5.1 A2Xml
A2Xml is dedicated to convert plaint text files into XML files compliant with the analysis programs of MetaQTL.
5.1.1 Command Line Options
| Option | Usage | Type | Explanation
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-i,--ifile | required | string | The file to convert in XML.
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-x,--xmlfile | required | string | The output XML file.
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-t,--type | required | string | The type of the input file.
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-f,--format | optional | string | The format of the input file.
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Presently, the command --type have two possible values:
map : the input file is a marker and/or QTL map.
onto : the input file is an ontology.
%java org.metatqtl.main.A2Xml \
> -i map.txt -x map.xml -t map -f chart
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The command -f,--format allows user to convert into XML different input file formats. This option works only when -t,--type is set to map. In this case 3 different input file formats can be used:
tab : the map is in tabulated format as for the GLMdb tables See GLMdb.
mch : the map is formatted like a MapChart (Voorrips 2002) input file.
mmk : the map is formatted like a MapMaker (Lander 1987) output.
For example, suppose we have a map file map.txt in tabulated format as follows,
group marker position
1 umc11 0.0
1 gsy27 18.0
1 umc67 54.0
1 umc58 75.0
1 umc83a 115.0
1 umc66b 140.0
1 gsy56 153.0
1 umc161 168.0
1 umc84 189.0
1 bnl6.32 198.0
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Then we can convert it into a XML file using the command
%java org.metatqtl.main.A2Xml \
> -i map.txt -x map.xml -t map -f tab
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This creates a file named map.xml which looks like this
<?xml version="1.0" encoding="UTF-8"?>
<genome-map name="">
<linkage-group name="1">
<locus name="umc83a" type="M" position="115.0"/>
<locus name="bnl6.32" type="M" position="198.0"/>
<locus name="gsy27" type="M" position="18.0"/>
<locus name="umc58" type="M" position="75.0"/>
<locus name="umc161" type="M" position="168.0"/>
<locus name="umc66b" type="M" position="140.0"/>
<locus name="umc11" type="M" position="0.0"/>
<locus name="gsy56" type="M" position="153.0"/>
<locus name="umc67" type="M" position="54.0"/>
<locus name="umc84" type="M" position="189.0"/>
</linkage-group>
</genome-map>
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The XML file will be the same if instead using a tabulated format we have used a MapChart format as input
group 1
umc11 0
gsy27 18
umc67 54
umc58 75
umc83a 115
umc66b 140
gsy56 153
umc161 168
umc84 189
bnl6.32 198
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and the command
%java org.metatqtl.main.A2Xml \
> -i map.txt -x map.xml -t map -f chart
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or if we have used a MapMaker like format
*1
>map
===========================================================================
Map:
Markers Distance
1 umc11 18 cM
2 gsy27 36 cM
3 umc67 21 cM
4 umc58 40 cM
5 umc83a 25 cM
6 umc66b 13 cM
7 gsy56 15 cM
8 umc161 21 cM
9 umc84 9 cM
10 bnl6.32 ----------
198 cM 10 markers log-likelihood=
===========================================================================
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and the command
%java org.metatqtl.main.A2Xml \
> -i map.txt -x map.xml -t map -f mm
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