pgd
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pgd [2011/07/07 15:50] – heidi | pgd [2011/10/11 15:54] – heidi | ||
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Version 1.0\\ | Version 1.0\\ | ||
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- | PGD (Population Genetics Data) is a file format designed to contain population genetics data. The aim of this format is to facilitate the transfer among several population genetics software packages. PGD plays an important role in the new data format converter PGDSpider. | + | PGD (Population Genetics Data) is a file format designed to contain population genetics data. The aim of this format is to facilitate the transfer among several population genetics software packages. PGD plays an important role in the new data format converter PGDSpider.\\ |
- | PGD is written in XML and is therefore independent of any particular computer system and extensible for future needs. The XML structure can easily be processed by computer programs. An additional XSLT style sheet makes it possible to display the data in an understandable and comprehensive way. This XSLT style sheet is delivered within the PGDSpider download. | + | |
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+ | PGD is written in XML and is therefore independent of any particular computer system and extensible for future needs. The XML structure can easily be processed by computer programs. An additional XSLT style sheet makes it possible to display the data in an understandable and comprehensive way. This XSLT style sheet is delivered within the PGDSpider download.\\ | ||
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+ | The PGDSpider distribution also includes an XML Schema (PGD_schema.xsd), | ||
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PGD is able to handle following data types: | PGD is able to handle following data types: | ||
* DNA | * DNA | ||
- | * UHTS (Ultra High-Throughput | + | * NGS (Next-Generation |
* Microsat (coded as number of repeats!) | * Microsat (coded as number of repeats!) | ||
* RFLP | * RFLP | ||
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==== Header block: ==== | ==== Header block: ==== | ||
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* Value: Character | * Value: Character | ||
* Character which codes missing values | * Character which codes missing values | ||
- | * <gap> (mandatory): | + | * <gap> (optional): |
* Value: Character | * Value: Character | ||
* Character which codes gaps | * Character which codes gaps | ||
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* distanceMatrix: | * distanceMatrix: | ||
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| **header** (attribute: title) | organism ||| o | o | o | | | **header** (attribute: title) | organism ||| o | o | o | | ||
| | numPop ||| x | x | x | | | | numPop ||| x | x | x | | ||
- | | | ploidy * //(--> mixed/ | + | | | ploidy * //(--> mixed/ |
| | missing ||| x | x | | | | | missing ||| x | x | | | ||
- | | | gap ||| | + | | | gap ||| |
| | gameticPhase //(--> known/ | | | gameticPhase //(--> known/ | ||
| | recessiveData //(--> yes/ | | | recessiveData //(--> yes/ | ||
^^^^^^^^^^^ | ^^^^^^^^^^^ | ||
| **dataDescription** (o) | numLoci ||| x | x | | | | **dataDescription** (o) | numLoci ||| x | x | | | ||
- | | | dataType * //(--> mixed/ | + | | | dataType * //(--> mixed/ |
- | | | locus (attribute: id) | locusDataType //(--> DNA/ | + | | | locus (attribute: id) | locusDataType //(--> DNA/ |
| || locusChromosome //(--> number/ | | || locusChromosome //(--> number/ | ||
| || locusLocation || o | o | | | | || locusLocation || o | o | | | ||
| || locusGenic //(--> coding/ | | || locusGenic //(--> coding/ | ||
| || locusLength || o | o | | | | || locusLength || o | o | | | ||
- | | || locusLinks || o | o | | | + | | || locusLinks |
| || locusComments || o | o | | | | || locusComments || o | o | | | ||
^^^^^^^^^^^ | ^^^^^^^^^^^ | ||
| **population** (attribute: name) | popSize ||| x | x | x | | | **population** (attribute: name) | popSize ||| x | x | x | | ||
- | | | popGeogCoord * //(lon, lat)// | + | | | popGeogCoord * //(lon, lat)// |
- | | | popLingGroup * ||| o (a4) | o (a4) | o | | + | | | popLingGroup * ||| o (a3) | o (a3) | o | |
- | | | popPloidy * //(--> mixed/ | + | | | popPloidy * //(--> mixed/ |
| | popLoci *< | | | popLoci *< | ||
- | | | ind (attribute: name) | indGeogCoord //(lon, lat)// | + | | | ind (attribute: name) | indGeogCoord //(lon, lat)// |
- | | || indLingGroup || o (a4) | o (a4) | | | + | | || indLingGroup || o (a3) | o (a3) | | |
- | | || indLoci *< | + | | || indLoci *< |
- | | || indPloidy // | + | | || indPloidy // |
| || indFreq //(absolute Freq)// || o | o | x | | | || indFreq //(absolute Freq)// || o | o | x | | ||
- | | || data *< | + | | || data *< |
- | | || read *< | + | | || read *< |
- | | ||| length *< | + | | ||| length *< |
- | | ||| data *< | + | | ||| data *< |
- | | ||| quality *< | + | | ||| quality *< |
^^^^^^^^^^^ | ^^^^^^^^^^^ | ||
| **structure** (attribute: name) (o) | numGroups ||| x | x | x | | | **structure** (attribute: name) (o) | numGroups ||| x | x | x | | ||
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| | matrixLabels //(name, name,...)// ||| x | x | x | | | | matrixLabels //(name, name,...)// ||| x | x | x | | ||
| | matrix //(number (line break) | | | matrix //(number (line break) | ||
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*< | *< | ||
*< | *< | ||
- | *< | + | *< |
- | *< | + | *< |
- | *< | + | *< |
- | *< | + | |
- | *< | + | |
x: obligatory\\ | x: obligatory\\ | ||
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===== PGD file examples: ===== | ===== PGD file examples: ===== | ||
- | * aligned | + | * Data of two loci with Standard |
- | * alinged data with different data types: [[PGD_aligned_DiffDataTypes]] | + | * Data of two loci with different data types (Standard and DNA) from two diploid populations: [[PGD_diffDataTypes]] |
- | * UHTS data with mixed number | + | * NGS data of two loci from three haploid populations: [[PGD_NGS]] |
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pgd.txt · Last modified: 2016/02/22 15:41 by heidi