MACS.py - Parser for MACS output

Author:Andreas Heger Release:$Id$ Date:December 09, 2013 Tags:Python

The Pipeline module contains various utility functions for parsing MACS output.

API

class WrapperMACS.MacsPeak

Bases: tuple

MacsPeak(contig, start, end, length, summit, tags, pvalue, fold, fdr)

contig

Alias for field number 0

count(value) → integer -- return number of occurrences of value

end

Alias for field number 2

fdr

Alias for field number 8

fold

Alias for field number 7

index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

length

Alias for field number 3

pvalue

Alias for field number 6

start

Alias for field number 1

summit

Alias for field number 4

tags

Alias for field number 5

WrapperMACS.iterateMacsPeaks(infile)

iterate over peaks.xls file and return parsed data. The fdr is converted from percent to values between 0 and 1.

class WrapperMACS.Macs2Peak

Bases: tuple

Macs2Peak(contig, start, end, length, summit, pileup, pvalue, fold, fdr, name)

contig

Alias for field number 0

count(value) → integer -- return number of occurrences of value

end

Alias for field number 2

fdr

Alias for field number 8

fold

Alias for field number 7

index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

length

Alias for field number 3

name

Alias for field number 9

pileup

Alias for field number 5

pvalue

Alias for field number 6

start

Alias for field number 1

summit

Alias for field number 4

WrapperMACS.iterateMacs2Peaks(infile)

iterate over peaks.xls file and return parsed data. The fdr is converted from percent to values between 0 and 1.