diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md index 1781b77..b32791b 100644 --- a/docs/CHANGELOG.md +++ b/docs/CHANGELOG.md @@ -1,3 +1,8 @@ +# 0.4.1 + +- 📝 Add more examples regarding #20 +- 🐛 Fix devpars by default a Namespace rather than a dict (#21, #22) + # 0.4.0 - ⬆️ Drop support for python 3.8 (brentp/cyvcf2#181) diff --git a/examples/multiallelic.vcf b/examples/multiallelic.vcf new file mode 100644 index 0000000..2cf0142 --- /dev/null +++ b/examples/multiallelic.vcf @@ -0,0 +1,84 @@ +##fileformat=VCFv4.1 +##samtoolsVersion=0.1.18-r572 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##source_20120424.1=vcf-annotate(r735) --fill-AC-AN -f + +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##INFO= +##INFO= +##source_20120424.2=vcf-annotate(r735) --fill-AC-AN -f + +##FILTER= +##source_20120710.1=vcf-annotate(r761) -f q=30 mpileup-v1/merged.filt.vcf.gz +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B C D +1 10492 . 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A G 89 PASS DP=304;VDB=0.0327;AF1=0.125;AC1=1;DP4=99,171,10,15;MQ=30;FQ=89;PV4=0.83,0.3,0.035,1;AN=8;AC=1 GT:PL:DP 0/0:0,95,255:11 0/0:0,72,255:11 0/0:0,101,255:11 1:255,0:11 diff --git a/examples/mymacros.py b/examples/mymacros.py index 8bc53ab..51939e9 100644 --- a/examples/mymacros.py +++ b/examples/mymacros.py @@ -1,4 +1,4 @@ -from vcfstats.macros import continuous +from vcfstats.macros import continuous, categorical @continuous @@ -27,3 +27,15 @@ def N_MISSING(variant): def Percent_HETs(variant): """Get % of HETs per locus""" return variant.num_het / float(len(variant.gt_types)) + + +@categorical +def Allelic_Type(variant): + """Get allelic type, either biallelic or multiallelic""" + return "biallelic" if len(variant.ALT) == 1 else "multi-allelic" + + +@categorical +def N_Allelic(variant): + """Get number of alleles""" + return len(variant.ALT) + 1 diff --git a/examples/number-of-biallelics-and-multiallelics.col.png b/examples/number-of-biallelics-and-multiallelics.col.png new file mode 100644 index 0000000..6c4754a Binary files /dev/null and b/examples/number-of-biallelics-and-multiallelics.col.png differ diff --git a/examples/number-of-variants-with-different-number-of-alleles.col.png b/examples/number-of-variants-with-different-number-of-alleles.col.png new file mode 100644 index 0000000..025b1d0 Binary files /dev/null and b/examples/number-of-variants-with-different-number-of-alleles.col.png differ diff --git a/poetry.lock b/poetry.lock index 6796e48..ab65cd2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -61,7 +61,7 @@ varname = ">=0.8,<0.9" [[package]] name = "colorama" -version = "0.4.4" +version = "0.4.5" description = "Cross-platform colored terminal text." category = "main" optional = false @@ -94,14 +94,14 @@ test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"] [[package]] name = "coverage" -version = "6.3.2" +version = "6.4.1" description = "Code coverage measurement for Python" category = "dev" optional = false python-versions = ">=3.7" [package.dependencies] -tomli = {version = "*", optional = true, markers = "extra == \"toml\""} +tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""} [package.extras] toml = ["tomli"] @@ -140,23 +140,22 @@ numpy = "*" [[package]] name = "datar" -version = "0.8.2" +version = "0.8.5" description = "Port of dplyr and other related R packages in python, using pipda." category = "main" optional = false python-versions = ">=3.7.1,<4.0.0" [package.dependencies] -diot = ">=0.1,<0.2" pandas = ">=1.3,<2.0" -pipda = ">=0.5,<0.6" +pipda = ">=0.6,<0.7" python-simpleconf = {version = ">=0.5,<0.6", extras = ["toml"]} -python-slugify = ">=6,<7" -scipy = ">=1.6,<2.0" -wcwidth = ">=0.2,<0.3" [package.extras] pdtypes = ["pdtypes (>=0.0,<0.1)"] +scipy = ["scipy (>=1.6,<2.0)"] +wcwidth = ["wcwidth (>=0.2,<0.3)"] +slugify = ["python-slugify (>=6,<7)"] modin = ["modin (>=0.10,<0.11)"] [[package]] @@ -240,7 +239,7 @@ python-versions = "*" [[package]] name = "kiwisolver" -version = "1.4.2" +version = "1.4.3" description = "A fast implementation of the Cassowary constraint solver" category = "main" optional = false @@ -299,7 +298,7 @@ testing = ["flake8", "pytest-cov"] [[package]] name = "numpy" -version = "1.22.3" +version = "1.23.0" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false @@ -326,7 +325,7 @@ python-versions = "*" [[package]] name = "pandas" -version = "1.4.2" +version = "1.4.3" description = "Powerful data structures for data analysis, time series, and statistics" category = "main" optional = false @@ -362,7 +361,7 @@ test = ["pytest", "pytest-cov", "scipy"] [[package]] name = "pillow" -version = "9.1.0" +version = "9.1.1" description = "Python Imaging Library (Fork)" category = "main" optional = false @@ -374,17 +373,15 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa [[package]] name = "pipda" -version = "0.5.9" +version = "0.6.0" description = "A framework for data piping in python" category = "main" optional = false python-versions = ">=3.7,<4.0" [package.dependencies] -diot = "*" -executing = "*" -pure_eval = "<1.0.0" -varname = "*" +diot = ">=0.1,<0.2" +varname = ">=0.8,<0.9" [[package]] name = "plotnine" @@ -461,7 +458,7 @@ python-versions = ">=3.6" [[package]] name = "pyparam" -version = "0.5.1" +version = "0.5.3" description = "Powerful parameter processing." category = "main" optional = false @@ -540,7 +537,7 @@ six = ">=1.5" [[package]] name = "python-simpleconf" -version = "0.5.4" +version = "0.5.6" description = "Simple configuration management with python." category = "main" optional = false @@ -548,14 +545,14 @@ python-versions = ">=3.7,<4.0" [package.dependencies] diot = ">=0.1,<0.2" -rtoml = {version = ">=0.7,<0.8", optional = true, markers = "extra == \"toml\" or extra == \"all\""} +rtoml = {version = ">=0.8,<0.9", optional = true, markers = "extra == \"toml\" or extra == 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--cov-report xml:.coverage.xml --cov-report term-missing" +addopts = "-vv -p 'no:asyncio' --cov-config=.coveragerc --cov=vcfstats --cov-report xml:.coverage.xml --cov-report term-missing" filterwarnings = [ - #"error" + # "error" ] console_output_style = "progress" junit_family = "xunit1" diff --git a/vcfstats/__init__.py b/vcfstats/__init__.py index 24a1e17..ebb4eda 100644 --- a/vcfstats/__init__.py +++ b/vcfstats/__init__.py @@ -3,4 +3,4 @@ from . import macros -__version__ = "0.4.0" +__version__ = "0.4.1" diff --git a/vcfstats/cli.py b/vcfstats/cli.py index 5567f2a..abbed6b 100644 --- a/vcfstats/cli.py +++ b/vcfstats/cli.py @@ -6,7 +6,7 @@ from os import path from cyvcf2 import VCF -from pyparam import Params +from pyparam import Params, Namespace from rich.console import Console from rich.table import Table from simpleconf import Config @@ -87,6 +87,10 @@ def get_instances(opts, samples): ggs = opts["ggs"][i] if i < len(opts["ggs"]) else None figtype = opts["figtype"][i] if i < len(opts["figtype"]) else None figfmt = opts["figfmt"][i] if i < len(opts["figfmt"]) else None + + if isinstance(devpars[i], Namespace): + devpars[i] = vars(devpars[i]) + ret.append( Instance( formula,