From 33d9fac3e8da4624bbe0c4a73bd6f5bd4629e578 Mon Sep 17 00:00:00 2001 From: dpryan79 Date: Tue, 3 Sep 2019 14:18:30 +0200 Subject: [PATCH 1/3] Fix #868 --- deeptools/plotCorrelation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deeptools/plotCorrelation.py b/deeptools/plotCorrelation.py index 1259c13bc..fba77f817 100644 --- a/deeptools/plotCorrelation.py +++ b/deeptools/plotCorrelation.py @@ -28,7 +28,7 @@ def parse_arguments(args=None): multiBigwigSummary. Pearson or Spearman methods are available to compute correlation coefficients. Results can be saved as multiple scatter plots depicting the pairwise correlations or as a clustered heatmap, -where the colors represent the correlation coefficients and the clusters are joined using the Nearest Point Algorithm (also known as "single"). +where the colors represent the correlation coefficients and the clusters are constructed using complete linkage. Optionally, the values can be saved as tables, too. From 09d7f6734ecb28350d318a107aa115cb124636d1 Mon Sep 17 00:00:00 2001 From: dpryan79 Date: Tue, 3 Sep 2019 14:25:54 +0200 Subject: [PATCH 2/3] Fix #867 --- CHANGES.txt | 1 + deeptools/bigwigCompare.py | 3 +-- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGES.txt b/CHANGES.txt index 819521098..3a4025db5 100644 --- a/CHANGES.txt +++ b/CHANGES.txt @@ -4,6 +4,7 @@ * Fixed compatibility with matplotlib 3 and restrict to at least that version. * The Y-axis labels should once again appear in both plotHeatmap and plotProfile (issue #844). This was related to the previous point. * Testing is no longer performed with python 2.7, which will reach end of life in a couple months. + * Various documentation updates (issues #868, #867 and #851). 3.3.0 diff --git a/deeptools/bigwigCompare.py b/deeptools/bigwigCompare.py index 80738840c..69cb11158 100644 --- a/deeptools/bigwigCompare.py +++ b/deeptools/bigwigCompare.py @@ -73,8 +73,7 @@ def parse_arguments(args=None): 'the negative of the inverse of the ratio ' 'if the ratio is less than 0. The resulting ' 'values are interpreted as negative fold changes. ' - '*NOTE*: Only with --operation subtract can --normalizeUsing RPGC or ' - '--normalizeUsing RPKM be used. Instead of performing a ' + 'Instead of performing a ' 'computation using both files, the scaled signal can ' 'alternatively be output for the first or second file using ' 'the \'--operation first\' or \'--operation second\'', From 0ae23138df7afb1b35ac57884db716dc21ac2eab Mon Sep 17 00:00:00 2001 From: dpryan79 Date: Tue, 3 Sep 2019 14:59:47 +0200 Subject: [PATCH 3/3] Default ALL the things! --- deeptools/alignmentSieve.py | 8 +++---- deeptools/bamCompare.py | 10 ++++---- deeptools/bamCoverage.py | 2 +- deeptools/bamPEFragmentSize.py | 10 ++++---- deeptools/bigwigCompare.py | 4 ++-- deeptools/computeGCBias.py | 4 ++-- deeptools/computeMatrix.py | 36 ++++++++++++++-------------- deeptools/computeMatrixOperations.py | 4 ++-- deeptools/estimateReadFiltering.py | 12 +++++----- deeptools/multiBamSummary.py | 4 ++-- deeptools/multiBigwigSummary.py | 4 ++-- deeptools/parserCommon.py | 22 ++++++++--------- deeptools/plotCorrelation.py | 6 ++--- deeptools/plotCoverage.py | 8 +++---- deeptools/plotEnrichment.py | 8 +++---- deeptools/plotFingerprint.py | 6 ++--- deeptools/plotPCA.py | 10 ++++---- 17 files changed, 79 insertions(+), 79 deletions(-) diff --git a/deeptools/alignmentSieve.py b/deeptools/alignmentSieve.py index c1dcea5d1..45851958b 100644 --- a/deeptools/alignmentSieve.py +++ b/deeptools/alignmentSieve.py @@ -30,7 +30,7 @@ def parseArguments(): general.add_argument('--numberOfProcessors', '-p', help='Number of processors to use. Type "max/2" to ' 'use half the maximum number of processors or "max" ' - 'to use all available processors.', + 'to use all available processors. (Default: %(default)s)', metavar="INT", type=parserCommon.numberOfProcessors, default=1, @@ -80,7 +80,7 @@ def parseArguments(): filtering.add_argument('--filterRNAstrand', help='Selects RNA-seq