commit: 20c8e6ec36a2cdd5af944030720b059fb8d10891 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Fri Apr 18 18:11:59 2014 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Apr 18 18:11:59 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=20c8e6ec
sci-biology/biopython: upstream patch to downgrade an assert to a warning Package-Manager: portage-2.2.7 --- sci-biology/biopython/ChangeLog | 11 ++ ...hon-1.63-r1.ebuild => biopython-1.62-r3.ebuild} | 5 +- ...hon-1.63-r1.ebuild => biopython-1.62-r4.ebuild} | 5 +- sci-biology/biopython/biopython-1.63-r1.ebuild | 3 +- sci-biology/biopython/files/SeqRecord.py.patch | 148 +++++++++++++++++++++ .../biopython/files/SffIO_broken_padding.patch | 27 ++++ .../biopython/files/adjust-trimpoints.patch | 76 +++++++++++ 7 files changed, 270 insertions(+), 5 deletions(-) diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog index 037227d..c326c4a 100644 --- a/sci-biology/biopython/ChangeLog +++ b/sci-biology/biopython/ChangeLog @@ -2,6 +2,17 @@ # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*biopython-1.62-r3 (18 Apr 2014) +*biopython-1.62-r4 (18 Apr 2014) + + 18 Apr 2014; Martin Mokrejs <[email protected]> + +biopython-1.62-r3.ebuild, +biopython-1.62-r4.ebuild, + +files/SeqRecord.py.patch, +files/SffIO_broken_padding.patch, + +files/adjust-trimpoints.patch, biopython-1.63-r1.ebuild, + files/SffIO_error_in_check_eof.patch, files/biopython-1.51-flex.patch, + files/biopython-1.62-SffIO.patch: + sci-biology/biopython: upstream patch to downgrade an assert to a warning + 23 Mar 2014; Martin Mokrejs <[email protected]> -biopython-1.62-r3.ebuild, -biopython-1.62-r4.ebuild, -biopython-1.63.ebuild, -files/SeqRecord.py.patch, -files/adjust-trimpoints.patch, diff --git a/sci-biology/biopython/biopython-1.63-r1.ebuild b/sci-biology/biopython/biopython-1.62-r3.ebuild similarity index 90% copy from sci-biology/biopython/biopython-1.63-r1.ebuild copy to sci-biology/biopython/biopython-1.62-r3.ebuild index e99f846..09e6ed7 100644 --- a/sci-biology/biopython/biopython-1.63-r1.ebuild +++ b/sci-biology/biopython/biopython-1.62-r3.ebuild @@ -23,7 +23,6 @@ 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}] @@ -35,8 +34,10 @@ DEPEND="${RDEPEND} DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) src_prepare() { - epatch "${FILESDIR}"/SffIO_error_in_check_eof.patch distutils-r1_src_prepare + epatch "${FILESDIR}/${PN}-1.62-SffIO.patch" + epatch "${FILESDIR}/SffIO_error_in_check_eof.patch" + epatch "${FILESDIR}/SffIO_broken_padding.patch" } python_test() { diff --git a/sci-biology/biopython/biopython-1.63-r1.ebuild b/sci-biology/biopython/biopython-1.62-r4.ebuild similarity index 90% copy from sci-biology/biopython/biopython-1.63-r1.ebuild copy to sci-biology/biopython/biopython-1.62-r4.ebuild index e99f846..09e6ed7 100644 --- a/sci-biology/biopython/biopython-1.63-r1.ebuild +++ b/sci-biology/biopython/biopython-1.62-r4.ebuild @@ -23,7 +23,6 @@ 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}] @@ -35,8 +34,10 @@ DEPEND="${RDEPEND} DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) src_prepare() { - epatch "${FILESDIR}"/SffIO_error_in_check_eof.patch distutils-r1_src_prepare + epatch "${FILESDIR}/${PN}-1.62-SffIO.patch" + epatch "${FILESDIR}/SffIO_error_in_check_eof.patch" + epatch "${FILESDIR}/SffIO_broken_padding.patch" } python_test() { diff --git a/sci-biology/biopython/biopython-1.63-r1.ebuild b/sci-biology/biopython/biopython-1.63-r1.ebuild index e99f846..b600748 100644 --- a/sci-biology/biopython/biopython-1.63-r1.ebuild +++ b/sci-biology/biopython/biopython-1.63-r1.ebuild @@ -35,7 +35,8 @@ DEPEND="${RDEPEND} DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) src_prepare() { - epatch "${FILESDIR}"/SffIO_error_in_check_eof.patch + epatch "${FILESDIR}/SffIO_error_in_check_eof.patch" + epatch "${FILESDIR}/SffIO_broken_padding.patch" distutils-r1_src_prepare } 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_broken_padding.patch b/sci-biology/biopython/files/SffIO_broken_padding.patch new file mode 100644 index 0000000..a009c58 --- /dev/null +++ b/sci-biology/biopython/files/SffIO_broken_padding.patch @@ -0,0 +1,27 @@ +diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py +index 735d55b..b89cf41 100644 +--- a/Bio/SeqIO/SffIO.py ++++ b/Bio/SeqIO/SffIO.py +@@ -933,12 +933,20 @@ def _check_eof(handle, index_offset, index_length): + "null padding region ended '.sff' which could " + "be the start of a concatenated SFF file? " + "See offset %i" % (padding, offset)) ++ if padding and not extra: ++ #TODO - Is this error harmless enough to just ignore? ++ import warnings ++ from Bio import BiopythonParserWarning ++ warnings.warn("Your SFF file is technically invalid as it is missing " ++ "a terminal %i byte null padding region." % padding, ++ BiopythonParserWarning) ++ return + if extra.count(_null) != padding: + import warnings + from Bio import BiopythonParserWarning + warnings.warn("Your SFF file is invalid, post index %i byte " +- "null padding region contained data." % padding, +- BiopythonParserWarning) ++ "null padding region contained data: %r" ++ % (padding, extra), BiopythonParserWarning) + + offset = handle.tell() + assert offset % 8 == 0, \ 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()
