PGpep/temp_mapping_params.xml at main · BISCodeRepo/PGpep · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
<?xml version="1.0" encoding="UTF-8"?>
<Params>
	<Mapping>
		<Environment>
			<!--
			PV: Mapping [P]rotein database first, then next [V]ariant splice graph.
			PS: Mapping [P]rotein database first, then next [S]ix-frame translation.
			VO: Mapping [V]ariant splice graph [O]nly.
			SO: Mapping [S]ix-frame translation [O]nly.
			-->
			<MappingMethod>VO</MappingMethod>

			<!-- Yes/No: consider isoleucine and leucine as the same. -->
			<ILSame>yes</ILSame>

			<!-- Path of a peptide list file that a user wants to map. -->
			<Input format="list" type="peptideList">ACTG/set1/1set_dn_pep_1014.txt</Input>

			<!-- Path of a folder where the output files will be located. -->
			<Output type="outputPath">ACTG/set1/IRCR_GBM15_774_T01/output</Output>
		</Environment>

		<ProteinDB>
			<!-- If a user sets "MappingMethod" as P[V|S], then the user should provide a folder path containing protein database. -->
			<Input format="FASTA" type="proteinDB">data/ProteinDB</Input>

			<!-- Yes/No: automatically consider single amino-acid variant when mapping on protein database. -->
			<SAVs>yes</SAVs>
		</ProteinDB>

		<VariantSpliceGraph>
			<!-- Serialization file path of the variant splice graph. -->
			<Input format="ser" type="graphFile">IRCR_GBM15_774_T01.ser</Input>

			<!-- Yes/No: consider junction variation events. -->
			<JunctionVariation>yes</JunctionVariation>

			<!-- Yes/No: consider single exon skipping events. -->
			<ExonSkipping>yes</ExonSkipping>

			<!-- Yes/No: consider intron mapping (exon-extension) events. -->
			<IntronMapping>yes</IntronMapping>

			<!-- If a user gives a VCF (variant call format), then this setting must be "yes". -->
			<Mutation>no</Mutation>

			<!-- If "Mutation" tag is set as "yes", then a user should provide the path of folder where VCF files are. -->
			<Input format="VCF" type="mutation">VCF</Input>
		</VariantSpliceGraph>

		<SixFrameTranslation>
			<!-- If a user sets "MappingMethod" as PS or SO, then the user should provide the path of folder where reference genome files are. -->
			<Input format="FASTA" type="referenceGenome">data/GRCh37.fa</Input>
		</SixFrameTranslation>
	</Mapping>

	<Systems>
		<!-- A user can set the number of threads. A proper setting can increase the speed of mapping. -->
		<TheNumberOfThreads>8</TheNumberOfThreads>
	</Systems>
</Params>