reads (single-end or paired-end) in ' - 'the given strand.', + 'the given strand. (Default: %(default)s)', choices=['forward', 'reverse'], default=None) @@ -129,7 +129,7 @@ def parseArguments(): help='The minimum fragment length needed for read/pair ' 'inclusion. This option is primarily useful ' 'in ATACseq experiments, for filtering mono- or ' - 'di-nucleosome fragments.', + 'di-nucleosome fragments. (Default: %(default)s)', metavar='INT', default=0, type=int, @@ -137,7 +137,7 @@ def parseArguments(): filtering.add_argument('--maxFragmentLength', help='The maximum fragment length needed for read/pair ' - 'inclusion.', + 'inclusion. A value of 0 indicates no limit. (Default: %(default)s)', metavar='INT', default=0, type=int, diff --git a/deeptools/bamCompare.py b/deeptools/bamCompare.py index 184b005fd..bbbbe848b 100644 --- a/deeptools/bamCompare.py +++ b/deeptools/bamCompare.py @@ -85,7 +85,7 @@ def getOptionalArgs(): 'If a method is specified, then it will be used to compensate ' 'for sequencing depth differences between the samples. ' 'As an alternative, this can be set to None and an option from ' - '--normalizeUsing can be used.', + '--normalizeUsing can be used. (Default: %(default)s)', choices=['readCount', 'SES', 'None'], default='readCount') @@ -97,14 +97,14 @@ def getOptionalArgs(): 'If you do not have a good sequencing depth for ' 'your samples consider increasing the sampling ' 'regions\' size to minimize the probability ' - 'that zero-coverage regions are used.', + 'that zero-coverage regions are used. (Default: %(default)s)', default=1000, type=int) optional.add_argument('--numberOfSamples', '-n', help='*Only relevant when SES is chosen for the ' 'scaleFactorsMethod.* Number of samplings taken ' - 'from the genome to compute the scaling factors.', + 'from the genome to compute the scaling factors. (Default: %(default)s)', default=1e5, type=int) @@ -125,7 +125,7 @@ def getOptionalArgs(): 'values are interpreted as negative fold changes. ' 'Instead of performing a computation using both files, the scaled signal can ' 'alternatively be output for the first or second file using ' - 'the \'--operation first\' or \'--operation second\'', + 'the \'--operation first\' or \'--operation second\'. (Default: %(default)s)', default='log2', choices=['log2', 'ratio', 'subtract', 'add', 'mean', 'reciprocal_ratio', 'first', 'second'], @@ -137,7 +137,7 @@ def getOptionalArgs(): 'You can specify different values as pseudocounts for ' 'the numerator and the denominator by providing two ' 'values (the first value is used as the numerator ' - 'pseudocount and the second the denominator pseudocount).', + 'pseudocount and the second the denominator pseudocount). (Default: %(default)s)', default=[1], type=float, nargs='+', diff --git a/deeptools/bamCoverage.py b/deeptools/bamCoverage.py index c97cadf57..f2bb2e423 100644 --- a/deeptools/bamCoverage.py +++ b/deeptools/bamCoverage.py @@ -67,7 +67,7 @@ def get_optional_args(): optional.add_argument('--scaleFactor', help='The computed scaling factor (or 1, if not applicable) will ' - 'be multiplied by this.', + 'be multiplied by this. (Default: %(default)s)', default=1.0, type=float, required=False) diff --git a/deeptools/bamPEFragmentSize.py b/deeptools/bamPEFragmentSize.py index fa458e36e..70764b484 100644 --- a/deeptools/bamPEFragmentSize.py +++ b/deeptools/bamPEFragmentSize.py @@ -51,7 +51,7 @@ def parse_arguments(): parser.add_argument('--numberOfProcessors', '-p', help='Number of processors to use. The default is ' - 'to use 1.', + 'to use 1. (Default: %(default)s)', metavar="INT", type=int, default=1, @@ -65,10 +65,10 @@ def parse_arguments(): nargs='+') parser.add_argument('--plotTitle', '-T', help='Title of the plot, to be printed on top of ' - 'the generated image. Leave blank for no title.', + 'the generated image. Leave blank for no title. (Default: %(default)s)', default='') parser.add_argument('--maxFragmentLength', - help='The maximum fragment length in the