update to 1.44 from Will Maier (new MAINTAINER)
ok merdely
This commit is contained in:
okan
parent
6206a1212d
commit
fc0db83b02
@ -1,14 +1,16 @@
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# $OpenBSD: Makefile,v 1.11 2008/01/11 09:28:20 winiger Exp $
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# $OpenBSD: Makefile,v 1.12 2008/01/12 02:00:24 okan Exp $
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SHARED_ONLY= Yes
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COMMENT= Python tools for computational molecular biology
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DISTNAME= biopython-1.41
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PKGNAME= py-${DISTNAME}p4
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DISTNAME= biopython-1.44
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PKGNAME= py-${DISTNAME}
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CATEGORIES= biology
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HOMEPAGE= http://www.biopython.org/
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MAINTAINER= Will Maier <willmaier@ml1.net>
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# BSD-like
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PERMIT_PACKAGE_CDROM= Yes
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PERMIT_PACKAGE_FTP= Yes
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@ -20,26 +22,28 @@ MASTER_SITES= ${HOMEPAGE}DIST/
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MODULES= lang/python
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PY_FLAVOR= python${MODPY_VERSION}
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WANTLIB+= stdc++
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BUILD_DEPENDS= ${MODPY_EXPAT_DEPENDS} \
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::math/py-Numeric
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::math/py-Numeric \
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::devel/swig
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RUN_DEPENDS= ${MODPY_EXPAT_DEPENDS} \
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:py-mxDateTime-*-${PY_FLAVOR}:devel/py-mxDateTime,${PY_FLAVOR} \
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:py-Numeric-*:math/py-Numeric \
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:py-reportlab-*:print/py-reportlab/reportlab
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REGRESS_DEPENDS=${RUN_DEPENDS}
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EXAMPLESDIR= ${PREFIX}/share/examples/py-biopython
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pre-configure:
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@echo '5\nm2\nwq' | ed -s ${WRKSRC}/Bio/Wise/dnal.py
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CFLAGS+= -fPIC
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post-install:
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${INSTALL_DATA_DIR} ${EXAMPLESDIR}
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cd ${WRKSRC}/Tests; tar cf - * | tar xf - -C ${EXAMPLESDIR}
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${INSTALL_DATA_DIR} ${PREFIX}/share/doc/py-biopython/
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${INSTALL_DATA_DIR} ${PREFIX}/share/examples/py-biopython/
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${INSTALL_DATA} ${WRKSRC}/Doc/*.txt ${PREFIX}/share/doc/py-biopython/
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cd ${WRKSRC}/Doc/examples; tar cf - * | \
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tar xf - -C ${PREFIX}/share/examples/py-biopython
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do-regress: fake
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@rm -f ${WRKSRC}/Tests/test_copen.py*
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@cd ${WRKSRC}/Tests && ${MAKE_ENV} \
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@cd ${WRKSRC}/Tests && \
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PYTHONPATH=${WRKINST}${MODPY_SITEPKG} \
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${MODPY_BIN} ./run_tests.py --no-gui
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@ -1,5 +1,5 @@
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MD5 (biopython-1.41.tar.gz) = A/jvwlj7SbB9GitkL6g2Lg==
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RMD160 (biopython-1.41.tar.gz) = 961eFwpqN0D6vjgocVuD/Ew+Fa4=
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SHA1 (biopython-1.41.tar.gz) = p6O6xgasxbW3ClZUAvnCgSCbqLk=
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SHA256 (biopython-1.41.tar.gz) = FbcIt2Nf2ZOq08U/1M/ChgHabUMysCfQmJnxy1F4zvk=
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SIZE (biopython-1.41.tar.gz) = 3807547
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MD5 (biopython-1.44.tar.gz) = dix6NYr53Fi3Eri0u5nQwg==
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RMD160 (biopython-1.44.tar.gz) = 7Lvi9G8OXRJNkQYy3Jp/0FEgLAs=
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SHA1 (biopython-1.44.tar.gz) = yio1yekqIZJW/k/CojLfUyj59dk=
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SHA256 (biopython-1.44.tar.gz) = 5HxKfGEuEctsHAUVJ0ziMWRrMbvxyeOsWJmJKMCtPHI=
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SIZE (biopython-1.44.tar.gz) = 3840036
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@ -1,216 +0,0 @@
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$OpenBSD: patch-Bio_Cluster_clustermodule_c,v 1.2 2007/10/18 15:22:15 ajacoutot Exp $
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--- Bio/Cluster/clustermodule.c.orig Wed Apr 27 10:09:08 2005
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+++ Bio/Cluster/clustermodule.c Thu Oct 18 17:11:50 2007
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@@ -111,7 +111,7 @@ parse_mask (PyObject* object, PyArrayObject** array, c
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return mask;
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}
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if(!PyArray_Check (object)) /* Try to convert object to a 2D double array */
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- { *array = (PyArrayObject*) PyArray_FromObject(object, PyArray_LONG, 2, 2);
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+ { *array = (PyArrayObject*) PyArray_FromObject(object, PyArray_INT, 2, 2);
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if (!(*array))
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{ strcpy (message, "mask cannot be converted to needed array");
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PyErr_SetString(ErrorObject, buffer);
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@@ -121,8 +121,8 @@ parse_mask (PyObject* object, PyArrayObject** array, c
