From 75a28929a759aad42c23aaf525f685678024fdf8 Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Wed, 7 Nov 2018 16:03:32 +0100 Subject: [PATCH] Renamed Cython alignment library in an attempt to limit some compilation bugs potentially involving name conflicts --- python/obitools3/commands/alignpairedend.pyx | 6 +++--- python/obitools3/commands/ngsfilter.pyx | 2 +- python/obitools3/{align => libalign}/__init__.py | 0 python/obitools3/{align => libalign}/_assemble.pxd | 0 python/obitools3/{align => libalign}/_assemble.pyx | 0 python/obitools3/{align => libalign}/_dynamic.pxd | 0 python/obitools3/{align => libalign}/_dynamic.pyx | 4 ++-- python/obitools3/{align => libalign}/_freeendgap.pxd | 0 python/obitools3/{align => libalign}/_freeendgap.pyx | 0 python/obitools3/{align => libalign}/_freeendgapfm.pxd | 0 python/obitools3/{align => libalign}/_freeendgapfm.pyx | 0 python/obitools3/{align => libalign}/_nws.pxd | 0 python/obitools3/{align => libalign}/_nws.pyx | 0 python/obitools3/{align => libalign}/_qsassemble.pyx | 0 python/obitools3/{align => libalign}/_qsrassemble.pyx | 0 python/obitools3/{align => libalign}/_rassemble.pxd | 0 python/obitools3/{align => libalign}/_rassemble.pyx | 0 python/obitools3/{align => libalign}/_solexapairend.pyx | 0 python/obitools3/{align => libalign}/solexapairend.py | 2 +- 19 files changed, 7 insertions(+), 7 deletions(-) rename python/obitools3/{align => libalign}/__init__.py (100%) rename python/obitools3/{align => libalign}/_assemble.pxd (100%) rename python/obitools3/{align => libalign}/_assemble.pyx (100%) rename python/obitools3/{align => libalign}/_dynamic.pxd (100%) rename python/obitools3/{align => libalign}/_dynamic.pyx (99%) rename python/obitools3/{align => libalign}/_freeendgap.pxd (100%) rename python/obitools3/{align => libalign}/_freeendgap.pyx (100%) rename python/obitools3/{align => libalign}/_freeendgapfm.pxd (100%) rename python/obitools3/{align => libalign}/_freeendgapfm.pyx (100%) rename python/obitools3/{align => libalign}/_nws.pxd (100%) rename python/obitools3/{align => libalign}/_nws.pyx (100%) rename python/obitools3/{align => libalign}/_qsassemble.pyx (100%) rename python/obitools3/{align => libalign}/_qsrassemble.pyx (100%) rename python/obitools3/{align => libalign}/_rassemble.pxd (100%) rename python/obitools3/{align => libalign}/_rassemble.pyx (100%) rename python/obitools3/{align => libalign}/_solexapairend.pyx (100%) rename python/obitools3/{align => libalign}/solexapairend.py (96%) diff --git a/python/obitools3/commands/alignpairedend.pyx b/python/obitools3/commands/alignpairedend.pyx index 803827f..3b5e2d3 100755 --- a/python/obitools3/commands/alignpairedend.pyx +++ b/python/obitools3/commands/alignpairedend.pyx @@ -11,9 +11,9 @@ from obitools3.dms.capi.obitypes cimport OBI_INT, OBI_STR, index_t, OBI_QUAL from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption from obitools3.uri.decode import open_uri from obitools3.apps.config import logger -from obitools3.align._qsassemble import QSolexaReverseAssemble -from obitools3.align._qsrassemble import QSolexaRightReverseAssemble -from obitools3.align._solexapairend import buildConsensus, buildJoinedSequence +from obitools3.libalign._qsassemble import QSolexaReverseAssemble +from obitools3.libalign._qsrassemble import QSolexaRightReverseAssemble +from obitools3.libalign._solexapairend import buildConsensus, buildJoinedSequence from obitools3.dms.obiseq cimport Nuc_Seq_Stored, Nuc_Seq import sys diff --git a/python/obitools3/commands/ngsfilter.pyx b/python/obitools3/commands/ngsfilter.pyx index 3dea800..1b79f2a 100755 --- a/python/obitools3/commands/ngsfilter.pyx +++ b/python/obitools3/commands/ngsfilter.pyx @@ -8,7 +8,7 @@ from obitools3.dms.column.column cimport Column, Column_line from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption from obitools3.uri.decode import open_uri from obitools3.apps.config import logger -from obitools3.align._freeendgapfm import FreeEndGapFullMatch +from obitools3.libalign._freeendgapfm import FreeEndGapFullMatch from obitools3.dms.obiseq cimport Nuc_Seq from obitools3.dms.capi.obitypes cimport OBI_SEQ, OBI_QUAL diff --git a/python/obitools3/align/__init__.py b/python/obitools3/libalign/__init__.py similarity index 