histogram. A value of 0 (the default) indicates to use twice the mean fragment length', + help='The maximum fragment length in the histogram. A value of 0 (the default) indicates to use twice the mean fragment length. (Default: %(default)s)', default=0, type=int) parser.add_argument('--logScale', @@ -76,7 +76,7 @@ def parse_arguments(): action='store_true') parser.add_argument('--binSize', '-bs', metavar='INT', - help='Length in bases of the window used to sample the genome. (default 1000)', + help='Length in bases of the window used to sample the genome. (Default: %(default)s)', default=1000, type=int) parser.add_argument('--distanceBetweenBins', '-n', @@ -87,7 +87,7 @@ def parse_arguments(): 'for high coverage samples, while smaller values are useful for ' 'lower coverage samples. Note that if you specify a value that ' 'results in too few (<1000) reads sampled, the value will be ' - 'decreased. (default 1000000)', + 'decreased. (Default: %(default)s)', default=1000000, type=int) parser.add_argument('--blackListFileName', '-bl', diff --git a/deeptools/bigwigCompare.py b/deeptools/bigwigCompare.py index 69cb11158..e4d69da20 100644 --- a/deeptools/bigwigCompare.py +++ b/deeptools/bigwigCompare.py @@ -54,7 +54,7 @@ def parse_arguments(args=None): 'You can specify different values as pseudocounts for ' 'the numerator and the denominator by providing two ' 'values (the first value is used as the numerator ' - 'pseudocount and the second the denominator pseudocount).', + 'pseudocount and the second the denominator pseudocount). (Default: %(default)s)', default=1, nargs='+', action=parserCommon.requiredLength(1, 2), @@ -76,7 +76,7 @@ def parse_arguments(args=None): 'Instead of performing a ' 'computation using both files, the scaled signal can ' 'alternatively be output for the first or second file using ' - 'the \'--operation first\' or \'--operation second\'', + 'the \'--operation first\' or \'--operation second\' (Default: %(default)s)', default='log2', choices=['log2', 'ratio', 'subtract', 'add', 'mean', 'reciprocal_ratio', 'first', 'second'], diff --git a/deeptools/computeGCBias.py b/deeptools/computeGCBias.py index af68ecf5e..cc27b88be 100644 --- a/deeptools/computeGCBias.py +++ b/deeptools/computeGCBias.py @@ -94,7 +94,7 @@ def getRequiredArgs(): optional.add_argument('--sampleSize', default=5e7, - help='Number of sampling points to be considered.', + help='Number of sampling points to be considered. (Default: %(default)s)', type=int) optional.add_argument('--extraSampling', @@ -130,7 +130,7 @@ def getRequiredArgs(): 'standard fragment size for Illumina machines. However, ' 'if the depth of sequencing is low, a larger bin size ' 'will be required, otherwise many bins will not ' - 'overlap with any read') + 'overlap with any read (Default: %(default)s)') return parser diff --git a/deeptools/computeMatrix.py b/deeptools/computeMatrix.py index 46b17905b..345bbc79a 100644 --- a/deeptools/computeMatrix.py +++ b/deeptools/computeMatrix.py @@ -144,7 +144,7 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]): default=1000, type=int, help='Distance in bases to which all regions will ' - 'be fit.') + 'be fit. (Default: %(default)s)') optional.add_argument('--startLabel', default='TSS', help='Label shown in the plot for the start of ' @@ -153,38 +153,38 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]): 'e.g. "peak start". Note that this is only ' 'useful if you plan to plot the results yourself ' 'and not, for example, with plotHeatmap, which ' - 'will override this.') + 'will override this. (Default: %(default)s)') optional.add_argument('--endLabel', default='TES', help='Label shown in the plot for the region ' 'end. Default is TES (transcription end site). ' 'See the --startLabel option for more ' - 'information. ') + 'information. (Default: %(default)s) ') optional.add_argument('--beforeRegionStartLength', '-b', '--upstream', default=0, type=int, help='Distance upstream of the start site of ' 'the regions defined