details: http://www.bx.psu.edu/hg/galaxy/rev/71b779fde315 changeset: 3126:71b779fde315 user: guru date: Mon Nov 30 11:56:58 2009 -0500 description: Added 'N' to the list of mask characters, as per Melissa's request.

diffstat:

tools/regVariation/maf_cpg_filter.py | 2 +- tools/regVariation/maf_cpg_filter.xml | 1 + tools/regVariation/quality_filter.py | 2 +- tools/regVariation/quality_filter.xml | 1 + 4 files changed, 4 insertions(+), 2 deletions(-)

diffs (46 lines):

diff -r a8234f4d7012 -r 71b779fde315 tools/regVariation/maf_cpg_filter.py --- a/tools/regVariation/maf_cpg_filter.py Mon Nov 30 09:35:21 2009 -0500 +++ b/tools/regVariation/maf_cpg_filter.py Mon Nov 30 11:56:58 2009 -0500 @@ -39,7 +39,7 @@ reader = bx.align.maf.Reader( open(inp_file, 'r') ) writer = bx.align.maf.Writer( open(out_file,'w') )

- mask_chr_dict = {0:'#', 1:'$', 2:'^', 3:'*', 4:'?'} + mask_chr_dict = {0:'#', 1:'$', 2:'^', 3:'*', 4:'?', 5:'N'} mask = mask_chr_dict[mask]

if sitetype == "CpG": diff -r a8234f4d7012 -r 71b779fde315 tools/regVariation/maf_cpg_filter.xml --- a/tools/regVariation/maf_cpg_filter.xml Mon Nov 30 09:35:21 2009 -0500 +++ b/tools/regVariation/maf_cpg_filter.xml Mon Nov 30 11:56:58 2009 -0500 @@ -21,6 +21,7 @@ <option value="2">^</option> <option value="3">*</option> <option value="4">?</option> + <option value="5">N</option> </param> <conditional name="masksite"> <param name="type" size="5" type="select" label="Sites to be masked"> diff -r a8234f4d7012 -r 71b779fde315 tools/regVariation/quality_filter.py --- a/tools/regVariation/quality_filter.py Mon Nov 30 09:35:21 2009 -0500 +++ b/tools/regVariation/quality_filter.py Mon Nov 30 11:56:58 2009 -0500 @@ -100,7 +100,7 @@ stop_err( "No mask species selected, try again by selecting at least one species to mask." )

mask_chr_count = 0 - mask_chr_dict = {0:'#', 1:'$', 2:'^', 3:'*', 4:'?'} + mask_chr_dict = {0:'#', 1:'$', 2:'^', 3:'*', 4:'?', 5:'N'} mask_reg_dict = {0:'Current pos', 1:'Current+Downstream', 2:'Current+Upstream', 3:'Current+Both sides'}

#ensure dbkey is present in the twobit loc file diff -r a8234f4d7012 -r 71b779fde315 tools/regVariation/quality_filter.xml --- a/tools/regVariation/quality_filter.xml Mon Nov 30 09:35:21 2009 -0500 +++ b/tools/regVariation/quality_filter.xml Mon Nov 30 11:56:58 2009 -0500 @@ -37,6 +37,7 @@ <option value="2">^</option> <option value="3">*</option> <option value="4">?</option> + <option value="5">N</option> </param> <conditional name="mask_region"> <param name="region" type="select" label="Mask region">