Mercurial > repos > greg > ideas
changeset 132:8ce93420010c draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 12 Dec 2017 10:47:26 -0500 |
| parents | 5150fcdcd0fa |
| children | 7d49fc24e06a |
| files | ideas.xml |
| diffstat | 1 files changed, 11 insertions(+), 6 deletions(-) [+] |
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--- a/ideas.xml Tue Dec 12 10:13:26 2017 -0500 +++ b/ideas.xml Tue Dec 12 10:47:26 2017 -0500 @@ -18,7 +18,9 @@ ## Create the config file and prepare the data ############################################## #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window -mkdir '$output_pdf_dir' && +#if str($output_heatmaps) == "yes": + mkdir '$output_pdf_dir' && +#end if mkdir '$output_txt_dir' && cp '$gen_prep_input_config' $prep_input_config && prepMat @@ -56,12 +58,12 @@ && cut -d' ' $prep_input_config -f1,2 > file1.txt && ls tmp/*.bed.gz > file2.txt && paste <(cat file1.txt) <(cat file2.txt) -d' ' > $prep_output_config -############################################## -## If using a genomic window bed file, categorize -## the window positions by chromosome to enable -## the IDEAS -inv option. -############################################## #if str($specify_genomic_window) == "yes": + ############################################## + ## Using a genomic window bed file, so categorize + ## the window positions by chromosome to enable + ## the IDEAS -inv option. + ############################################## #import collections #set window_positions_by_chroms = collections.OrderedDict() #for count, line in enumerate(open($specify_genomic_window_cond.bed_input.file_name, 'r')): @@ -127,6 +129,9 @@ #end for #else: + ############################################## + ## Not using a genomic window bed file. + ############################################## && ideas '$prep_output_config' $tmp_dir/*.bed