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Add --fixedStep option for bigwigCompare #1028

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merged 3 commits into from
May 12, 2023
Merged

Add --fixedStep option for bigwigCompare #1028

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a40e25d
Add --fixedStep option for bigwigCompare
icebert Dec 10, 2020
e55f24f
Merge branch 'deeptools:master' into master
icebert May 15, 2022
430c161
trigger new build
bgruening Apr 4, 2023
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7 changes: 6 additions & 1 deletion deeptools/bigwigCompare.py
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Original file line number Diff line number Diff line change
Expand Up @@ -93,6 +93,10 @@ def parse_arguments(args=None):
'zeros may be wrong and this option should be used ',
action='store_true')

parser.add_argument('--fixedStep',
help='Output in fixed step of bin size (as specified by --binSize), not merging '
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If anyone has a better phrasing here that would be great. I think the PR is fine but the sentences is a bit confusing for me.

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@WardDeb any idea?

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Agreed the wording is a bit confusing.
Perhaps:
'Write out all bins (of size --binSize) instead of merging neighbouring bins with equal values.' ?

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I'll take it along in develop for now and will make the change afterwards.

'neighboring bins with same values in the output file',
action='store_true')
return parser


Expand Down Expand Up @@ -168,7 +172,8 @@ def main(args=None):
format=args.outFileFormat,
smoothLength=False,
missingDataAsZero=not args.skipNonCoveredRegions,
extendPairedEnds=False)
extendPairedEnds=False,
fixedStep=args.fixedStep)

# Clean up temporary bigWig files, if applicable
if not args.deepBlueKeepTemp:
Expand Down
14 changes: 7 additions & 7 deletions deeptools/writeBedGraph_bam_and_bw.py
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Expand Up @@ -45,7 +45,7 @@ def writeBedGraph_wrapper(args):
def writeBedGraph_worker(
chrom, start, end, tileSize, defaultFragmentLength,
bamOrBwFileList, func, funcArgs, extendPairedEnds=True, smoothLength=0,
skipZeroOverZero=False, missingDataAsZero=False, fixed_step=False):
skipZeroOverZero=False, missingDataAsZero=False, fixedStep=False):
r"""
Writes a bedgraph having as base a number of bam files.

Expand Down Expand Up @@ -103,12 +103,12 @@ def writeBedGraph_worker(

value = func(tileCoverage, funcArgs)

if fixed_step:
if fixedStep:
writeStart = start + tileIndex * tileSize
writeEnd = min(writeStart + tileSize, end)
try:
_file.write(toBytes("%s\t%d\t%d\t%.2f\n" % (chrom, writeStart,
writeEnd, value)))
_file.write(toBytes("{0}\t{1}\t{2}\t{3:g}\n".format(chrom, writeStart,
writeEnd, value)))
except TypeError:
_file.write(toBytes("{}\t{}\t{}\t{}\n".format(chrom, writeStart,
writeEnd, value)))
Expand All @@ -130,7 +130,7 @@ def writeBedGraph_worker(
writeStart = writeEnd
writeEnd = min(writeStart + tileSize, end)

if not fixed_step:
if not fixedStep:
# write remaining value if not a nan
if previousValue and writeStart != end and \
not np.isnan(previousValue):
Expand All @@ -146,7 +146,7 @@ def writeBedGraph(
bamOrBwFileList, outputFileName, fragmentLength,
func, funcArgs, tileSize=25, region=None, blackListFileName=None, numberOfProcessors=1,
format="bedgraph", extendPairedEnds=True, missingDataAsZero=False,
skipZeroOverZero=False, smoothLength=0, fixed_step=False, verbose=False):
skipZeroOverZero=False, smoothLength=0, fixedStep=False, verbose=False):
r"""
Given a list of bamfiles, a function and a function arguments,
this method writes a bedgraph file (or bigwig) file
Expand Down Expand Up @@ -205,7 +205,7 @@ def writeBedGraph(

res = mapReduce.mapReduce((tileSize, fragmentLength, bamOrBwFileList,
func, funcArgs, extendPairedEnds, smoothLength,
skipZeroOverZero, missingDataAsZero, fixed_step),
skipZeroOverZero, missingDataAsZero, fixedStep),
writeBedGraph_wrapper,
chromNamesAndSize,
genomeChunkLength=genomeChunkLength,
Expand Down