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comparison pal_finder_macros.xml @ 8:4e625d3672ba draft

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Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
author pjbriggs
date Wed, 16 May 2018 07:39:16 -0400
parents 5e133b7b79a6
children
comparison
equal deleted inserted replaced
7:5e133b7b79a6 8:4e625d3672ba
12 <has_line line="broken:&#009;2" /> 12 <has_line line="broken:&#009;2" />
13 <has_line line="compound:&#009;2" /> 13 <has_line line="compound:&#009;2" />
14 <has_line line="readsWithMicrosat:&#009;13" /> 14 <has_line line="readsWithMicrosat:&#009;13" />
15 <has_line line="totalBases:&#009;2320" /> 15 <has_line line="totalBases:&#009;2320" />
16 <has_line line="totalReads:&#009;20&#009;(2 x 10)" /> 16 <has_line line="totalReads:&#009;20&#009;(2 x 10)" />
17 <has_line line="readsWithBadRanges:&#009;0" />
17 <has_line line="Microsat Type&#009;monomer length&#009;total loci&#009;loci w/ primers&#009;reads with loci&#009;total bases&#009;extended&#009;extended w/ primers&#009;spanning&#009;spanning w/ primers" /> 18 <has_line line="Microsat Type&#009;monomer length&#009;total loci&#009;loci w/ primers&#009;reads with loci&#009;total bases&#009;extended&#009;extended w/ primers&#009;spanning&#009;spanning w/ primers" />
18 <has_line_matching expression="(AC|TG)\t2\t7\t4\t7\t116\t0?\t0?\t0?\t0?" /> 19 <has_line_matching expression="(AC|TG)\t2\t7\t4\t7\t116\t0?\t0?\t0?\t0?" />
19 <has_line_matching expression="(AT|CG)\t2\t8\t0\t6\t106\t0?\t0?\t0?\t0?" /> 20 <has_line_matching expression="(AT|CG)\t2\t8\t0\t6\t106\t0?\t0?\t0?\t0?" />
20 <has_line_matching expression="(AG|TC)\t2\t2\t1\t2\t26\t0?\t0?\t0?\t0?" /> 21 <has_line_matching expression="(AG|TC)\t2\t2\t1\t2\t26\t0?\t0?\t0?\t0?" />
22 </assert_contents>
23 </output>
24 </xml>
25 <xml name="output_illumina_microsat_subset_summary">
26 <output name="output_microsat_summary">
27 <assert_contents>
28 <has_line line="allExtended:&#009;0" />
29 <has_line line="allSpan:&#009;0" />
30 <has_line line="broken:&#009;0" />
31 <has_line line="compound:&#009;2" />
32 <has_line line="readsWithMicrosat:&#009;7" />
33 <has_line line="totalBases:&#009;1160" />
34 <has_line line="totalReads:&#009;10&#009;(2 x 5)" />
35 <has_line line="Microsat Type&#009;monomer length&#009;total loci&#009;loci w/ primers&#009;reads with loci&#009;total bases&#009;extended&#009;extended w/ primers&#009;spanning&#009;spanning w/ primers" />
36 <has_line_matching expression="(AC|TG)\t2\t6\t3\t6\t104\t0?\t0?\t0?\t0?" />
37 <has_line_matching expression="(AT|CG)\t2\t3\t0\t3\t38\t0?\t0?\t0?\t0?" />
38 <has_line_matching expression="(AG|TC)\t2\t0\t0\t0\t0\t0?\t0?\t0?\t0?" />
39 </assert_contents>
40 </output>
41 </xml>
42 <xml name="output_illumina_microsat_summary_bad_ranges">
43 <output name="output_microsat_summary">
44 <assert_contents>
45 <has_line line="allExtended:&#009;2" />
46 <has_line line="allSpan:&#009;0" />
47 <has_line line="broken:&#009;0" />
48 <has_line line="compound:&#009;4" />
49 <has_line line="readsWithMicrosat:&#009;12" />
50 <has_line line="totalBases:&#009;2231" />
51 <has_line line="totalReads:&#009;12&#009;(2 x 6)" />
52 <has_line line="readsWithBadRanges:&#009;2" />
53 <has_line line="Microsat Type&#009;monomer length&#009;total loci&#009;loci w/ primers&#009;reads with loci&#009;total bases&#009;extended&#009;extended w/ primers&#009;spanning&#009;spanning w/ primers" />
54 <!--
55 I'd like to do a basic check on the remainder of the file but
56 there are too many lines for the 'assert_contents' method (and
57 the tag doesn't provide the functionality to do a simple line
58 count
59 -->
21 </assert_contents> 60 </assert_contents>
22 </output> 61 </output>
23 </xml> 62 </xml>
24 <xml name="output_454_microsat_summary"> 63 <xml name="output_454_microsat_summary">
25 <output name="output_microsat_summary"> 64 <output name="output_microsat_summary">