API library interface¶
sequenza.izip¶
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class
sequenza.izip.
zip_coordinates
(item1, item2)[source]¶ Merge two object that have coordinate chromosome/position. The format of the objects must be a tuple with (coordinates, data) where coordinate is a tuple with chromosome,position_start, position_end and data is a tuple with the data. The data of the two object will be merged for matching lines. For the first object only the start coordinate is taken into account.
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sequenza.izip.
zip_fast
(item1, item2)[source]¶ Use the native implementation of the heapq algorithm to sort and merge files chromosome-coordinate ordered. It assumes that the two files are position ordered and both files have the same chromosome order. It differs from zip_coordinates by the fact that this return all the position present in both files, group together the lines present in both
sequenza.wig¶
sequenza.fasta¶
sequenza.pileup¶
sequenza.samtools¶
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class
sequenza.samtools.
bam_mpileup
(bam, fasta, q=20, Q=20, samtools_bin='samtools', regions=[])[source]¶ Use samtools via subprocess and return an iterable object.
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class
sequenza.samtools.
indexed_pileup
(pileup, tabix_bin='tabix', regions=[])[source]¶ Use tabix via subprocess to slice the pileup data and return an iterable object