100% rename from python/obitools3/align/__init__.py rename to python/obitools3/libalign/__init__.py diff --git a/python/obitools3/align/_assemble.pxd b/python/obitools3/libalign/_assemble.pxd similarity index 100% rename from python/obitools3/align/_assemble.pxd rename to python/obitools3/libalign/_assemble.pxd diff --git a/python/obitools3/align/_assemble.pyx b/python/obitools3/libalign/_assemble.pyx similarity index 100% rename from python/obitools3/align/_assemble.pyx rename to python/obitools3/libalign/_assemble.pyx diff --git a/python/obitools3/align/_dynamic.pxd b/python/obitools3/libalign/_dynamic.pxd similarity index 100% rename from python/obitools3/align/_dynamic.pxd rename to python/obitools3/libalign/_dynamic.pxd diff --git a/python/obitools3/align/_dynamic.pyx b/python/obitools3/libalign/_dynamic.pyx similarity index 99% rename from python/obitools3/align/_dynamic.pyx rename to python/obitools3/libalign/_dynamic.pyx index 46c6a88..4ccea93 100755 --- a/python/obitools3/align/_dynamic.pyx +++ b/python/obitools3/libalign/_dynamic.pyx @@ -6,8 +6,8 @@ Created on 14 sept. 2009 @author: coissac ''' -from obitools3.align import AlignedSequence -from obitools3.align import Alignment +from obitools3.libalign import AlignedSequence +from obitools3.libalign import Alignment from copy import deepcopy diff --git a/python/obitools3/align/_freeendgap.pxd b/python/obitools3/libalign/_freeendgap.pxd similarity index 100% rename from python/obitools3/align/_freeendgap.pxd rename to python/obitools3/libalign/_freeendgap.pxd diff --git a/python/obitools3/align/_freeendgap.pyx b/python/obitools3/libalign/_freeendgap.pyx similarity index 100% rename from python/obitools3/align/_freeendgap.pyx rename to python/obitools3/libalign/_freeendgap.pyx diff --git a/python/obitools3/align/_freeendgapfm.pxd b/python/obitools3/libalign/_freeendgapfm.pxd similarity index 100% rename from python/obitools3/align/_freeendgapfm.pxd rename to python/obitools3/libalign/_freeendgapfm.pxd diff --git a/python/obitools3/align/_freeendgapfm.pyx b/python/obitools3/libalign/_freeendgapfm.pyx similarity index 100% rename from python/obitools3/align/_freeendgapfm.pyx rename to python/obitools3/libalign/_freeendgapfm.pyx diff --git a/python/obitools3/align/_nws.pxd b/python/obitools3/libalign/_nws.pxd similarity index 100% rename from python/obitools3/align/_nws.pxd rename to python/obitools3/libalign/_nws.pxd diff --git a/python/obitools3/align/_nws.pyx b/python/obitools3/libalign/_nws.pyx similarity index 100% rename from python/obitools3/align/_nws.pyx rename to python/obitools3/libalign/_nws.pyx diff --git a/python/obitools3/align/_qsassemble.pyx b/python/obitools3/libalign/_qsassemble.pyx similarity index 100% rename from python/obitools3/align/_qsassemble.pyx rename to python/obitools3/libalign/_qsassemble.pyx diff --git a/python/obitools3/align/_qsrassemble.pyx b/python/obitools3/libalign/_qsrassemble.pyx similarity index 100% rename from python/obitools3/align/_qsrassemble.pyx rename to python/obitools3/libalign/_qsrassemble.pyx diff --git a/python/obitools3/align/_rassemble.pxd b/python/obitools3/libalign/_rassemble.pxd similarity index 100% rename from python/obitools3/align/_rassemble.pxd rename to python/obitools3/libalign/_rassemble.pxd diff --git a/python/obitools3/align/_rassemble.pyx b/python/obitools3/libalign/_rassemble.pyx similarity index 100% rename from python/obitools3/align/_rassemble.pyx rename to python/obitools3/libalign/_rassemble.pyx diff --git a/python/obitools3/align/_solexapairend.pyx b/python/obitools3/libalign/_solexapairend.pyx similarity index 100% rename from python/obitools3/align/_solexapairend.pyx rename to python/obitools3/libalign/_solexapairend.pyx diff --git a/python/obitools3/align/solexapairend.py b/python/obitools3/libalign/solexapairend.py similarity index 96% rename from python/obitools3/align/solexapairend.py rename to python/obitools3/libalign/solexapairend.py index db9dd53..63c797e 100755 --- a/python/obitools3/align/solexapairend.py +++ b/python/obitools3/libalign/solexapairend.py @@ -6,7 +6,7 @@ Created on 17 mai 2010 @author: coissac ''' -from obitools3.align import columnIterator +from obitools3.libalign import columnIterator def iterOnAligment(ali):