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else /* User passed an array */
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{ *array = (PyArrayObject*) object;
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Py_INCREF(object);
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- if ((*array)->descr->type_num != PyArray_LONG)
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- { PyArrayObject* av = (PyArrayObject*) PyArray_Cast (*array, PyArray_LONG);
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+ if ((*array)->descr->type_num != PyArray_INT)
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+ { PyArrayObject* av = (PyArrayObject*) PyArray_Cast (*array, PyArray_INT);
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Py_DECREF((PyObject*) *array);
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*array = av;
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if (!(*array))
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@@ -281,7 +281,7 @@ parse_initialid(PyObject* object, int* nclusters, int
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PyArrayObject* array;
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/* -- First we create the clusterid variable ------------------------ */
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PyArrayObject* clusterid =
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- (PyArrayObject*) PyArray_FromDims(1, &nitems, PyArray_LONG);
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+ (PyArrayObject*) PyArray_FromDims(1, &nitems, PyArray_INT);
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if (!clusterid)
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{ strcpy(message, "Could not create clusterid array -- too big?");
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PyErr_SetString (ErrorObject, buffer);
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@@ -291,7 +291,7 @@ parse_initialid(PyObject* object, int* nclusters, int
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if (object==NULL) return clusterid;
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/* -- Check if the specified object is an array --------------------- */
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if(!PyArray_Check (object))
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- { array = (PyArrayObject*) PyArray_FromObject(object, PyArray_LONG,1,1);
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+ { array = (PyArrayObject*) PyArray_FromObject(object, PyArray_INT,1,1);
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if (!array)
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{ strcpy (message, "initialid cannot be converted to needed array.");
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PyErr_SetString(ErrorObject, buffer);
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@@ -304,8 +304,8 @@ parse_initialid(PyObject* object, int* nclusters, int
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Py_INCREF(object);
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}
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/* -- Check if the array contains integers -------------------------- */
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- if (array->descr->type_num != PyArray_LONG)
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- { PyArrayObject* av = (PyArrayObject*) PyArray_Cast(array, PyArray_LONG);
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+ if (array->descr->type_num != PyArray_INT)
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+ { PyArrayObject* av = (PyArrayObject*) PyArray_Cast(array, PyArray_INT);
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Py_DECREF((PyObject*) array);
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array = av;
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if (!array)
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@@ -394,7 +394,7 @@ parse_clusterid(PyObject* object, PyArrayObject** arra
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}
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/* -- The user specified something. Let's see if it is an array ----- */
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if(!PyArray_Check (object))
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- { *array = (PyArrayObject*) PyArray_FromObject(object, PyArray_LONG,1,1);
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+ { *array = (PyArrayObject*) PyArray_FromObject(object, PyArray_INT,1,1);
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if (!(*array))
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{ strcpy (message, "clusterid cannot be converted to needed array.");
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PyErr_SetString(ErrorObject, buffer);
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@@ -406,8 +406,8 @@ parse_clusterid(PyObject* object, PyArrayObject** arra
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Py_INCREF(object);
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}
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/* -- Check if the array contains integers -------------------------- */
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- if ((*array)->descr->type_num != PyArray_LONG)
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- { PyArrayObject* av = (PyArrayObject*) PyArray_Cast(*array, PyArray_LONG);
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+ if ((*array)->descr->type_num != PyArray_INT)
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+ { PyArrayObject* av = (PyArrayObject*) PyArray_Cast(*array, PyArray_INT);
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Py_DECREF((PyObject*) (*array));
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*array = av;
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if (!(*array))
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@@ -663,7 +663,7 @@ parse_index(PyObject* object, PyArrayObject** array, i
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/* Check if the user specified an array */
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if(!PyArray_Check (object)) /* Try to convert to an array of type long */
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{ *array = (PyArrayObject*)
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- PyArray_ContiguousFromObject(object, PyArray_LONG, 1, 1);
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+ PyArray_ContiguousFromObject(object, PyArray_INT, 1, 1);
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if (!(*array))
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{ strcpy(message, "index argument cannot be converted to needed type.");