in the region file. If the ' 'regions are genes, this would be the distance ' - 'upstream of the transcription start site.') + 'upstream of the transcription start site. (Default: %(default)s)') optional.add_argument('--afterRegionStartLength', '-a', '--downstream', default=0, type=int, help='Distance downstream of the end site ' 'of the given regions. If the ' 'regions are genes, this would be the distance ' - 'downstream of the transcription end site.') + 'downstream of the transcription end site. (Default: %(default)s)') optional.add_argument("--unscaled5prime", default=0, type=int, help='Number of bases at the 5-prime end of the ' 'region to exclude from scaling. By default, ' - 'each region is scaled to a given length (see the --regionBodyLength option). In some cases it is useful to look at unscaled signals around region boundaries, so this setting specifies the number of unscaled bases on the 5-prime end of each boundary.') + 'each region is scaled to a given length (see the --regionBodyLength option). In some cases it is useful to look at unscaled signals around region boundaries, so this setting specifies the number of unscaled bases on the 5-prime end of each boundary. (Default: %(default)s)') optional.add_argument("--unscaled3prime", default=0, type=int, help='Like --unscaled5prime, but for the 3-prime ' - 'end.') + 'end. (Default: %(default)s)') elif case == 'reference-point': optional.add_argument('--referencePoint', @@ -195,7 +195,7 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]): 'region end (TES) or the center of the region. ' 'Note that regardless of what you specify, ' 'plotHeatmap/plotProfile will default to using "TSS" as the ' - 'label.') + 'label. (Default: %(default)s)') # set region body length to zero for reference point mode optional.add_argument('--regionBodyLength', help=argparse.SUPPRESS, @@ -207,13 +207,13 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]): type=int, metavar='INT bp', help='Distance upstream of the reference-point ' - 'selected.') + 'selected. (Default: %(default)s)') optional.add_argument('--afterRegionStartLength', '-a', '--downstream', default=1500, metavar='INT bp', type=int, help='Distance downstream of the ' - 'reference-point selected.') + 'reference-point selected. (Default: %(default)s)') optional.add_argument('--nanAfterEnd', action='store_true', help='If set, any values after the region end ' @@ -225,7 +225,7 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]): optional.add_argument('--binSize', '-bs', help='Length, in bases, of the non-overlapping ' 'bins for averaging the score over the ' - 'regions length.', + 'regions length. (Default: %(default)s)', type=int, default=10) @@ -240,7 +240,7 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]): 'the input files. If you require the output order to ' 'match that of the input regions, then either specify ' '"keep" or use computeMatrixOperations to resort the ' - 'results file.', + 'results file. (Default: %(default)s)', choices=["descend", "ascend", "no", "keep"], default='keep') @@ -249,7 +249,7 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]): 'sorting. The value is computed for each row.' 'Note that the region_length option will lead ' 'to a dotted line within the heatmap that indicates ' - 'the end of the regions.', + 'the end of the regions. (Default: %(default)s)', choices=["mean", "median", "max", "min", "sum", "region_length"], default='mean') @@ -268,7 +268,7 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]): help='Define the type of statistic that should be ' 'used over the bin size range. The ' 'options are: "mean", "median", "min", "max", "sum" ' - 'and "std". The default is "mean".') + 'and "std". The default is "mean". (Default: %(default)s)') optional.add_argument('--missingDataAsZero', help='If set, missing data (NAs) will be treated as zeros. ' @@ -291,7 +291,7 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]): 'will be skipped. This is useful to skip, ' 