[gentoo-commits] proj/sci:master commit in: sci-biology/biopython/, sci-biology/biopython/files/

[Martin Mokrejs]

commit:     031391850b6768a55ed2c98a93eeb255954b51d2
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 16:07:50 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 16:07:50 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=03139185

sci-biology/biopython-1.63-r1: added missing deps on dev-python/rdflib to sync with official sci-biology/biopython-1.63; dropping sci-biology/biopython-1.63 from overlay

Package-Manager: portage-2.2.7

---
 sci-biology/biopython/ChangeLog                    |   8 ++
 sci-biology/biopython/biopython-1.62-r3.ebuild     |  51 -------
 sci-biology/biopython/biopython-1.62-r4.ebuild     |  51 -------
 sci-biology/biopython/biopython-1.63-r1.ebuild     |   1 +
 sci-biology/biopython/biopython-1.63.ebuild        |  50 -------
 sci-biology/biopython/files/SeqRecord.py.patch     | 148 ---------------------
 .../biopython/files/adjust-trimpoints.patch        |  76 -----------
 7 files changed, 9 insertions(+), 376 deletions(-)

diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
index 6dfe5e2..037227d 100644
--- a/sci-biology/biopython/ChangeLog
+++ b/sci-biology/biopython/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  23 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
+  -biopython-1.62-r3.ebuild, -biopython-1.62-r4.ebuild, -biopython-1.63.ebuild,
+  -files/SeqRecord.py.patch, -files/adjust-trimpoints.patch,
+  biopython-1.63-r1.ebuild:
+  sci-biology/biopython-1.63-r1: added missing deps on dev-python/rdflib to sync
+  with official sci-biology/biopython-1.63; dropping sci-biology/biopython-1.63
+  from overlay
+
 *biopython-1.62-r3 (23 Mar 2014)
 *biopython-1.62-r4 (23 Mar 2014)
 *biopython-1.63-r1 (23 Mar 2014)

diff --git a/sci-biology/biopython/biopython-1.62-r3.ebuild b/sci-biology/biopython/biopython-1.62-r3.ebuild
deleted file mode 100644
index 1eed5a9..0000000
--- a/sci-biology/biopython/biopython-1.62-r3.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.62.ebuild,v 1.1 2013/09/17 16:07:56 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_6,2_7} )
-
-inherit distutils-r1 eutils
-
-DESCRIPTION="Python modules for computational molecular biology"
-HOMEPAGE="http://www.biopython.org/ http://pypi.python.org/pypi/biopython/"
-SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz"
-
-LICENSE="HPND"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="mysql postgres"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pygraphviz[${PYTHON_USEDEP}]
-	dev-python/reportlab[${PYTHON_USEDEP}]
-	media-gfx/pydot[${PYTHON_USEDEP}]
-	mysql? ( dev-python/mysql-python[${PYTHON_USEDEP}] )
-	postgres? ( dev-python/psycopg[${PYTHON_USEDEP}] )"
-DEPEND="${RDEPEND}
-	sys-devel/flex"
-
-DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
-
-src_prepare() {
-	distutils-r1_src_prepare
-	epatch "${FILESDIR}/${PN}-1.62-SffIO.patch"
-}
-
-python_test() {
-	cd Tests || die
-	${PYTHON} run_tests.py || die
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	dodir /usr/share/${PN}
-	cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die
-}

diff --git a/sci-biology/biopython/biopython-1.62-r4.ebuild b/sci-biology/biopython/biopython-1.62-r4.ebuild
deleted file mode 100644
index 1eed5a9..0000000
--- a/sci-biology/biopython/biopython-1.62-r4.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.62.ebuild,v 1.1 2013/09/17 16:07:56 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_6,2_7} )
-
-inherit distutils-r1 eutils
-
-DESCRIPTION="Python modules for computational molecular biology"
-HOMEPAGE="http://www.biopython.org/ http://pypi.python.org/pypi/biopython/"
-SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz"
-
-LICENSE="HPND"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="mysql postgres"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pygraphviz[${PYTHON_USEDEP}]
-	dev-python/reportlab[${PYTHON_USEDEP}]
-	media-gfx/pydot[${PYTHON_USEDEP}]
-	mysql? ( dev-python/mysql-python[${PYTHON_USEDEP}] )
-	postgres? ( dev-python/psycopg[${PYTHON_USEDEP}] )"
-DEPEND="${RDEPEND}
-	sys-devel/flex"
-
-DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
-
-src_prepare() {
-	distutils-r1_src_prepare
-	epatch "${FILESDIR}/${PN}-1.62-SffIO.patch"
-}
-
-python_test() {
-	cd Tests || die
-	${PYTHON} run_tests.py || die
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	dodir /usr/share/${PN}
-	cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die
-}