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PyErr_SetString (ErrorObject, buffer);
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@@ -672,7 +672,7 @@ parse_index(PyObject* object, PyArrayObject** array, i
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}
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}
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/* If an array, make sure it contains integers */
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- else if ((*array)->descr->type_num == PyArray_LONG)
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+ else if ((*array)->descr->type_num == PyArray_INT)
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{ *array = (PyArrayObject*) object;
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Py_INCREF(object);
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}
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@@ -697,7 +697,7 @@ parse_index(PyObject* object, PyArrayObject** array, i
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}
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if (!(*array)->flags & CONTIGUOUS)
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{ PyObject* av =
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- PyArray_ContiguousFromObject((PyObject*) array, PyArray_LONG, 0, 0);
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+ PyArray_ContiguousFromObject((PyObject*) array, PyArray_INT, 0, 0);
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Py_DECREF(object); /* can only happen if *array==(PyArrayObject*)object */
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if(!av)
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{ strcpy(message, "Failed making argument index contiguous.");
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@@ -800,7 +800,7 @@ py_kcluster (PyObject* self, PyObject* args, PyObject*
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"dist",
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"initialid",
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NULL };
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- if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|lOOllccO", kwlist,
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+ if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|iOOiiccO", kwlist,
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&DATA,
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&NCLUSTERS,
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&MASK,
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@@ -899,7 +899,7 @@ py_kcluster (PyObject* self, PyObject* args, PyObject*
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free_weight(aWEIGHT, weight);
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/* --------------------------------------------------------------------- */
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- return Py_BuildValue("Ndl", aCLUSTERID, ERROR, IFOUND);
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+ return Py_BuildValue("Ndi", aCLUSTERID, ERROR, IFOUND);
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}
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/* end of wrapper for kcluster */
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@@ -1015,7 +1015,7 @@ py_kmedoids (PyObject* self, PyObject* args, PyObject*
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strcpy(message, "Unknown error in kmedoids");
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return NULL;
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}
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- return Py_BuildValue("Ndl",aCLUSTERID, ERROR, IFOUND);
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+ return Py_BuildValue("Ndi",aCLUSTERID, ERROR, IFOUND);
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}
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/* end of wrapper for kmedoids */
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@@ -1091,7 +1091,7 @@ py_treecluster (PyObject* self, PyObject* args, PyObje
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"dist",
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"distancematrix",
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NULL };
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- if(!PyArg_ParseTupleAndKeywords(args, keywords, "|OOOlccO", kwlist,
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+ if(!PyArg_ParseTupleAndKeywords(args, keywords, "|OOOiccO", kwlist,
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&DATA,
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&MASK,
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&WEIGHT,
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@@ -1165,7 +1165,7 @@ py_treecluster (PyObject* self, PyObject* args, PyObje
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/* -- Create the output variable tree ---------------------------------- */
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shape[0] = nnodes;
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shape[1] = 2;
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- aRESULT = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_LONG);
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+ aRESULT = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_INT);
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if (!aRESULT)
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{ strcpy(message, "Could not create array for return value -- too big?");
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PyErr_SetString(ErrorObject, buffer);
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@@ -1228,7 +1228,7 @@ py_treecluster (PyObject* self, PyObject* args, PyObje
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/* -- Create the output variable tree ---------------------------------- */
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shape[0] = nnodes;
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shape[1] = 2;
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- aRESULT = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_LONG);
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+ aRESULT = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_INT);
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if (!aRESULT)
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{ strcpy(message, "Could not create array for return value -- too big?");
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PyErr_SetString(ErrorObject, buffer);
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@@ -1341,7 +1341,7 @@ py_somcluster (PyObject* self, PyObject* args, PyObjec
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"niter",
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"dist",
