wip/py-mappy: import mappy version 2.18 as wip/py-mappy

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

Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <brook%nmsu.edu@localhost>
Pushed By:	brook
Date:		Tue Jun 8 09:21:37 2021 -0600
Changeset:	ef9a468962ac2cfcbb11126459416c025e029123

Modified Files:
	Makefile
Added Files:
	py-mappy/DESCR
	py-mappy/Makefile
	py-mappy/PLIST
	py-mappy/distinfo

Log Message:
wip/py-mappy: import mappy version 2.18 as wip/py-mappy

==============================
Mappy: Minimap2 Python Binding
==============================

Mappy provides a convenient interface to minimap2
<https://github.com/lh3/minimap2>, a fast and accurate C program to
align genomic and transcribe nucleotide sequences.

Mappy implements two classes and two global functions.

Class mappy.Aligner: performs alignment with the following methods and
property:

- mappy.Aligner(fn_idx_in=None, preset=None, ...)
- mappy.Aligner.map(seq, seq2=None, cs=False, MD=False)
- mappy.Aligner.seq(name, start=0, end=0x7fffffff)
- mappy.Aligner.seq_names

Class mappy.Alignment: describes a single alignment

mappy.fastx_read(fn, read_comment=False): generator for a FASTA/FASTQ
file

mappy.revcomp(seq): return the reverse complement of DNA string

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=ef9a468962ac2cfcbb11126459416c025e029123

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

diffstat:
 Makefile          |  1 +
 py-mappy/DESCR    | 24 ++++++++++++++++++++++++
 py-mappy/Makefile | 25 +++++++++++++++++++++++++
 py-mappy/PLIST    |  7 +++++++
 py-mappy/distinfo |  6 ++++++
 5 files changed, 63 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 9dabaea2fd..ec1aceb174 100644
--- a/Makefile
+++ b/Makefile
@@ -3976,6 +3976,7 @@ SUBDIR+=	py-mailcap-fix
 SUBDIR+=	py-mailingstats
 SUBDIR+=	py-mailq
 SUBDIR+=	py-mapcode
+SUBDIR+=	py-mappy
 SUBDIR+=	py-mapy-package
 SUBDIR+=	py-mark
 SUBDIR+=	py-markovchain
diff --git a/py-mappy/DESCR b/py-mappy/DESCR
new file mode 100644
index 0000000000..2e3167b367
--- /dev/null
+++ b/py-mappy/DESCR
@@ -0,0 +1,24 @@
+==============================
+Mappy: Minimap2 Python Binding
+==============================
+
+Mappy provides a convenient interface to minimap2
+<https://github.com/lh3/minimap2>, a fast and accurate C program to
+align genomic and transcribe nucleotide sequences.
+
+Mappy implements two classes and two global functions.
+
+Class mappy.Aligner: performs alignment with the following methods and
+property:
+
+- mappy.Aligner(fn_idx_in=None, preset=None, ...)
+- mappy.Aligner.map(seq, seq2=None, cs=False, MD=False)
+- mappy.Aligner.seq(name, start=0, end=0x7fffffff)
+- mappy.Aligner.seq_names
+
+Class mappy.Alignment: describes a single alignment
+
+mappy.fastx_read(fn, read_comment=False): generator for a FASTA/FASTQ
+file
+
+mappy.revcomp(seq): return the reverse complement of DNA string
diff --git a/py-mappy/Makefile b/py-mappy/Makefile
new file mode 100644
index 0000000000..356174b2af
--- /dev/null
+++ b/py-mappy/Makefile
@@ -0,0 +1,25 @@
+# $NetBSD$
+
+DISTNAME=	mappy-2.18
+PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
+CATEGORIES=	biology python
+MASTER_SITES=	https://files.pythonhosted.org/packages/a2/d7/284160aed169db536db7ac823bddcf3c86d22258497ae0db28475c68330e/
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/lh3/minimap2
+COMMENT=	Minimap2 python binding
+LICENSE=	mit
+
+USE_TOOLS+=	gmake
+
+INSTALLATION_DIRS+=	share/examples/mappy
+
+post-install:
+	${RM} ${DESTDIR}${PREFIX}/bin/minimap2.py
+	${INSTALL_DATA} ${WRKSRC}/python/README.rst ${DESTDIR}${PREFIX}/share/examples/mappy
+
+BUILDLINK_DEPENDS.py-cython+=	build
+BUILDLINK_API_DEPENDS.py-cython+=	${PYPKGPREFIX}-cython>=0.29.23
+.include "../../devel/py-cython/buildlink3.mk"
+.include "../../lang/python/egg.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/py-mappy/PLIST b/py-mappy/PLIST
new file mode 100644
index 0000000000..1e1fcde1b2
--- /dev/null
+++ b/py-mappy/PLIST
@@ -0,0 +1,7 @@
+@comment $NetBSD$
+share/examples/mappy/README.rst
+${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
+${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
+${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/mappy.so
diff --git a/py-mappy/distinfo b/py-mappy/distinfo
new file mode 100644
index 0000000000..8cfad26f37
--- /dev/null
+++ b/py-mappy/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (mappy-2.18.tar.gz) = 6e95645f8a741ce1a89f79dab6bbae12cf701d53
+RMD160 (mappy-2.18.tar.gz) = 7b2ccbb0e989928c747487e18602bf43c86828c6
+SHA512 (mappy-2.18.tar.gz) = 36d02374249cf9a87e885e0be5098b0123727215a8d8e14ef86db920e0f17ffaf8da4158a41b62264aaa5a888d1273bdef4081593db7fb0a7d37a609353a0e32
+Size (mappy-2.18.tar.gz) = 130502 bytes