wip/nanomath: import nanomath version 1.2.1.20210604 as wip/nanomath

[Brook Milligan <brook%nmsu.edu@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <brook%nmsu.edu@localhost>
Pushed By:	brook
Date:		Mon Jun 7 18:17:03 2021 -0600
Changeset:	260131b147ab4b7b0c3a17b1fedec9817d316348

Modified Files:
	Makefile
Added Files:
	nanomath/DESCR
	nanomath/Makefile
	nanomath/PLIST
	nanomath/distinfo

Log Message:
wip/nanomath: import nanomath version 1.2.1.20210604 as wip/nanomath

This module provides a few simple math and statistics functions for
other scripts processing Oxford Nanopore sequencing data

## Functions

* Calculate read N50 from a set of lengths `get_N50(readlenghts)`

* Remove extreme length outliers from a dataset
  `remove_length_outliers(dataframe, columname)`

* Calculate the average Phred quality of a read `ave_qual(qualscores)`

* Write out the statistics report after calling readstats function
  `write_stats(dataframe, outputname)`

* Compute a number of statistics, return a dictionary
  `calc_read_stats(dataframe)`

If you use this tool, please consider citing our publication:
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=260131b147ab4b7b0c3a17b1fedec9817d316348

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile          |  1 +
 nanomath/DESCR    | 20 ++++++++++++++++++++
 nanomath/Makefile | 28 ++++++++++++++++++++++++++++
 nanomath/PLIST    | 18 ++++++++++++++++++
 nanomath/distinfo |  6 ++++++
 5 files changed, 73 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index b468f7ca30..49823d5215 100644
--- a/Makefile
+++ b/Makefile
@@ -2463,6 +2463,7 @@ SUBDIR+=	n2n
 SUBDIR+=	naev
 SUBDIR+=	nag
 SUBDIR+=	nagios-plugin-mysql_health
+SUBDIR+=	nanomath
 SUBDIR+=	naqsh-ttf
 SUBDIR+=	nary
 SUBDIR+=	natali
diff --git a/nanomath/DESCR b/nanomath/DESCR
new file mode 100644
index 0000000000..48248c4c45
--- /dev/null
+++ b/nanomath/DESCR
@@ -0,0 +1,20 @@
+This module provides a few simple math and statistics functions for
+other scripts processing Oxford Nanopore sequencing data
+
+## Functions
+
+* Calculate read N50 from a set of lengths `get_N50(readlenghts)`
+
+* Remove extreme length outliers from a dataset
+  `remove_length_outliers(dataframe, columname)`
+
+* Calculate the average Phred quality of a read `ave_qual(qualscores)`
+
+* Write out the statistics report after calling readstats function
+  `write_stats(dataframe, outputname)`
+
+* Compute a number of statistics, return a dictionary
+  `calc_read_stats(dataframe)`
+
+If you use this tool, please consider citing our publication:
+https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939.
diff --git a/nanomath/Makefile b/nanomath/Makefile
new file mode 100644
index 0000000000..cfbe701982
--- /dev/null
+++ b/nanomath/Makefile
@@ -0,0 +1,28 @@
+# $NetBSD$
+
+GITHUB_PROJECT=	nanomath
+GITHUB_TAG=	79b7f85
+DISTNAME=	nanomath-1.2.1.20210604
+CATEGORIES=	biology python
+MASTER_SITES=	${MASTER_SITE_GITHUB:=wdecoster/}
+DIST_SUBDIR=	${GITHUB_PROJECT}
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/wdecoster/nanomath
+COMMENT=	Math functions for other Oxford Nanopore processing scripts
+LICENSE=	gnu-gpl-v3
+
+DEPENDS+=	${PYPKGPREFIX}-pandas>=1.2.4:../../math/py-pandas
+
+WRKSRC=		${WRKDIR}/nanomath-79b7f85d004763a07c56b9eb594713ae7349ff93
+USE_LANGUAGES=	# none
+
+EGG_NAME=	${DISTNAME:C/\.[[:digit:]]+$$//}
+
+post-install:
+	rm ${DESTDIR}${PREFIX}/LICENSE
+
+BUILDLINK_API_DEPENDS.py-numpy+=	${PYPKGPREFIX}-numpy>1.8
+.include "../../math/py-numpy/buildlink3.mk"
+.include "../../lang/python/egg.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/nanomath/PLIST b/nanomath/PLIST
new file mode 100644
index 0000000000..0573e09330
--- /dev/null
+++ b/nanomath/PLIST
@@ -0,0 +1,18 @@
+@comment $NetBSD$
+${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
+${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
+${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/requires.txt
+${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/nanomath/__init__.py
+${PYSITELIB}/nanomath/__init__.pyc
+${PYSITELIB}/nanomath/__init__.pyo
+${PYSITELIB}/nanomath/nanomath.py
+${PYSITELIB}/nanomath/nanomath.pyc
+${PYSITELIB}/nanomath/nanomath.pyo
+${PYSITELIB}/nanomath/test_nanomath.py
+${PYSITELIB}/nanomath/test_nanomath.pyc
+${PYSITELIB}/nanomath/test_nanomath.pyo
+${PYSITELIB}/nanomath/version.py
+${PYSITELIB}/nanomath/version.pyc
+${PYSITELIB}/nanomath/version.pyo
diff --git a/nanomath/distinfo b/nanomath/distinfo
new file mode 100644
index 0000000000..04c2548e9b
--- /dev/null
+++ b/nanomath/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (nanomath/nanomath-1.2.1.20210604-79b7f85.tar.gz) = 64c169e3194ba320719c642ade88ff596aeafa74
+RMD160 (nanomath/nanomath-1.2.1.20210604-79b7f85.tar.gz) = fce15a2081c87495d00d629d91d704a25cb4024c
+SHA512 (nanomath/nanomath-1.2.1.20210604-79b7f85.tar.gz) = cc59c9014a5df1f2fb1587811224c225838870a5bc21ea8ca22954f7a219105a138b555cb937da3b5853a12b137261ff4491bf3c8897f296d426a74d632f53d4
+Size (nanomath/nanomath-1.2.1.20210604-79b7f85.tar.gz) = 17571 bytes