: m6a Basemods object

msp: Ranges object for msp features

nuc: Ranges object for nuc features

offset: offset for centering the fiber

qname: Name of the read

rg: Read group

rq: Read quality

sam_flag: SAM flag

seq: Read sequence

start: Chromosome start

strand: Strand

class pyft.Basemods(starts, reference_starts, ml)

Bases: object

Class for describing base modifications within fiberseq data. For example, m6a and 5mC (cpg) features.

get_ends(): return ends, start + 1

get_reference_ends(): return reference ends, start + 1

ml: Basemod ML

reference_starts: Basemod reference starts

starts: Basemod starts

class pyft.Ranges(starts, lengths, qual, reference_starts, reference_lengths)

Bases: object

Class for describing ranges within fiberseq data. For example, nucleosomes and msp features.

ends: Range ends

lengths: Range lengths

qual: quals

reference_ends: Reference ends

reference_lengths: Reference lengths

reference_starts: Reference starts

starts: Range starts

class pyft.Fiberwriter(output_bam_path, template_bam_path)

Bases: object

write(fiberdata): Write a Fiberdata object to a bam file.

utils.empty_data_dict()[source]

utils.footprint_code_to_vec(footprint_code, n_modules)[source]: Convert a footprint code to a boolean vector of length n_modules

utils.read_footprint_table(f, long=False)[source]: Read a ft-footprint bed into a pandas dataframe

utils.read_and_center_footprint_table(f)[source]: Read a ft-footprint bed into a pandas dataframe and reformat the data to reflect ft-center output

utils.read_center_table(f)[source]: Read a ft-center bed into a pandas dataframe

utils.region_to_centered_df(fiberbam, region, strand='+', max_flank=None, min_basemod_qual=125)[source]: Takes a fiberbam and a region and returns a pandas dataframe with reference centered positions

utils.region_to_df(fiberbam, region, min_basemod_qual=125)[source]: Takes a fiberbam and a region and returns a pandas dataframe with fibers that overlap the region