From 4279415d2a561f99037b03b88e18ccd2d0f7e24d Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Mon, 26 Jan 2009 14:48:45 -0500 Subject: [PATCH 1/2] Fix For MAF Filter tool. Looks like when grouping parameter types were updated to be recursively wrapped properly, this tool was not updated. --- tools/maf/maf_filter.xml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tools/maf/maf_filter.xml b/tools/maf/maf_filter.xml index 70e4e88c8d8..0771c628530 100644 --- a/tools/maf/maf_filter.xml +++ b/tools/maf/maf_filter.xml @@ -104,22 +104,22 @@ def maf_block_pass_filter( maf_block ): #if $len( $maf_filter['species1_attributes']['filter_condition'] ) == 0: #continue #end if - primary_component = maf_block.get_component_by_src_start( """$maf_filter['species1'].encode( 'string_escape' )""".decode( 'string_escape' ) ) + primary_component = maf_block.get_component_by_src_start( """$maf_filter['species1'].value.encode( 'string_escape' )""".decode( 'string_escape' ) ) if primary_component is not None: #if $maf_filter['species1_attributes']['species1_attribute_type'] == 'attribute_chr': - if primary_component.src.split( "." )[-1] $is_isnot_valid.get( $maf_filter['species1_attributes']['species1_is_isnot'].strip(), 'is in' ) """$maf_filter['species1_attributes']['species1_attribute'].encode( 'string_escape' )""".decode( 'string_escape' ).split( "," ): + if primary_component.src.split( "." )[-1] $is_isnot_valid.get( $maf_filter['species1_attributes']['species1_is_isnot'].value.strip(), 'is in' ) """$maf_filter['species1_attributes']['species1_attribute'].value.encode( 'string_escape' )""".decode( 'string_escape' ).split( "," ): #else - if primary_component.strand $is_isnot_valid.get( $maf_filter['species1_attributes']['species1_is_isnot'].strip(), '==' ) """$maf_filter['species1_attributes']['species1_attribute'].encode( 'string_escape' )""".decode( 'string_escape' ): + if primary_component.strand $is_isnot_valid.get( $maf_filter['species1_attributes']['species1_is_isnot'].value.strip(), '==' ) """$maf_filter['species1_attributes']['species1_attribute'].value.encode( 'string_escape' )""".decode( 'string_escape' ): #end if #for $filter_condition in $maf_filter['species1_attributes']['filter_condition']: - secondary_component = maf_block.get_component_by_src_start( """$filter_condition['species2'].encode( 'string_escape' )""".decode( 'string_escape' ) ) + secondary_component = maf_block.get_component_by_src_start( """$filter_condition['species2'].value.encode( 'string_escape' )""".decode( 'string_escape' ) ) #if $filter_condition['species2_attributes']['species2_attribute_type'] == 'attribute_chr': if secondary_component is not None: - if not ( secondary_component.src.split( "." )[-1] $is_isnot_valid.get( $filter_condition['species2_attributes']['species2_is_isnot'].strip(), 'is in' ) """$filter_condition['species2_attributes']['species2_attribute'].encode( 'string_escape' )""".decode( 'string_escape' ).split( "," ) ): + if not ( secondary_component.src.split( "." )[-1] $is_isnot_valid.get( $filter_condition['species2_attributes']['species2_is_isnot'].value.strip(), 'is in' ) """$filter_condition['species2_attributes']['species2_attribute'].value.encode( 'string_escape' )""".decode( 'string_escape' ).split( "," ) ): return False #else: if secondary_component is not None: - if not ( secondary_component.strand $is_isnot_valid.get( $filter_condition['species2_attributes']['species2_is_isnot'].strip(), '==' ) """$filter_condition['species2_attributes']['species2_attribute'].encode( 'string_escape' )""".decode( 'string_escape' ) ): + if not ( secondary_component.strand $is_isnot_valid.get( $filter_condition['species2_attributes']['species2_is_isnot'].value.strip(), '==' ) """$filter_condition['species2_attributes']['species2_attribute'].value.encode( 'string_escape' )""".decode( 'string_escape' ) ): return False #end if #end for From 4f9735fb31a4a9adf46421c54efe7e81adea0156 Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Tue, 27 Jan 2009 14:48:51 -0500 Subject: [PATCH 2/2] upgrade bx-python to rev 460 --- eggs.ini | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/eggs.ini b/eggs.ini index debb4c3c43c..43f226b378e 100644 --- a/eggs.ini +++ b/eggs.ini @@ -55,12 +55,12 @@ pysqlite = _3.5.4_static MySQL_python = _5.0.67_static python_lzo = _static flup = .dev_r2311 -bx_python = _dev_r459 +bx_python = _dev_r460 nose = .dev_r101 ; source location, necessary for scrambling [source] -bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r459.tar.bz2 +bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r460.tar.bz2 Cheetah = http://voxel.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar.gz DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python-1.2.2.tar.gz http://mysql.mirrors.pair.com/Downloads/MySQL-5.0/mysql-5.0.67.tar.gz