diff --git a/sci-biology/biopython/biopython-1.63-r1.ebuild b/sci-biology/biopython/biopython-1.63-r1.ebuild
index aac2bdf..e99f846 100644
--- a/sci-biology/biopython/biopython-1.63-r1.ebuild
+++ b/sci-biology/biopython/biopython-1.63-r1.ebuild
@@ -23,6 +23,7 @@ RDEPEND="${PYTHON_DEPS}
 	dev-python/matplotlib[${PYTHON_USEDEP}]
 	dev-python/networkx[${PYTHON_USEDEP}]
 	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/rdflib[${PYTHON_USEDEP}]
 	dev-python/pygraphviz[${PYTHON_USEDEP}]
 	dev-python/reportlab[${PYTHON_USEDEP}]
 	media-gfx/pydot[${PYTHON_USEDEP}]

diff --git a/sci-biology/biopython/biopython-1.63.ebuild b/sci-biology/biopython/biopython-1.63.ebuild
deleted file mode 100644
index 5180b33..0000000
--- a/sci-biology/biopython/biopython-1.63.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.62.ebuild,v 1.1 2013/09/17 16:07:56 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_6,2_7} )
-
-inherit distutils-r1 eutils
-
-DESCRIPTION="Python modules for computational molecular biology"
-HOMEPAGE="http://www.biopython.org/ http://pypi.python.org/pypi/biopython/"
-SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz"
-
-LICENSE="HPND"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="mysql postgres"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pygraphviz[${PYTHON_USEDEP}]
-	dev-python/reportlab[${PYTHON_USEDEP}]
-	media-gfx/pydot[${PYTHON_USEDEP}]
-	mysql? ( dev-python/mysql-python[${PYTHON_USEDEP}] )
-	postgres? ( dev-python/psycopg[${PYTHON_USEDEP}] )"
-DEPEND="${RDEPEND}
-	sys-devel/flex"
-
-DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
-
-src_prepare() {
-	distutils-r1_src_prepare
-}
-
-python_test() {
-	cd Tests || die
-	${PYTHON} run_tests.py || die
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	dodir /usr/share/${PN}
-	cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die
-}