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NULL };
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- if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|OOllldlc", kwlist,
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+ if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|OOiiidic", kwlist,
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&DATA,
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&MASK,
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&WEIGHT,
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@@ -1403,7 +1403,7 @@ py_somcluster (PyObject* self, PyObject* args, PyObjec
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/* --------------------------------------------------------------------- */
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shape[0] = nitems;
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shape[1] = 2;
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- aCLUSTERID = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_LONG);
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+ aCLUSTERID = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_INT);
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if (!aCLUSTERID)
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{ strcpy(buffer, "somcluster: Could not create clusterid array -- too big?");
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PyErr_SetString (ErrorObject, buffer);
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@@ -1656,7 +1656,7 @@ py_clusterdistance (PyObject* self, PyObject* args, Py
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"dist",
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"transpose",
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NULL };
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- if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|OOOOccl", kwlist,
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+ if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|OOOOcci", kwlist,
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&DATA,
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&MASK,
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&WEIGHT,
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@@ -1826,7 +1826,7 @@ py_clustercentroid (PyObject* self, PyObject* args, Py
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for (i=0; i<shape[0]; i++)
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cdata[i] = ((double*) (aCDATA->data)) + i*shape[1];
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/* -- Create the centroid mask output variable ------------------------- */
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- aCMASK = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_LONG);
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+ aCMASK = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_INT);
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if (!aCMASK)
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{ strcpy(message, "Could not create centroids array -- too big?");
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PyErr_SetString (ErrorObject, buffer);
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@@ -1934,7 +1934,7 @@ py_distancematrix (PyObject* self, PyObject* args, PyO
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"transpose",
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"dist",
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NULL };
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- if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|OOlc", kwlist,
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+ if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|OOic", kwlist,
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&DATA,
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&MASK,
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&WEIGHT,
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@@ -2056,7 +2056,7 @@ py_cuttree (PyObject* self, PyObject* args, PyObject*
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{ aTREE = (PyArrayObject*) TREE;
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Py_INCREF((PyObject*) aTREE);
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}
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- if (aTREE->descr->type_num != PyArray_LONG)
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+ if (aTREE->descr->type_num != PyArray_INT)
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{ PyErr_SetString (ErrorObject,
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"cuttree: Argument tree should contain integer values only");
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return NULL;
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@@ -2095,7 +2095,7 @@ py_cuttree (PyObject* self, PyObject* args, PyObject*
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return NULL;
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}
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/* -- Create the clusterid output variable ----------------------------- */
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- aCLUSTERID = (PyArrayObject*) PyArray_FromDims(1, &NELEMENTS, PyArray_LONG);
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+ aCLUSTERID = (PyArrayObject*) PyArray_FromDims(1, &NELEMENTS, PyArray_INT);
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if (!aCLUSTERID) {
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PyErr_SetString (ErrorObject,
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"cuttree: Could not create array for return value -- too big?");
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@ -1,7 +1,7 @@
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$OpenBSD: patch-Tests_run_tests_py,v 1.1 2005/12/03 22:34:52 alek Exp $
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--- Tests/run_tests.py.orig Sun Nov 20 16:29:24 2005
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+++ Tests/run_tests.py Sun Nov 20 16:29:35 2005
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@@ -37,11 +37,11 @@ def main(argv):
|
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$OpenBSD: patch-Tests_run_tests_py,v 1.2 2008/01/12 02:00:24 okan Exp $
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--- Tests/run_tests.py.orig Thu Oct 11 20:39:07 2007
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+++ Tests/run_tests.py Fri Dec 21 16:45:24 2007
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@@ -39,11 +39,11 @@ def main(argv):
|
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# A. Because Martel may not be in ../build/lib.*
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test_path = sys.path[0] or "."