'for example, genes where the read count is zero ' 'for any of the bins. This could be the result of ' - 'unmappable areas and can bias the overall results.') + 'unmappable areas and can bias the overall results. (Default: %(default)s)') optional.add_argument('--maxThreshold', default=None, @@ -301,7 +301,7 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]): 'will be skipped. The maxThreshold is useful to ' 'skip those few regions with very high read counts ' '(e.g. micro satellites) that may bias the average ' - 'values.') + 'values. (Default: %(default)s)') optional.add_argument('--blackListFileName', '-bl', help="A BED file containing regions that should be excluded from all analyses. Currently this works by rejecting genomic chunks that happen to overlap an entry. Consequently, for BAM files, if a read partially overlaps a blacklisted region or a fragment spans over it, then the read/fragment might still be considered.", @@ -336,13 +336,13 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]): optional.add_argument('--scale', help='If set, all values are multiplied by ' - 'this number.', + 'this number. (Default: %(default)s)', type=float, default=1) optional.add_argument('--numberOfProcessors', '-p', help='Number of processors to use. Type "max/2" to ' 'use half the maximum number of processors or "max" ' - 'to use all available processors.', + 'to use all available processors. (Default: %(default)s)', metavar="INT", type=numberOfProcessors, default=1, diff --git a/deeptools/computeMatrixOperations.py b/deeptools/computeMatrixOperations.py index 0029b4c86..1324c22df 100644 --- a/deeptools/computeMatrixOperations.py +++ b/deeptools/computeMatrixOperations.py @@ -270,7 +270,7 @@ def sortArgs(): default='transcript', help='When a GTF file is used to provide regions, only ' 'entries with this value as their feature (column 2) ' - 'will be processed as transcripts.') + 'will be processed as transcripts. (Default: %(default)s)') optional.add_argument('--transcript_id_designator', default='transcript_id', @@ -281,7 +281,7 @@ def sortArgs(): '\'transcript_id "ACTB"\', for a key of transcript_id ' 'and a value of ACTB). In some cases it can be ' 'convenient to use a different identifier. To do so, set ' - 'this to the desired key.') + 'this to the desired key. (Default: %(default)s)') return parser diff --git a/deeptools/estimateReadFiltering.py b/deeptools/estimateReadFiltering.py index c4b526815..464fe0999 100644 --- a/deeptools/estimateReadFiltering.py +++ b/deeptools/estimateReadFiltering.py @@ -62,7 +62,7 @@ def parseArguments(): general.add_argument('--binSize', '-bs', metavar='INT', - help='Length in bases of the window used to sample the genome. (default 1000000)', + help='Length in bases of the window used to sample the genome. (Default: %(default)s)', default=1000000, type=int) @@ -74,14 +74,14 @@ def parseArguments(): 'for high coverage samples, while smaller values are useful for ' 'lower coverage samples. Note that if you specify a value that ' 'results in too few (<1000) reads sampled, the value will be ' - 'decreased. (default 10000)', + 'decreased. (Default: %(default)s)', default=10000, type=int) general.add_argument('--numberOfProcessors', '-p', help='Number of processors to use. Type "max/2" to ' 'use half the maximum number of processors or "max" ' - 'to use all available processors.', + 'to use all available processors. (Default: %(default)s)', metavar="INT", type=parserCommon.numberOfProcessors, default=1, @@ -98,7 +98,7 @@ def parseArguments(): filtering.add_argument('--filterRNAstrand', help='Selects RNA-seq reads (single-end or paired-end) in ' - 'the given strand.', + 'the given strand. (Default: %(default)s)', choices=['forward', 'reverse'], default=None) @@ -121,7 +121,7 @@ def parseArguments(): 'to get only reads that are the first mate, use a flag of 64. ' 'This is useful to count properly paired reads only once, ' 'as otherwise the second mate will be also considered for the ' - 'coverage.', + 'coverage. (Default: %(default)s)', metavar='INT', default=None, type=int, @@ -131,7 +131,7 @@ def parseArguments(): help='Exclude reads based on the SAM flag. For example, ' 'to get only reads that map to the forward strand, use ' '--samFlagExclude 16, where 16 is the SAM flag for reads ' - 'that map to the reverse strand.', + 'that map to the reverse strand. (Default: %(default)s)', metavar='INT', default=None, type=int, diff --git a/deeptools/multiBamSummary.py b/deeptools/multiBamSummary.py index 5d0ca554d..3a0bf8361 100644 --- a/deeptools/multiBamSummary.py +++ b/deeptools/multiBamSummary.py @@ -128,7 +128,7 @@ def bamcorrelate_args(case='bins'): optional.add_argument('--binSize', '-bs', metavar='INT', help='Length in bases of the window used ' - 'to sample the genome.', + 'to sample the genome. (Default: %(default)s)', default=10000, type=int) @@ -138,7 +138,7 @@ def bamcorrelate_args(case='bins'): 'bins of the specified --binSize. However, to ' 'reduce the computation time, a larger distance ' 'between bins can by given. Larger distances ' - 'result in fewer bins considered.', + 'result in fewer bins considered. (Default: %(default)s)', default=0, type=int) diff --git a/deeptools/multiBigwigSummary.py b/deeptools/multiBigwigSummary.py index 9c18151ed..8d89421f1 100644 --- a/deeptools/multiBigwigSummary.py +++ b/deeptools/multiBigwigSummary.py @@ -155,7 +155,7 @@ def multiBigwigSummaryArgs(case='bins'): optional.add_argument('--binSize', '-bs', metavar='INT', help='Size (in bases) of the windows sampled ' - 'from the genome.', + 'from the genome. (Default: %(default)s)', default=10000, type=int) @@ -165,7 +165,7 @@ def multiBigwigSummaryArgs(case='bins'): 'bins of the specified --binSize. However, to ' 'reduce the computation time, a larger distance ' 'between bins can be given. Larger distances ' - 'results in fewer considered bins.', + 'results in fewer considered bins. (Default: %(default)s)', default=0, type=int) diff --git a/deeptools/parserCommon.py b/deeptools/parserCommon.py index cdd15d1a0..2090d60e8 100644 --- a/deeptools/parserCommon.py +++ b/deeptools/parserCommon.py @@ -100,7 +100,7 @@ def read_options(): 'to get only reads that are the first mate, use a flag of 64. ' 'This is useful to count properly paired reads only once, ' 'as otherwise the second mate will be also considered for the ' - 'coverage.', + 'coverage. (Default: %(default)s)', metavar='INT', default=None, type=int, @@ -110,7 +110,7 @@ def read_options(): help='Exclude reads based on the SAM flag. For example, ' 'to get only reads that map to the forward strand, use ' '--samFlagExclude 16, where 16 is the SAM flag for reads ' - 'that map to the reverse strand.', + 'that map to the reverse strand. (Default: %(default)s)', metavar='INT', default=None, type=int, @@ -120,7 +120,7 @@ def read_options(): help='The minimum fragment length needed for read/pair ' 'inclusion. This option is primarily useful ' 'in ATACseq experiments, for filtering mono- or ' - 'di-nucleosome fragments.', + 'di-nucleosome fragments. (Default: %(default)s)', metavar='INT', default=0, type=int, @@ -128,7 +128,7 @@ def read_options(): group.add_argument('--maxFragmentLength', help='The maximum fragment length needed for read/pair ' - 'inclusion.', + 'inclusion. (Default: %(default)s)', metavar='INT', default=0, type=int, @@ -156,7 +156,7 @@ def gtf_options(suppress=False): rather than using the genomic interval defined by the \ 5-prime and 3-prime most transcript bound (i.e., columns \ 2 and 3 of a BED file). If a BED3 or BED6 file is used \ - as input, then columns 2 and 3 are used as an exon.' + as input, then columns 2 and 3 are used as an exon. (Default: %(default)s)' group.add_argument('--metagene', help=help, @@ -166,7 +166,7 @@ def gtf_options(suppress=False): if suppress is False: help = 'When a GTF file is used to provide regions, only \ entries with this value as their feature (column 2) \ - will be processed as transcripts.' + will