coverage¶
coverage module have 3 functions
- one which is an interface to pysam.
- an other with the same api to call the wig.chromosomes
- the third is a function selector accordingly the data input, wig or bam.
get_bam_coverage¶
Get coverage from pysam for reference (chromosome) for an interval of positions, a quality on both strand.
and convert the coverage return by pysam. A score on each position for each base (ACGT)) in a global coverage for this
position.
It also aligned all coverages return by pysam on the reference position by padding left and right by None
.
This function is called for each entry of the annotation file.
get_wig_coverage¶
Get coverage from craw.wig.Genome
instance for reference (chromosome) for an interval of positions, on both strand.
The quality parameter is here just to have the same signature as get_bam_coverage but will be ignores .
It also aligned all coverages return by the Chromosome on the reference position by padding left and right by None
.
This function is called for each entry of the annotation file.
coverage API reference¶
craw.coverage.
get_bam_coverage
(sam_file, annot_entry, start=None, stop=None, qual_thr=15, max_left=0, max_right=0)[source]¶Compute the coverage for a region position by position on each strand
Parameters:
- sam_file (
pysam.AlignmentFile
object.) – the samfile openend with pysam- annot_entry (
annotation.Entry
object) – an entry of the annotation file- start (int) – The position to start to compute the coverage(coordinates are 0-based, start position is included).
- stop (int) – The position to start to compute the coverage (coordinates are 0-based, stop position is excluded).
- qual_thr (int) – The quality threshold
- max_left (int) – The highest number of base before the reference position to take in account.
- max_right (int) – The highest number of base after the reference position to take in account.
Returns: the coverage (all bases)
Return type: tuple of 2 list containing int
craw.coverage.
get_coverage_function
(input)[source]¶
Parameters: input ( wig.Genome
orpysam.calignmentfile.AlignmentFile
object) – the input either a samfile (see pysam library) or a genome build from a wig file (see wig module)Returns: get_wig_coverage or get_bam_coverage according the type of input Return type: function Raises RuntimeError: when input is not instance of pysam.calignmentfile.AlignmentFile
orwig.Genome
craw.coverage.
get_wig_coverage
(genome, annot_entry, start=None, stop=None, max_left=0, max_right=0, qual_thr=None)[source]¶
Parameters:
- annot_entry (
annotation.Entry
object) – an entry of the annotation file- start (int) – The position to start to compute the coverage(coordinates are 0-based, start position is included).
- stop (int) – The position to start to compute the coverage (coordinates are 0-based, stop position is excluded).
- max_left (int) – The highest number of base before the reference position to take in account.
- max_right (int) – The highest number of base after the reference position to take in account.
- qual_thr (None) – this parameter is not used, It’s here to have the same api as get_bam_coverage.
Returns: the coverage (all bases)
Return type: tuple of 2 list containing int