diff --git a/sci-biology/biopython/files/SeqRecord.py.patch b/sci-biology/biopython/files/SeqRecord.py.patch
deleted file mode 100644
index ac3785f..0000000
--- a/sci-biology/biopython/files/SeqRecord.py.patch
+++ /dev/null
@@ -1,148 +0,0 @@
-diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
-index 1971dba..43b38fd 100644
---- a/Bio/SeqIO/SffIO.py
-+++ b/Bio/SeqIO/SffIO.py
-@@ -539,8 +539,15 @@ _valid_UAN_read_name = re.compile(r'^[a-zA-Z0-9]{14}$')
- 
- 
- def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
--                         key_sequence, alphabet, trim=False):
--    """Parse the next read in the file, return data as a SeqRecord (PRIVATE)."""
-+                         key_sequence, alphabet, trim=False, interpret_qual_trims=True, interpret_adapter_trims=False):
-+    """Parse the next read in the file, return data as a SeqRecord (PRIVATE).
-+    Allow user to specify which type of clipping values should be applied
-+    while reading the SFF stream. To be backwards compatible, we interpret
-+    only the quality-based trim points by default. That results in lower-cased
-+    sequences in the low-qual region, regardless what adapter-based clip points
-+    say. This should be the desired behavior. More discussion at
-+    https://redmine.open-bio.org/issues/3437
-+    """
-     #Now on to the reads...
-     #the read header format (fixed part):
-     #read_header_length     H
-@@ -589,20 +596,41 @@ def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
-             warnings.warn("Post quality %i byte padding region contained data, SFF data is not broken"
-                              % padding)
-     #Follow Roche and apply most aggressive of qual and adapter clipping.
--    #Note Roche seems to ignore adapter clip fields when writing SFF,
--    #and uses just the quality clipping values for any clipping.
--    clip_left = max(clip_qual_left, clip_adapter_left)
--    #Right clipping of zero means no clipping
--    if clip_qual_right:
--        if clip_adapter_right:
--            clip_right = min(clip_qual_right, clip_adapter_right)
-+    #Note Roche does not use adapter clip fields when writing SFF files
-+    #but instead combines the adapter clipping information with quality-based
-+    #values and writes the most aggressive combination into clip fields (as
-+    #allowed by SFF specs).
-+
-+    if interpret_qual_trims:
-+        if interpret_adapter_trims:
-+            clip_left = max(clip_qual_left, clip_adapter_left)
-+            #Right clipping of zero means no clipping
-+            if clip_qual_right:
-+                if clip_adapter_right:
-+                    clip_right = min(clip_qual_right, clip_adapter_right)
-+                else:
-+                    #Typical case with Roche SFF files
-+                    clip_right = clip_qual_right
-+            elif clip_adapter_right:
-+                clip_right = clip_adapter_right
-+            else:
-+                clip_right = seq_len
-         else:
--            #Typical case with Roche SFF files
--            clip_right = clip_qual_right
--    elif clip_adapter_right:
--        clip_right = clip_adapter_right
-+	    clip_left = clip_qual_left
-+	    if clip_qual_right:
-+	        clip_right = clip_qual_right
-+            else:
-+	        clip_right = seq_len
-+    elif interpret_adapter_trims:
-+        clip_left = clip_adapter_left
-+	if clip_adapter_right:
-+	    clip_right = clip_adapter_right
-+	else:
-+	    clip_right = seq_len
-     else:
--        clip_right = seq_len
-+        clip_left = 0
-+	clip_right = seq_len
-+
-     #Now build a SeqRecord
-     if trim:
-         seq = seq[clip_left:clip_right].upper()
-diff --git a/Bio/SeqRecord.py b/Bio/SeqRecord.py
-index c90e13b..66bdea0 100644
---- a/Bio/SeqRecord.py
-+++ b/Bio/SeqRecord.py
-@@ -14,6 +14,8 @@ __docformat__ = "epytext en"  # Simple markup to show doctests nicely
- # also BioSQL.BioSeq.DBSeq which is the "Database Seq" class)
- 
- 
-+from Bio.Seq import Seq
-+
- class _RestrictedDict(dict):
-     """Dict which only allows sequences of given length as values (PRIVATE).
- 
-@@ -76,7 +78,7 @@ class _RestrictedDict(dict):
-         if not hasattr(value, "__len__") or not hasattr(value, "__getitem__") \
-         or (hasattr(self, "_length") and len(value) != self._length):
-             raise TypeError("We only allow python sequences (lists, tuples or "
--                            "strings) of length %i." % self._length)
-+                            "strings) of length %i whereas you passed an object of length %s." % (self._length, str(len(value))))
-         dict.__setitem__(self, key, value)
- 
-     def update(self, new_dict):
-@@ -290,10 +292,11 @@ class SeqRecord(object):
-         """)
- 
-     def _set_seq(self, value):
--        #TODO - Add a deprecation warning that the seq should be write only?
--        if self._per_letter_annotations:
--            #TODO - Make this a warning? Silently empty the dictionary?
--            raise ValueError("You must empty the letter annotations first!")
-+        # we should be much more user friendly and accept even a plain sequence string
-+	# and make the Seq or MutableSeq object ourselves
-+        if not isinstance(value, Seq):
-+            raise ValueError("You must pass a Seq object containing the new sequence instead of just plain string.")
-+        else:
-         self._seq = value
-         try:
-             self._per_letter_annotations = _RestrictedDict(length=len(self.seq))
-@@ -696,7 +699,7 @@ class SeqRecord(object):
-         SeqIO.write(self, handle, format_spec)
-         return handle.getvalue()
- 
--    def __len__(self):
-+    def __len__(self, trim=False, interpret_qual_trims=True, interpret_adapter_trims=False):
-         """Returns the length of the sequence.
- 
-         For example, using Bio.SeqIO to read in a FASTA nucleotide file:
-@@ -707,6 +710,10 @@ class SeqRecord(object):
-         309
-         >>> len(record.seq)
-         309
-+
-+	It should be possible to get length of a raw object, of trimmed
-+	object by quality or adapter criteria or both, whenever user wants
-+	to, not only when data is parsed from input.
-         """
-         return len(self.seq)
- 
-@@ -725,6 +732,13 @@ class SeqRecord(object):
-         """
-         return True
- 
-+    def apply_trimpoints(self, trim=False, interpret_qual_trims=False, interpret_adapter_trims=False):
-+        """We should apply either of the quality-based or adapter-based annotated
-+	trim points and return a new, sliced object.
-+	"""
-+	pass
-+
-+
-     def __add__(self, other):
-         """Add another sequence or string to this sequence.
- 

