Commit 67a8dbe9 authored by Remi  PLANEL's avatar Remi PLANEL
Browse files

one data source per strains

parent a03b6581
...@@ -3,26 +3,225 @@ ...@@ -3,26 +3,225 @@
<property name="common.os.prefix" value="common"/> <property name="common.os.prefix" value="common"/>
<sources> <sources>
<!-- Legio paris -->
<source name="legiolist-gff-297246" type="gff">
<!-- 1 Legio paris -->
<source name="LegioParis-chromosome-fasta" type="fasta" dump="true">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/>
<property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila str. Paris chromosome sequence"/>
<property name="fasta.taxonId" value="297246"/>
<property name="fasta.includes" value="LegioParis_10-05-2012_LegioList.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta"/>
</source>
<source name="LegioParis-gff" type="gff">
<property name="gff3.taxonId" value="297246"/> <property name="gff3.taxonId" value="297246"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila str. Paris"/> <property name="gff3.seqDataSourceName" value="LegioList LegioParis"/>
<property name="gff3.dataSourceName" value="LegioList Legionella pneumophila str. Paris"/> <property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/> <property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="LegioList Legionella pneumophila str. Paris"/> <property name="gff3.dataSetTitle" value="LegioList Legionella pneumophila str. Paris genome annotation"/>
<property name="fasta.includes" value="LegioParis_10-05-2012_LegioList.genbank.gff3"/> <property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/LegioParis"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff"/>
</source> </source>
<source name="legiolist-chromosome-fasta-297246" type="fasta" dump="true">
<!-- <source name="Lfallonii-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/> <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/> <property name="fasta.dataSourceName" value="LegioList"/>
<property name="fasta.dataSetTitle" value="LegioList chromosome sequence"/> <property name="fasta.dataSetTitle" value="LegioList Legionella fallonii chromosome sequence"/>
<property name="fasta.taxonId" value="297246"/> <property name="fasta.taxonId" value="96230"/>
<property name="fasta.includes" value="LegioParis_10-05-2012_LegioList.fasta"/> <property name="fasta.includes" value="Lfallonii.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta"/> <property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta"/>
</source> </source>
<source name="Lfallonii-gff" type="gff">
<property name="gff3.taxonId" value="96230"/>
<property name="gff3.seqDataSourceName" value="LegioList Lfalloni"/>
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella fallonii genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Lfallonii"/>
</source>
-->
<!--
<source name="Lhackeliae-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/>
<property name="fasta.dataSetTitle" value="LegioList Legionella hackeliae chromosome sequence"/>
<property name="fasta.taxonId" value="449"/>
<property name="fasta.includes" value="Lhackeliae.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta"/>
</source>
<source name="Lhackeliae-gff" type="gff">
<property name="gff3.taxonId" value="449"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella hackeliae"/>
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella hackeliae genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Lhackeliae"/>
</source>
-->
<!--
<source name="Lmicadei-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/>
<property name="fasta.dataSetTitle" value="LegioList Legionella micdadei chromosome sequence"/>
<property name="fasta.taxonId" value="451"/>
<property name="fasta.includes" value="Lmicadei.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta"/>
</source>
<source name="Lmicadei-gff" type="gff">
<property name="gff3.taxonId" value="451"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella micdadei"/>
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella micdadei genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Lmicadei"/>
</source>
-->
<!-- <source name="Long_Mage-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/>
<property name="fasta.dataSetTitle" value="LegioList Legionella longbeachae NSW150 chromosome sequence"/>
<property name="fasta.taxonId" value="661367"/>
<property name="fasta.includes" value="Long_Mage.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta"/>
</source>
<source name="Long_Mage-gff" type="gff">
<property name="gff3.taxonId" value="661367"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella longbeachae NSW150"/>
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella longbeachae NSW150 genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Long_Mage"/>
</source> -->
<!-- pneumophila Lorraine -->
<!-- <source name="lorraine-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/>
<property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila subsp. pneumophila str. Lorraine chromosome sequence"/>
<property name="fasta.taxonId" value="1046632"/>
<property name="fasta.includes" value="Lorraine.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta"/>
</source>
<source name="Lorraine-gff" type="gff">
<property name="gff3.taxonId" value="1046632"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila subsp. pneumophila str. Lorraine"/>
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella pneumophila subsp. pneumophila str. Lorraine genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/Lorraine"/>
</source> -->
<!-- Legionella pneumophila 2300/99 Alcoy -->
<!-- <source name="LpAlcoy-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/>
<property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila 2300/99 Alcoy chromosome sequence"/>
<property name="fasta.taxonId" value="423212"/>
<property name="fasta.includes" value="LpAlcoy.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta"/>
</source>
<source name="LpAlcoy-gff" type="gff">
<property name="gff3.taxonId" value="423212"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila 2300/99 Alcoy"/>
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella pneumophila 2300/99 Alcoy genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/LpAlcoy"/>
</source> -->
<!-- pneumophila Corby -->
<!-- <source name="LpCorby-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/>
<property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila str. Corby chromosome sequence"/>
<property name="fasta.taxonId" value="400673"/>
<property name="fasta.includes" value="LpCorby.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta"/>
</source>
<source name="LpCorby-gff" type="gff">
<property name="gff3.taxonId" value="400673"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila str. Corby"/>
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella pneumophila str. Corby genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/LpCorby"/>
</source>
-->
<!-- Legionella pneumophila str. Lens -->
<!--
<source name="LpLens-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/>
<property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila str. Lens chromosome sequence"/>
<property name="fasta.taxonId" value="297245"/>
<property name="fasta.includes" value="LpLens.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta"/>
</source>
<source name="LpLens-gff" type="gff">
<property name="gff3.taxonId" value="297245"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila str. Lens"/>
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella pneumophila str. Lens genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/LpLens"/>
</source>
-->
<!-- Legionella pneumophila subsp. pneumophila str. Philadelphia 1 -->
<!--
<source name="LpPhila-chromosome-fasta" type="fasta">
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.dataSourceName" value="LegioList"/>
<property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila subsp. pneumophila str. Philadelphia 1 chromosome sequence"/>
<property name="fasta.taxonId" value="272624"/>
<property name="fasta.includes" value="LpPhila.fasta"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/fasta"/>
</source>
<source name="LpPhila-gff" type="gff">
<property name="gff3.taxonId" value="272624"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila subsp. pneumophila str. Philadelphia 1"/>
<property name="gff3.dataSourceName" value="LegioList"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSetTitle" value="Legionella pneumophila subsp. pneumophila str. Philadelphia 1 genome annotation"/>
<property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/gff/legiolist-gff/LpPhila"/>
</source> -->
<source name="entrez-organism" type="entrez-organism"> <source name="entrez-organism" type="entrez-organism">
<property name="src.data.file" location="organisms.xml"/> <property name="src.data.file" location="organisms.xml"/>
</source> </source>
...@@ -32,6 +231,7 @@ ...@@ -32,6 +231,7 @@
<post-processing> <post-processing>
<post-process name="create-references"/> <post-process name="create-references"/>
<post-process name="transfer-sequences" dump="true"/>
<post-process name="create-chromosome-locations-and-lengths"/> <post-process name="create-chromosome-locations-and-lengths"/>
<post-process name="transfer-sequences" dump="true"/> <post-process name="transfer-sequences" dump="true"/>
<post-process name="do-sources" /> <post-process name="do-sources" />
......
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