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source_path = os.path.abspath("%s/.." % test_path)
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|
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@ -1,15 +1,22 @@
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$OpenBSD: patch-setup_py,v 1.4 2005/12/18 20:33:17 alek Exp $
|
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--- setup.py.orig Fri Oct 28 21:41:02 2005
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+++ setup.py Sun Dec 18 19:26:31 2005
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@@ -65,6 +65,7 @@ def check_dependencies_once():
|
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$OpenBSD: patch-setup_py,v 1.5 2008/01/12 02:00:24 okan Exp $
|
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--- setup.py.orig Sat Oct 27 02:11:01 2007
|
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+++ setup.py Fri Dec 21 16:56:57 2007
|
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@@ -65,6 +65,14 @@ def check_dependencies_once():
|
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return _CHECKED
|
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|
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def check_dependencies():
|
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+ NUMPY_PACKAGES.append("Bio.KDTree")
|
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+ NUMPY_EXTENSIONS.append(
|
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+ CplusplusExtension('Bio.KDTree._CKDTree',
|
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+ ["Bio/KDTree/KDTree.cpp",
|
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+ "Bio/KDTree/KDTree.swig.cpp"],
|
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+ libraries=["stdc++"],
|
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+ language="c++"))
|
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+ return 1
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"""Return whether the installation should continue."""
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# There should be some way for the user to tell specify not to
|
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# check dependencies. For example, it probably should not if
|
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@@ -254,7 +255,10 @@ def is_Martel_installed():
|
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@@ -285,7 +293,10 @@ def is_Martel_installed():
|
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bundled_martel_version = m.__version__
|
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else:
|
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bundled_martel_version = None
|
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|
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2
biology/py-biopython/pkg/PFRAG.shared
Normal file
2
biology/py-biopython/pkg/PFRAG.shared
Normal file
@ -0,0 +1,2 @@
|
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@comment $OpenBSD: PFRAG.shared,v 1.1 2008/01/12 02:00:24 okan Exp $
|
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lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/_CKDTree.so
|
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@ -1,4 +1,5 @@
|
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@comment $OpenBSD: PLIST,v 1.5 2007/11/02 10:10:11 ajacoutot Exp $
|
||||
@comment $OpenBSD: PLIST,v 1.6 2008/01/12 02:00:24 okan Exp $
|
||||
%%SHARED%%
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/
|
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lib/python${MODPY_VERSION}/site-packages/Bio/Affy/
|
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lib/python${MODPY_VERSION}/site-packages/Bio/Affy/CelFile.py
|
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@ -8,8 +9,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Affy/__init__.pyc
|
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lib/python${MODPY_VERSION}/site-packages/Bio/Ais/
|
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lib/python${MODPY_VERSION}/site-packages/Bio/Ais/__init__.py
|
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lib/python${MODPY_VERSION}/site-packages/Bio/Ais/__init__.pyc
|
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lib/python${MODPY_VERSION}/site-packages/Bio/Ais/example_ais2.py
|
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lib/python${MODPY_VERSION}/site-packages/Bio/Ais/example_ais2.pyc
|
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lib/python${MODPY_VERSION}/site-packages/Bio/Align/
|
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lib/python${MODPY_VERSION}/site-packages/Bio/Align/AlignInfo.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Align/AlignInfo.pyc
|
||||
@ -78,8 +77,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/cluster.so
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/data.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/data.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Compass/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Compass/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Compass/__init__.pyc
|
||||
@ -252,6 +249,8 @@ lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/LocationParser.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/LocationParser.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/Record.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/Record.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/Scanner.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/Scanner.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/utils.py
|
||||
@ -261,8 +260,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Geo/Record.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Geo/Record.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Geo/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Geo/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Geo/geo_format.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Geo/geo_format.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Gobase/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Gobase/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Gobase/__init__.pyc
|
||||
@ -302,31 +299,25 @@ lib/python${MODPY_VERSION}/site-packages/Bio/IntelliGenetics/intelligenetics_for
