Top-Level Namespace

Everything below is importable directly from finaletoolkit without knowing the internal submodule layout:

import finaletoolkit as ftk

results = ftk.coverage("sample.bam", "intervals.bed", output_file=None)
motifs = ftk.end_motifs("sample.bam", "hg38.2bit", k=4)
gaps = ftk.GenomeGaps.hg38()

You can also import each feature from its submodule:

from finaletoolkit.frag import wps, multi_wps, delfi
from finaletoolkit.utils import frag_generator, agg_bw, filter_file
from finaletoolkit.genome import GenomeGaps, ContigGaps
from finaletoolkit.io import ReferenceWrapper, AlignmentWrapper, Fragment

Fragmentation features

  • frag_length, frag_length_bins, frag_length_intervals

  • coverage, single_coverage

  • wps, multi_wps, adjust_wps

  • cleavage_profile, multi_cleavage_profile

  • delfi, delfi_gc_correct, delfi_merge_bins

  • end_motifs, region_end_motifs, interval_end_motifs

  • breakpoint_motifs, region_breakpoint_motifs, interval_breakpoint_motifs

  • end_motif / breakpoint_motif

Result and container types

  • CoverageResult, FragLengthStats

  • EndMotifFreqs, EndMotifsIntervals

  • BreakpointMotifFreqs, BreakpointMotifsIntervals

Utilities

  • frag_generator, frag_array, frags_in_region, frag_bam_to_bed

  • agg_bw, filter_file

  • get_intervals, overlaps, gen_kmers, reverse_complement

  • chrom_sizes_to_dict, chrom_sizes_to_list, low_quality_read_pairs

I/O and genome annotations

  • ReferenceWrapper, AlignmentWrapper, Fragment

  • GenomeGaps, ContigGaps

  • ucsc_hg19_gap_bed, b37_gap_bed, ucsc_hg38_gap_bed

Exceptions

See Exceptions.