diff --git a/sci-biology/biopython/files/adjust-trimpoints.patch b/sci-biology/biopython/files/adjust-trimpoints.patch
deleted file mode 100644
index dd6d548..0000000
--- a/sci-biology/biopython/files/adjust-trimpoints.patch
+++ /dev/null
@@ -1,76 +0,0 @@
-diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
-index 1971dba..43b38fd 100644
---- a/Bio/SeqIO/SffIO.py
-+++ b/Bio/SeqIO/SffIO.py
-@@ -539,8 +539,15 @@ _valid_UAN_read_name = re.compile(r'^[a-zA-Z0-9]{14}$')
- 
- 
- def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
--                         key_sequence, alphabet, trim=False):
--    """Parse the next read in the file, return data as a SeqRecord (PRIVATE)."""
-+                         key_sequence, alphabet, trim=False, interpret_qual_trims=True, interpret_adapter_trims=False):
-+    """Parse the next read in the file, return data as a SeqRecord (PRIVATE).
-+    Allow user to specify which type of clipping values should be applied
-+    while reading the SFF stream. To be backwards compatible, we interpret
-+    only the quality-based trim points by default. That results in lower-cased
-+    sequences in the low-qual region, regardless what adapter-based clip points
-+    say. This should be the desired behavior. More discussion at
-+    https://redmine.open-bio.org/issues/3437
-+    """
-     #Now on to the reads...
-     #the read header format (fixed part):
-     #read_header_length     H
-@@ -589,20 +596,41 @@ def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
-             warnings.warn("Post quality %i byte padding region contained data, SFF data is not broken"
-                              % padding)
-     #Follow Roche and apply most aggressive of qual and adapter clipping.
--    #Note Roche seems to ignore adapter clip fields when writing SFF,
--    #and uses just the quality clipping values for any clipping.
--    clip_left = max(clip_qual_left, clip_adapter_left)
--    #Right clipping of zero means no clipping
--    if clip_qual_right:
--        if clip_adapter_right:
--            clip_right = min(clip_qual_right, clip_adapter_right)
-+    #Note Roche does not use adapter clip fields when writing SFF files
-+    #but instead combines the adapter clipping information with quality-based
-+    #values and writes the most aggressive combination into clip fields (as
-+    #allowed by SFF specs).
-+
-+    if interpret_qual_trims:
-+        if interpret_adapter_trims:
-+            clip_left = max(clip_qual_left, clip_adapter_left)
-+            #Right clipping of zero means no clipping
-+            if clip_qual_right:
-+                if clip_adapter_right:
-+                    clip_right = min(clip_qual_right, clip_adapter_right)
-+                else:
-+                    #Typical case with Roche SFF files
-+                    clip_right = clip_qual_right
-+            elif clip_adapter_right:
-+                clip_right = clip_adapter_right
-+            else:
-+                clip_right = seq_len
-         else:
--            #Typical case with Roche SFF files
--            clip_right = clip_qual_right
--    elif clip_adapter_right:
--        clip_right = clip_adapter_right
-+	    clip_left = clip_qual_left
-+	    if clip_qual_right:
-+	        clip_right = clip_qual_right
-+            else:
-+	        clip_right = seq_len
-+    elif interpret_adapter_trims:
-+        clip_left = clip_adapter_left
-+	if clip_adapter_right:
-+	    clip_right = clip_adapter_right
-+	else:
-+	    clip_right = seq_len
-     else:
--        clip_right = seq_len
-+        clip_left = 0
-+	clip_right = seq_len
-+
-     #Now build a SeqRecord
-     if trim:
-         seq = seq[clip_left:clip_right].upper()