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

[Martin Mokrejs]

commit:     b6bc96d05888bcfb2a2ebac3a477663d1915c57c
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 15:52:18 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 15:52:18 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b6bc96d0

sci-biology/biopython-1.63-r1: version bump and an upstream patch to improve error message

Package-Manager: portage-2.2.7

---
 sci-biology/biopython/ChangeLog                    |  17 +++
 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     |  51 +++++++
 sci-biology/biopython/biopython-1.63.ebuild        |  50 +++++++
 sci-biology/biopython/files/SeqRecord.py.patch     | 148 +++++++++++++++++++++
 .../biopython/files/SffIO_error_in_check_eof.patch |  14 ++
 .../biopython/files/adjust-trimpoints.patch        |  76 +++++++++++
 .../biopython/files/biopython-1.51-flex.patch      |  21 +++
 .../biopython/files/biopython-1.62-SffIO.patch     |  36 +++++
 sci-biology/biopython/metadata.xml                 |   5 +
 11 files changed, 520 insertions(+)

diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
new file mode 100644
index 0000000..6dfe5e2
--- /dev/null
+++ b/sci-biology/biopython/ChangeLog
@@ -0,0 +1,17 @@
+# ChangeLog for sci-biology/biopython
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*biopython-1.62-r3 (23 Mar 2014)
+*biopython-1.62-r4 (23 Mar 2014)
+*biopython-1.63-r1 (23 Mar 2014)
+*biopython-1.63 (23 Mar 2014)
+
+  23 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
+  +biopython-1.62-r3.ebuild, +biopython-1.62-r4.ebuild,
+  +biopython-1.63-r1.ebuild, +biopython-1.63.ebuild, +files/SeqRecord.py.patch,
+  +files/SffIO_error_in_check_eof.patch, +files/adjust-trimpoints.patch,
+  +files/biopython-1.51-flex.patch, +files/biopython-1.62-SffIO.patch,
+  +metadata.xml:
+  sci-biology/biopython-1.63-r1: version bump and an upstream patch to improve
+  error message

diff --git a/sci-biology/biopython/biopython-1.62-r3.ebuild b/sci-biology/biopython/biopython-1.62-r3.ebuild
new file mode 100644
index 0000000..1eed5a9
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.62-r3.ebuild
@@ -0,0 +1,51 @@
+# 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
new file mode 100644
index 0000000..1eed5a9
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.62-r4.ebuild
@@ -0,0 +1,51 @@
+# 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
new file mode 100644
index 0000000..aac2bdf
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.63-r1.ebuild
@@ -0,0 +1,51 @@
+# 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() {
+	epatch "${FILESDIR}"/SffIO_error_in_check_eof.patch
+	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/biopython-1.63.ebuild b/sci-biology/biopython/biopython-1.63.ebuild
new file mode 100644
index 0000000..5180b33
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.63.ebuild
@@ -0,0 +1,50 @@
+# 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
new file mode 100644
index 0000000..ac3785f
--- /dev/null
+++ b/sci-biology/biopython/files/SeqRecord.py.patch
@@ -0,0 +1,148 @@
+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/SffIO_error_in_check_eof.patch b/sci-biology/biopython/files/SffIO_error_in_check_eof.patch
new file mode 100644
index 0000000..9059604
--- /dev/null
+++ b/sci-biology/biopython/files/SffIO_error_in_check_eof.patch
@@ -0,0 +1,14 @@
+diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
+index 2bb0dac..735d55b 100644
+--- a/Bio/SeqIO/SffIO.py
++++ b/Bio/SeqIO/SffIO.py
+@@ -941,7 +941,8 @@ def _check_eof(handle, index_offset, index_length):
+                       BiopythonParserWarning)
+ 
+     offset = handle.tell()
+-    assert offset % 8 == 0
++    assert offset % 8 == 0, \
++        "Wanted offset %i %% 8 = %i to be zero" % (offset, offset % 8)
+     # Should now be at the end of the file...
+     extra = handle.read(4)
+     if extra == _sff:

