changeset 3:0f30d19bc378 draft

Uploaded

--- a/parse.conf	Wed Nov 30 13:33:56 2016 -0500
+++ b/parse.conf	Wed Nov 30 13:34:10 2016 -0500
@@ -1,3 +1,4 @@
+
 <filter>
 SNV_FILTER
 SNV_FILTER_NUM
@@ -6,23 +7,42 @@
 
 <files>
 ROOT
-CNV
-SNV
-MART 
-CIRCOS 
+cnv = data/cnv.txt
+cnvlg = data/cnv.large.scale.txt
+sv = data/snv.txt
+mart = data/biomart.txt
+CIRCOS
+mask = data/genes_to_hide.txt
+genes = data/genes_to_label.txt
 </files>
 
+
+<map>
+log2 = avg:sprintf("%.2f",2*2**x)
+</map>
+
+# 0-indexed column numbers and names
 <fields>
+<cnvlg>
+key = chr
+0   = chr
+1   = start
+2   = end
+3   = type:lc
+</cnvlg>
 <cnv>
 key = sample,chr
-0   = sample
+0   = sample 
 1   = chr
 2   = start
 3   = end
-5   = avg
-6   = category:lc
+# :map(x,y) will create a new field x based on intervals defined in a block
+#
+# e.g.
+# value of 2*2**(log2) (see <map> block above) will be used to assign key "category"
+# based on <cnv><log2> intervals
+5   = log2:map(category,cnv/log2)
 </cnv>
-
 <sv>
 key = id,sample
 4   = chr
@@ -33,14 +53,13 @@
 47  = id
 53  = aa
 </sv>
-
 <genes>
 key = chr
 0   = id
-2   = end
-3   = start
-4   = chr
-5   = name
+3   = end
+2   = start
+1   = chr
+4   = name
 </genes>
 </fields>
 
@@ -54,10 +73,32 @@
 homd  = 5
 hlamp = 0
 </types>
+# assign log2 ranges to CNV event categories
+#
+# ( indicates open interval
+# [ indicates closed interval
+#
+# e.g. (1,2] is 1 <  x <= 2
+#      [2,3) is 2 <= x <  3
+#
+# The intervals must be disjoint and completely cover
+# all possible values you're going to test. 
+<log2>
+# max = category
+(,1)  = homd
+[1,2) = hetd
+2     = neut
+(2,3] = gain
+(3,)  = amp
+</log2>
 </cnv>
 
 <sv>
+# only pay attention to SV types listed <types>
 filter     = yes
+# only consider the most damaging type of mutation in a patient
+# (one with top score in <types> 
+# the absolute value of the damage weight is unimportant, only order matters
 top_damage_only   = yes
 <types>
 nonsense_mutation = 35
@@ -69,4 +110,4 @@
 nonstop_mutation  = 5
 missense_mutation = 1
 </types>
-</sv>
\ No newline at end of file
+</sv>