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Sun, 23 Mar 2014 16:09:15 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1395590870.031391850b6768a55ed2c98a93eeb255954b51d2.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/biopython/, sci-biology/biopython/files/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/biopython/ChangeLog sci-biology/biopython/biopython-1.62-r3.ebuild sci-biology/biopython/biopython-1.62-r4.ebuild sci-biology/biopython/biopython-1.63-r1.ebuild sci-biology/biopython/biopython-1.63.ebuild sci-biology/biopython/files/SeqRecord.py.patch sci-biology/biopython/files/adjust-trimpoints.patch X-VCS-Directories: sci-biology/biopython/ sci-biology/biopython/files/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 031391850b6768a55ed2c98a93eeb255954b51d2 X-VCS-Branch: master Date: Sun, 23 Mar 2014 16:09:15 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: e0467ab2-bc1e-4097-8ad0-5f20d793365b X-Archives-Hash: bc032ac303748dca14d462b59f674f76 commit: 031391850b6768a55ed2c98a93eeb255954b51d2 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Sun Mar 23 16:07:50 2014 +0000 Commit: Martin Mokrejs fold natur cuni 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 + -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()