X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=blobdiff_plain;f=examples%2Fdirectory.mupa;fp=examples%2Fdirectory.mupa;h=f57d81ba7d12b5ff98527590b33951a0d2abe189;hp=0000000000000000000000000000000000000000;hb=27fcfad1ecefd7f8d021108d10e70fdd4a870f63;hpb=5427fa1cc2b43ae32fa13ec0c86bc10974a61f1e

diff --git a/examples/directory.mupa b/examples/directory.mupa
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+#
+# Used to make sure that we properly report an error when
+# an annotation is not a file.
+# 
+
+
+# name of anaylsis directory and stem for associated files
+ANA_NAME directory
+
+# if APPEND vars true, a _wXX and/or _tYY added to analysis name
+# where XX = WINDOW and YY = THRESHOLD
+# Highly recommeded with use of command line override of WINDOW or THRESHOLD
+APPEND_WIN true
+APPEND_THRES true
+  
+# first sequence info
+SEQUENCE seq/mouse_mck_pro.fa
+ANNOTATION mm_mck3test.annot
+SEQ_START 300
+
+# the second sequence info
+SEQUENCE seq/human_mck_pro.fa
+ANNOTATION seq
+SEQ_START 300
+
+# analyses parameters: command line args -w -t will override these
+WINDOW 30
+THRESHOLD 20