The gtftk.bam.bam_coverage_matrix module¶
A module to compute bigwig coverage over a set of regions (bed).
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pygtftk.bwig.bw_coverage.
bw_cov_mp
(bw_list=None, region_file=None, labels=None, bin_nb=None, nb_proc=None, n_highest=None, zero_to_na=False, pseudo_count=None, stat='mean', verbose=False)¶ Compute bigwig coverage (multi-processed) for a set of regions.
Parameters: - bw_list – the list of bigWig files to be processed.
- region_file – the bed file containing the region for which coverage is to be computed.
- labels – shortname for bigwigs.
- bin_nb – The number of bin into which the region should be splitted.
- nb_proc – Number of threads to be used.
- n_highest – compute the mean coverage based on the n highest values in the bins.
- pseudo_count – The value for a pseudo-count.
- verbose – run in verbose mode.
- stat – mean (default) or sum.
- zero_to_na – Convert missing values to NA, not zero.
Returns a file.
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pygtftk.bwig.bw_coverage.
bw_profile_mp
(in_bed_file=None, nb_proc=None, big_wig=None, bin_nb=None, pseudo_count=0, stranded=True, type=None, labels=None, outputfile=None, zero_to_na=False, bed_format=False, add_score=False, stat='mean', verbose=False)¶ Compute bigwig profile for a set of regions.
Parameters: - in_bed_file – the bed file containing the region for which coverage is to be computed.
- nb_proc – Number of threads to be used.
- big_wig – The bigWig files to be processed.
- bin_nb – The number of bin into which the region should be splitted.
- pseudo_count – The value for a pseudo-count.
- stranded – controls whether the profile should be ordered based on strand.
- type – This string will be added to the output to indicate the type of region (e.g tss, promoter,…).
- labels – shortname for bigwigs.
- outputfile – output file name.
- zero_to_na – Convert missing values to NA, not zero.
- bed_format – Force Bed format. Default is to write columns in the following way: bwig, chrom, start, end, gene/feature, strand…
- add_score – add a ‘score’ column (“.”). Just for downstream compatibility).
- stat – mean (default) or sum.
- verbose – run in verbose mode.
Returns a file.