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/InterPro/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/InterPro/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/InterPro/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/CKDTree.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/CKDTree.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/KDTree.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/KDTree.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Compound/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Compound/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Compound/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Compound/compound_format.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Compound/compound_format.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Enzyme/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Enzyme/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Enzyme/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Enzyme/enzyme_format.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Enzyme/enzyme_format.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Map/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Map/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Map/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Map/map_format.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Map/map_format.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/Record.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/Record.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/kabat_format.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/kabat_format.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/LocusLink/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/LocusLink/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/LocusLink/__init__.pyc
|
||||
@ -490,6 +481,8 @@ lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PDBList.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PDBList.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PDBParser.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PDBParser.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PSEA.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PSEA.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/Polypeptide.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/Polypeptide.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/Residue.py
|
||||
@ -511,7 +504,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/PDB/Vector.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/mmCIF/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/mmCIF/MMCIFlex.so
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/mmCIF/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/mmCIF/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/parse_pdb_header.py
|
||||
@ -535,6 +527,28 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/Rep/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/Rep/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/Async/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/Async/Local.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/Async/Local.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/Async/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/Async/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/Async.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/Async.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/Controller.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/Controller.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/Utils.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/Utils.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/Utils.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/Utils.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PropertyManager.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/PropertyManager.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Prosite/
|
||||
@ -549,10 +563,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/PubMed.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Rebase/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Rebase/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Rebase/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/RecordFile.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/RecordFile.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/ReseekFile.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/ReseekFile.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Restriction/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Restriction/DNAUtils.so
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Restriction/PrintFormat.py
|
||||
@ -596,8 +606,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer/SVDSuperimposer.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer/SVDSuperimposer.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SVM.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SVM.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Saf/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Saf/Record.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Saf/Record.pyc
|
||||
@ -612,8 +620,24 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Seq.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqFeature.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqFeature.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/ClustalIO.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/ClustalIO.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/FASTA.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/FASTA.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/FastaIO.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/FastaIO.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/InsdcIO.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/InsdcIO.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/Interfaces.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/Interfaces.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/NexusIO.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/NexusIO.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/PhylipIO.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/PhylipIO.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/StockholmIO.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/StockholmIO.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/SwissIO.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/SwissIO.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/generic.py
|
||||
@ -621,6 +645,8 @@ lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/generic.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqRecord.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqRecord.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/CheckSum.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/CheckSum.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/CodonUsage.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/CodonUsage.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/CodonUsageIndices.py
|
||||
@ -635,6 +661,8 @@ lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/ProtParamData.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/ProtParamData.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/lcc.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/lcc.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/Ace.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/Ace.pyc
|
||||
@ -710,9 +738,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/builders/SeqRecord/sequence.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/builders/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/builders/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/cMarkovModel.so
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/cSVM.so
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/cdistance.so
