cutcounts submodule#
This modules contains classes and functions to compute cleavage counts directly from an alignment file.
- exception footprint_tools.cutcounts.GenotypeError#
- exception footprint_tools.cutcounts.ReadError(e)#
- ERROR_5PROXIMITY = (1, "Variant too close to 5' end of tag")#
- ERROR_ALIGNMENT = (0, 'Read alignment problematic (QC fail, duplicate, or MAPQ < 1)')#
- ERROR_BASEQ = (2, 'Base quality < 20')#
- ERROR_GENOTYPE = (3, 'Base does not match reference or expected alternate allele')#
- ERROR_MISMATCH = (4, 'Read contains too many mismatches')#
- class footprint_tools.cutcounts.bamfile(filepath, min_qual=1, remove_dups=False, remove_qcfail=True, offset=(0, - 1))#
Class to access BAM files
- Attributes
- min_qualint
Filter reads by minimim mapping quality (MAPQ)
- offsettuple
Position offsets to apply to the + and - strands,. DNase I data (0, -1). Tn5-derived data would use (4,-5). (default = (0, -1))
- remove_dupsbool
Remove reads with duplicate flag (512) set
- remove_qcfailbool
Remove reads with QC fail flag (1024) set
- samfilepysam.Samfile
SAM/BAM file object
- close()#
Closes BAM file
- lookup(interval)#
Lookup reads in a defined genomic region
- Parameters
- intervals: iterable (genomic_interval)
- Returns
- counts: dict
Dictionary of read counts (keys: ‘+’ or ‘-), which contain arrays with counts on each strand
- lookup_allelic(chrom, start, end, pos, ref, alt, flip=False)#
Lookup function for allelically resolved counts
- Parameters
- Returns
- read_pair_generator(chrom, start, end)#
Generator function that returns sequencing tags within a given region
- Parameters
- chromstr
Chromosome
- startint
Start coordinate
- endint
End coordinate
- Yields
- reads: tuple
A tuple of
pysam.AlignedSegment. Elements may be NoneType if single-end sequencing or one of pairs falls outisde of query range.
- validate_read(read)#
Validate BAM tag
- Parameters
- read
pysam.AlignedSegment Read from BAM/SAM file
- read
- Returns
- read:class:pysam.AlignedSegment
Same read as input
- Raises
- ReadError
Raises error if read fails QC flag, is a duplicate or MAPQ < minimum