be processed as transcripts. (Default: %(default)s)' group.add_argument('--transcriptID', help=help, @@ -176,7 +176,7 @@ def gtf_options(suppress=False): help = 'When a GTF file is used to provide regions, only \ entries with this value as their feature (column 2) \ will be processed as exons. CDS would be another common \ - value for this.' + value for this. (Default: %(default)s)' group.add_argument('--exonID', help=help, @@ -190,7 +190,7 @@ def gtf_options(suppress=False): \'transcript_id "ACTB"\', for a key of transcript_id \ and a value of ACTB). In some cases it can be \ convenient to use a different identifier. To do so, set \ - this to the desired key.' + this to the desired key. (Default: %(default)s)' group.add_argument('--transcript_id_designator', help=help, @@ -242,7 +242,7 @@ def normalization_options(): 'for the sample to match the 1x coverage. This option requires --effectiveGenomeSize. ' 'Each read is considered independently, ' 'if you want to only count one mate from a pair in ' - 'paired-end data, then use the --samFlagInclude/--samFlagExclude options.', + 'paired-end data, then use the --samFlagInclude/--samFlagExclude options. (Default: %(default)s)', choices=['RPKM', 'CPM', 'BPM', 'RPGC', 'None'], default=None, required=False) @@ -302,7 +302,7 @@ def getParentArgParse(args=None, binSize=True, blackList=True): if binSize: optional.add_argument('--binSize', '-bs', help='Size of the bins, in bases, for the output ' - 'of the bigwig/bedgraph file.', + 'of the bigwig/bedgraph file. (Default: %(default)s)', metavar="INT bp", type=int, default=50) @@ -327,7 +327,7 @@ def getParentArgParse(args=None, binSize=True, blackList=True): optional.add_argument('--numberOfProcessors', '-p', help='Number of processors to use. Type "max/2" to ' 'use half the maximum number of processors or "max" ' - 'to use all available processors.', + 'to use all available processors. (Default: %(default)s)', metavar="INT", type=numberOfProcessors, default=1, diff --git a/deeptools/plotCorrelation.py b/deeptools/plotCorrelation.py index fba77f817..c72e43bfc 100644 --- a/deeptools/plotCorrelation.py +++ b/deeptools/plotCorrelation.py @@ -91,7 +91,7 @@ def plot_correlation_args(): optional.add_argument('--plotTitle', '-T', help='Title of the plot, to be printed on top of ' - 'the generated image. Leave blank for no title.', + 'the generated image. Leave blank for no title. (Default: %(default)s)', default='') optional.add_argument('--plotFileFormat', @@ -162,12 +162,12 @@ def heatmap_options(): heatmap = parser.add_argument_group('Heatmap options') heatmap.add_argument('--plotHeight', - help='Plot height in cm.', + help='Plot height in cm. (Default: %(default)s)', type=float, default=9.5) heatmap.add_argument('--plotWidth', - help='Plot width in cm. The minimum value is 1 cm.', + help='Plot width in cm. The minimum value is 1 cm. (Default: %(default)s)', type=float, default=11) diff --git a/deeptools/plotCoverage.py b/deeptools/plotCoverage.py index dcc3cc068..7b647f3ba 100644 --- a/deeptools/plotCoverage.py +++ b/deeptools/plotCoverage.py @@ -102,7 +102,7 @@ def required_args(): optional.add_argument('--plotTitle', '-T', help='Title of the plot, to be printed on top of ' - 'the generated image. Leave blank for no title.', + 'the generated image. Leave blank for no title. (Default: %(default)s)', default='') optional.add_argument('--skipZeros', @@ -113,7 +113,7 @@ def required_args(): required=False) optional.add_argument('--numberOfSamples', '-n', - help='Number of 1 bp regions to sample. Default 1 million.', + help='Number of 1 bp regions to sample. (Default: %(default)s)', required=False, type=int, default=1000000) @@ -147,12 +147,12 @@ def required_args(): 'high as the given threshold. This can be specified multiple times.') optional.add_argument('--plotHeight', - help='Plot height in cm.', + help='Plot height in cm. (Default: %(default)s)', type=float, default=5.0) optional.add_argument('--plotWidth', - help='Plot width