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/ckMeans.so
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/clistfns.so
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/cmathfns.so
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/config/
|
||||
@ -808,8 +834,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/formatdefs/sequence.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/formatdefs/sequence.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/formatdefs/swissprot.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/formatdefs/swissprot.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/kMeans.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/kMeans.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/kNN.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/kNN.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/lcc.py
|
||||
@ -820,8 +844,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/mathfns.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/mathfns.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/pairwise2.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/pairwise2.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/sequtils.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/sequtils.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/stringfns.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/stringfns.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/trie.so
|
||||
@ -841,8 +863,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/writers/SeqRecord/fasta.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/writers/SeqRecord/fasta.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/writers/__init__.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/writers/__init__.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/xkMeans.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Bio/xkMeans.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/BioSQL/
|
||||
lib/python${MODPY_VERSION}/site-packages/BioSQL/BioSeq.py
|
||||
lib/python${MODPY_VERSION}/site-packages/BioSQL/BioSeq.pyc
|
||||
@ -885,622 +905,35 @@ lib/python${MODPY_VERSION}/site-packages/Martel/optimize.py
|
||||
lib/python${MODPY_VERSION}/site-packages/Martel/optimize.pyc
|
||||
@comment lib/python${MODPY_VERSION}/site-packages/Martel/setup.py
|
||||
@comment lib/python${MODPY_VERSION}/site-packages/Martel/setup.pyc
|
||||
lib/python${MODPY_VERSION}/site-packages/biopython-1.41-py${MODPY_VERSION}.egg-info
|
||||
lib/python${MODPY_VERSION}/site-packages/biopython-1.44-py${MODPY_VERSION}.egg-info
|
||||
share/doc/py-biopython/
|
||||
share/doc/py-biopython/CDD.txt
|
||||
share/doc/py-biopython/Crystal.txt
|
||||
share/doc/py-biopython/ECell.txt
|
||||
share/doc/py-biopython/FilteredReader.txt
|
||||
share/doc/py-biopython/Geo.txt
|
||||
share/doc/py-biopython/IntelliGenetics.txt
|
||||
share/doc/py-biopython/InterPro.txt
|
||||
share/doc/py-biopython/NetCatch.txt
|
||||
share/doc/py-biopython/References.txt
|
||||
share/doc/py-biopython/SGMLExtractor.txt
|
||||
share/doc/py-biopython/Saf.txt
|
||||
share/doc/py-biopython/Tutorial.txt
|
||||
share/examples/py-biopython/
|
||||
share/examples/py-biopython/Ace/
|
||||
share/examples/py-biopython/Ace/contig1.ace
|
||||
share/examples/py-biopython/Amino/
|
||||
share/examples/py-biopython/Amino/aster.pro
|
||||
share/examples/py-biopython/Amino/loveliesbleeding.pro
|
||||
share/examples/py-biopython/Amino/rose.pro
|
||||
share/examples/py-biopython/Amino/rosemary.pro
|
||||
share/examples/py-biopython/BioSQL/
|
||||
share/examples/py-biopython/BioSQL/biosqldb-mysql.sql
|
||||
share/examples/py-biopython/BioSQL/biosqldb-pg.sql
|
||||
share/examples/py-biopython/Blast/
|
||||
share/examples/py-biopython/Blast/README
|
||||
share/examples/py-biopython/Blast/bt001
|
||||
share/examples/py-biopython/Blast/bt002
|
||||
share/examples/py-biopython/Blast/bt003
|
||||
share/examples/py-biopython/Blast/bt004
|
||||
share/examples/py-biopython/Blast/bt005
|
||||
share/examples/py-biopython/Blast/bt006
|
||||
share/examples/py-biopython/Blast/bt007
|
||||
share/examples/py-biopython/Blast/bt009
|
||||
share/examples/py-biopython/Blast/bt010
|
||||
share/examples/py-biopython/Blast/bt011
|
||||
share/examples/py-biopython/Blast/bt012
|
||||
share/examples/py-biopython/Blast/bt013
|
||||
share/examples/py-biopython/Blast/bt014
|
||||
share/examples/py-biopython/Blast/bt015
|
||||
share/examples/py-biopython/Blast/bt016
|
||||
share/examples/py-biopython/Blast/bt017
|
||||
share/examples/py-biopython/Blast/bt018
|
||||
share/examples/py-biopython/Blast/bt019
|
||||
share/examples/py-biopython/Blast/bt020
|
||||
share/examples/py-biopython/Blast/bt021
|
||||
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share/examples/py-biopython/test_HotRand.py
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share/examples/py-biopython/test_IsoelectricPoint.py
|
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share/examples/py-biopython/test_KDTree.py
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share/examples/py-biopython/test_KEGG.py
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share/examples/py-biopython/test_KeyWList.py
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|
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share/examples/py-biopython/test_MarkovModel.py
|
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share/examples/py-biopython/test_NCBIStandalone.py
|
||||
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|
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|
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|
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share/examples/py-biopython/test_SCOP_Astral.py
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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share/examples/py-biopython/test_metatool.py
|
||||
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|
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share/examples/py-biopython/test_ndb.py
|
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share/examples/py-biopython/test_pairwise2.py
|
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share/examples/py-biopython/test_prodoc.py
|
||||
share/examples/py-biopython/test_property_manager.py
|
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|
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|
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|
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|
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|
||||
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|
||||
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|
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|
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|
||||
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
share/examples/py-biopython/pubmed_search.py
|
||||
share/examples/py-biopython/query_entrez.py
|
||||
share/examples/py-biopython/swissprot.py
|
||||
share/examples/py-biopython/www_blast.py
|
||||
|
||||
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Reference in New Issue
Block a user