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Close #868 #867 and #851 #869

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Sep 3, 2019
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Close #868 #867 and #851 #869

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33d9fac
Fix #868
dpryan79 Sep 3, 2019
09d7f67
Fix #867
dpryan79 Sep 3, 2019
0ae2313
Default ALL the things!
dpryan79 Sep 3, 2019
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1 change: 1 addition & 0 deletions CHANGES.txt
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Expand Up @@ -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

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8 changes: 4 additions & 4 deletions deeptools/alignmentSieve.py
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Expand Up @@ -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,
Expand Down Expand Up @@ -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)

Expand Down Expand Up @@ -129,15 +129,15 @@ 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,
required=False)

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,
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10 changes: 5 additions & 5 deletions deeptools/bamCompare.py
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Expand Up @@ -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 <method> can be used.',
'--normalizeUsing <method> can be used. (Default: %(default)s)',
choices=['readCount', 'SES', 'None'],
default='readCount')

Expand All @@ -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)

Expand All @@ -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'],
Expand All @@ -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='+',
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2 changes: 1 addition & 1 deletion deeptools/bamCoverage.py
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Expand Up @@ -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)
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10 changes: 5 additions & 5 deletions deeptools/bamPEFragmentSize.py
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Expand Up @@ -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,
Expand All @@ -65,18 +65,18 @@ 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',
help='Plot on the log scale',
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',
Expand All @@ -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',
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7 changes: 3 additions & 4 deletions deeptools/bigwigCompare.py
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Expand Up @@ -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),
Expand All @@ -73,11 +73,10 @@ 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\'',
'the \'--operation first\' or \'--operation second\' (Default: %(default)s)',
default='log2',
choices=['log2', 'ratio', 'subtract', 'add', 'mean',
'reciprocal_ratio', 'first', 'second'],
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4 changes: 2 additions & 2 deletions deeptools/computeGCBias.py
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Expand Up @@ -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',
Expand Down Expand Up @@ -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

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