in cm. The minimum value is 1 cm.', + help='Plot width in cm. The minimum value is 1 cm. (Default: %(default)s)', type=float, default=15.0) diff --git a/deeptools/plotEnrichment.py b/deeptools/plotEnrichment.py index adda203a1..b9843f420 100644 --- a/deeptools/plotEnrichment.py +++ b/deeptools/plotEnrichment.py @@ -118,7 +118,7 @@ def plot_enrichment_args(): optional.add_argument('--plotTitle', '-T', help='Title of the plot, to be printed on top of ' - 'the generated image. Leave blank for no title.', + 'the generated image. Leave blank for no title. (Default: %(default)s)', default='') optional.add_argument('--plotFileFormat', @@ -143,12 +143,12 @@ def plot_enrichment_args(): action='store_true') optional.add_argument('--plotHeight', - help='Plot height in cm.', + help='Plot height in cm. (Default: %(default)s)', type=float, default=20) optional.add_argument('--plotWidth', - help='Plot width in cm. The minimum value is 1 cm.', + help='Plot width in cm. The minimum value is 1 cm. (Default: %(default)s)', type=float, default=20) @@ -162,7 +162,7 @@ def plot_enrichment_args(): nargs='+') optional.add_argument('--numPlotsPerRow', - help='Number of plots per row', + help='Number of plots per row (Default: %(default)s)', type=int, default=4) diff --git a/deeptools/plotFingerprint.py b/deeptools/plotFingerprint.py index d2a1a3b12..b09e10bdf 100644 --- a/deeptools/plotFingerprint.py +++ b/deeptools/plotFingerprint.py @@ -104,13 +104,13 @@ def get_optional_args(): optional.add_argument('--binSize', '-bs', help='Window size in base pairs to ' - 'sample the genome. This times --numberOfSamples should be less than the genome size.', + 'sample the genome. This times --numberOfSamples should be less than the genome size. (Default: %(default)s)', default=500, type=int) optional.add_argument('--numberOfSamples', '-n', help='The number of bins that are sampled from the genome, ' - 'for which the overlapping number of reads is computed.', + 'for which the overlapping number of reads is computed. (Default: %(default)s)', default=5e5, type=int) @@ -125,7 +125,7 @@ def get_optional_args(): optional.add_argument('--plotTitle', '-T', help='Title of the plot, to be printed on top of ' - 'the generated image. Leave blank for no title.', + 'the generated image. Leave blank for no title. (Default: %(default)s)', default='') optional.add_argument('--skipZeros', diff --git a/deeptools/plotPCA.py b/deeptools/plotPCA.py index cc1a367f0..9df973e4b 100644 --- a/deeptools/plotPCA.py +++ b/deeptools/plotPCA.py @@ -64,7 +64,7 @@ def plotCorrelationArgs(): optional.add_argument('--plotTitle', '-T', help='Title of the plot, to be printed on top of ' - 'the generated image. Leave blank for no title.', + 'the generated image. Leave blank for no title. (Default: %(default)s)', default='') optional.add_argument('--plotFileFormat', @@ -76,12 +76,12 @@ def plotCorrelationArgs(): choices=['png', 'pdf', 'svg', 'eps', 'plotly']) optional.add_argument('--plotHeight', - help='Plot height in cm.', + help='Plot height in cm. (Default: %(default)s)', type=float, default=10) optional.add_argument('--plotWidth', - help='Plot width in cm. The minimum value is 1 cm.', + help='Plot width in cm. The minimum value is 1 cm. (Default: %(default)s)', type=float, default=10) @@ -101,14 +101,14 @@ def plotCorrelationArgs(): 'original matrix. Specifying 0 will result in all ' 'rows being used. If the matrix is to be transposed, ' 'rows with 0 variance are always excluded, even if a ' - 'values of 0 is specified. The default is 1000.', + 'values of 0 is specified. The default is 1000. (Default: %(default)s)', type=int, default=1000) optional.add_argument('--PCs', help='The principal components to plot. If specified, ' 'you must provide two different integers, greater ' - 'than zero, separated by a space. An example (and the default) is "1 2".', + 'than zero, separated by a space. An example (and the default) is "1 2". (Default: %(default)s)', type=int, nargs=2, default=[1, 2])