diff --git a/sci-biology/biopython/files/adjust-trimpoints.patch b/sci-biology/biopython/files/adjust-trimpoints.patch
new file mode 100644
index 0000000..dd6d548
--- /dev/null
+++ b/sci-biology/biopython/files/adjust-trimpoints.patch
@@ -0,0 +1,76 @@
+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/sci-biology/biopython/files/biopython-1.51-flex.patch b/sci-biology/biopython/files/biopython-1.51-flex.patch
new file mode 100644
index 0000000..afd5094
--- /dev/null
+++ b/sci-biology/biopython/files/biopython-1.51-flex.patch
@@ -0,0 +1,21 @@
+--- setup.py.old	2008-11-25 18:03:16.000000000 +0100
++++ setup.py	2008-11-25 18:04:14.000000000 +0100
+@@ -341,12 +341,12 @@
+               include_dirs=["Bio"]
+               ),
+ #Commented out due to the build dependency on flex, see Bug 2619
+-#   Extension('Bio.PDB.mmCIF.MMCIFlex',
+-#              ['Bio/PDB/mmCIF/lex.yy.c',
+-#               'Bio/PDB/mmCIF/MMCIFlexmodule.c'],
+-#              include_dirs=["Bio"],
+-#              libraries=["fl"]
+-#              ),
++    Extension('Bio.PDB.mmCIF.MMCIFlex',
++              ['Bio/PDB/mmCIF/lex.yy.c',
++               'Bio/PDB/mmCIF/MMCIFlexmodule.c'],
++              include_dirs=["Bio"],
++              libraries=["fl"]
++              ),
+     Extension('Bio.Nexus.cnexus',
+               ['Bio/Nexus/cnexus.c']
+               ),

diff --git a/sci-biology/biopython/files/biopython-1.62-SffIO.patch b/sci-biology/biopython/files/biopython-1.62-SffIO.patch
new file mode 100644
index 0000000..7f2208e
--- /dev/null
+++ b/sci-biology/biopython/files/biopython-1.62-SffIO.patch
@@ -0,0 +1,36 @@
+--- Bio/SeqIO/SffIO.py.ori	2013-09-25 13:28:51.000000000 +0200
++++ Bio/SeqIO/SffIO.py	2013-09-25 13:37:44.000000000 +0200
+@@ -383,7 +383,14 @@
+         if padding:
+             padding = 8 - padding
+             if handle.read(padding).count(_null) != padding:
+-                raise ValueError("Post quality %i byte padding region contained data"
++                import warnings
++                from Bio import BiopythonParserWarning
++                warnings.warn("Your SFF file is valid but post quality %i byte "
++                              "padding region contains UNUSED data. Was the "
++                              "SFF file created by SRA sff-dump >2.1.7 and <2.1.10? "
++                              "It did not clear some internal buffer while writing "
++                              "out new data so that previous values remained in the"
++                              "output unless overwritten by new real values."
+                                  % padding)
+         #print read, name, record_offset
+         yield name, record_offset
+--- Bio/SeqIO/SffIO.py.ori	2013-09-25 14:07:14.000000000 +0200
++++ Bio/SeqIO/SffIO.py	2013-09-25 14:08:59.000000000 +0200
+@@ -596,7 +596,14 @@
+     if padding:
+         padding = 8 - padding
+         if handle.read(padding).count(_null) != padding:
+-            raise ValueError("Post quality %i byte padding region contained data"
++            import warnings
++            from Bio import BiopythonParserWarning
++            warnings.warn("Your SFF file is valid but post quality %i byte "
++                          "padding region contains UNUSED data. Was the "
++                          "SFF file created by SRA sff-dump >2.1.7 and <2.1.10? "
++                          "It did not clear some internal buffer while writing "
++                          "out new data so that previous values remained in the"
++                          "output unless overwritten by new real values."
+                              % padding)
+     #Follow Roche and apply most aggressive of qual and adapter clipping.
+     #Note Roche seems to ignore adapter clip fields when writing SFF,

diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml
new file mode 100644
index 0000000..f17a827
--- /dev/null
+++ b/sci-biology/biopython/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>