Pyrodigal is a Python module that provides bindings to Prodigal using Cython.
Features:
The library now features everything from the original Prodigal CLI:
* run mode selection: Choose between single mode, using a training sequence
to count nucleotide hexamers, or metagenomic mode, using pre-trained data
from different organisms (prodigal -p).
* region masking: Prevent genes from being predicted across regions
containing unknown nucleotides (prodigal -m).
* closed ends: Genes will be identified as running over edges if they are
larger than a certain size, but this can be disabled (prodigal -c).
* training configuration: During the training process, a custom translation
table can be given (prodigal -g), and the Shine-Dalgarno motif search can
be forcefully bypassed (prodigal -n)
* output files: Output files can be written in a format mostly compatible
with the Prodigal binary, including the protein translations in FASTA
format (prodigal -a), the gene sequences in FASTA format (prodigal -d),
or the potential gene scores in tabular format (prodigal -s).
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above. NOTE: This is a Python port. Instead of py311-pyrodigal listed in the above command, you can pick from the names under the Packages section.
python.mk: rename PYTHON_EXT_SUFFIX to PYTHON_TAG, document, etc
EXT_SUFFIX, according to PEP 3149, refers to the full tag and
extension for compiled extension module objects, eg .cpython-311.so,
.cpython-313t.so, etc. We do not use the correct semantic meaning,
and this usage becomes ambiguous and confusing when tags do not
match between bytecode and compiled extension module objects.
Rename our PYTHON_EXT_SUFFIX to PYTHON_TAG to align with PEP 3147's
specification of a magic tag, which consists of implementation name
and shorthand version only. This is meant for bytecode and other
files containing this tag in their filename that do not depend on
a specific Python ABI for the same version. Chase all existing
consumers.
(Only the first 15 lines of the commit message are shown above )
Mk/Uses/python.mk: Introduce USE_PYTHON=cython3{,_run,_test}
- Update USE_PYTHON=cython{,_run,_test}
- Convert all cython3 occurrence to USE_PYTHON=cython3*
- While I'm here, fix incorrect usage of combining cython3 in BUILD_DEPENDS and
USE_PYTHON=cython
It is added to simplify the future transition from Cython 0.29 to 3.
The minimal version is set to 3.0.12 because it is required by
devel/py-propcache.
The upper bound of version is set to 3.1 because it is limited by multiple
ports.
all: remove explicit versions in USES=python for "3.x+"
The logic in USES=python will automatically convert this to 3.8+ by
itself.
Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.
finance/quickfix: mark BROKEN with PYTHON
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
^~~~~~~~~~
1 warning and 1 error generated.
Reviewed by: portmgr, vishwin, yuri
Differential Revision: <https://reviews.freebsd.org/D40568>
