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legiolist
Commit 9052f85b authored by Remi PLANEL's avatar Remi PLANEL
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remove version in project

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project.xml
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......@@ -5,7 +5,7 @@
<sources>
<!-- First gff and then fasta if you want to have the sequence available -->
<source name="LegioParis-gff" type="legiolist-gff" version="4.1.1">
<source name="LegioParis-gff" type="legiolist-gff">
<property name="gff3.taxonId" value="297246" />
<property name="gff3.seqDataSourceName" value="LegioList LegioParis" />
<property name="gff3.dataSourceName" value="LegioList" />
......@@ -14,7 +14,7 @@
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/LegioParis_10-05-2012_LegioList/" />
</source>
<source name="LegioParis-chromosome-fasta" type="fasta" version="4.1.1">
<source name="LegioParis-chromosome-fasta" type="fasta">
<property name="fasta.taxonId" value="297246" />
<property name="fasta.className" value="org.intermine.model.bio.Chromosome" />
<property name="fasta.dataSourceName" value="LegioList" />
......@@ -24,14 +24,14 @@
</source>
<source name="LegioParis-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<source name="LegioParis-protein-gene" type="legiolist-gene-prot">
<property name="legiolist.taxid" value="297246" />
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein" />
<property name="src.data.dir.includes" value="LegioParis_10-05-2012_LegioList-prot-gene.tsv" />
</source>
<source name="LegioParis-protein-fasta" type="fasta" version="4.1.1">
<source name="LegioParis-protein-fasta" type="fasta">
<property name="fasta.taxonId" value="297246" />
<property name="fasta.dataSetTitle" value="Legiolist protein sequence" />
<property name="fasta.className" value="org.intermine.model.bio.Protein" />
......@@ -44,7 +44,7 @@
</source>
<!--
<source name="Lfallonii-gff" type="legiolist-gff" version="4.1.1">
<source name="Lfallonii-gff" type="legiolist-gff" >
<property name="gff3.taxonId" value="96230"/>
<property name="gff3.seqDataSourceName" value="LegioList Lfalloni"/>
<property name="gff3.dataSourceName" value="LegioList"/>
......@@ -52,7 +52,7 @@
<property name="gff3.dataSetTitle" value="Legionella fallonii genome annotation"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/Lfallonii"/>
</source>
<source name="Lfallonii-chromosome-fasta" type="fasta" version="4.1.1">
<source name="Lfallonii-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 fallonii chromosome sequence"/>
......@@ -61,7 +61,7 @@
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
<source name="Lfallonii-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<source name="Lfallonii-protein-gene" type="legiolist-gene-prot" >
<property name="legiolist.taxid" value="96230"/>
<property name="legiolist-gene-prot.dataSetTitle" value="LegioList Legionella fallonii proteins"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
......@@ -69,7 +69,7 @@
</source>
<source name="Lfallonii-protein-fasta" type="fasta" version="4.1.1">
<source name="Lfallonii-protein-fasta" type="fasta" >
<property name="fasta.taxonId" value="96230"/>
<property name="fasta.dataSetTitle" value="Legiolist Lfallonii protein sequence"/>
<property name="fasta.className" value="org.intermine.model.bio.Protein"/>
......@@ -82,7 +82,7 @@
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
</source>
<source name="Lhackeliae-gff" type="legiolist-gff" version="4.1.1">
<source name="Lhackeliae-gff" type="legiolist-gff" >
<property name="gff3.taxonId" value="449"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella hackeliae"/>
<property name="gff3.dataSourceName" value="LegioList"/>
......@@ -90,7 +90,7 @@
<property name="gff3.dataSetTitle" value="Legionella hackeliae genome annotation"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/Lhackeliae"/>
</source>
<source name="Lhackeliae-chromosome-fasta" type="fasta" version="4.1.1">
<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"/>
......@@ -99,14 +99,14 @@
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
<source name="Lhackeliae-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<source name="Lhackeliae-protein-gene" type="legiolist-gene-prot" >
<property name="legiolist.taxid" value="449"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir.includes" value="Lhackeliae-prot-gene.tsv"/>
</source>
<source name="Lhackeliae-protein-fasta" type="fasta" version="4.1.1">
<source name="Lhackeliae-protein-fasta" type="fasta" >
<property name="fasta.taxonId" value="449"/>
<property name="fasta.dataSetTitle" value="Legiolist protein sequence"/>
<property name="fasta.className" value="org.intermine.model.bio.Protein"/>
......@@ -124,7 +124,7 @@
<source name="Lmicadei-gff" type="legiolist-gff" version="4.1.1">
<source name="Lmicadei-gff" type="legiolist-gff" >
<property name="gff3.taxonId" value="451"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella micdadei"/>
<property name="gff3.dataSourceName" value="LegioList"/>
......@@ -132,7 +132,7 @@
<property name="gff3.dataSetTitle" value="Legionella micdadei genome annotation"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/Lmicadei"/>
</source>
<source name="Lmicadei-chromosome-fasta" type="fasta" version="4.1.1">
<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"/>
......@@ -142,14 +142,14 @@
</source>
<source name="Lmicadei-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<source name="Lmicadei-protein-gene" type="legiolist-gene-prot" >
<property name="legiolist.taxid" value="451"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir.includes" value="Lmicadei-prot-gene.tsv"/>
</source>
<source name="Lmicadei-protein-fasta" type="fasta" version="4.1.1">
<source name="Lmicadei-protein-fasta" type="fasta" >
<property name="fasta.taxonId" value="451"/>
<property name="fasta.dataSetTitle" value="Legiolist protein sequence"/>
<property name="fasta.className" value="org.intermine.model.bio.Protein"/>
......@@ -164,7 +164,7 @@
<source name="Long_Mage-gff" type="legiolist-gff" version="4.1.1">
<source name="Long_Mage-gff" type="legiolist-gff" >
<property name="gff3.taxonId" value="661367"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella longbeachae NSW150"/>
<property name="gff3.dataSourceName" value="LegioList"/>
......@@ -172,7 +172,7 @@
<property name="gff3.dataSetTitle" value="Legionella longbeachae NSW150 genome annotation"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/Long_Mage"/>
</source>
<source name="Long_Mage-chromosome-fasta" type="fasta" version="4.1.1">
<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"/>
......@@ -181,13 +181,13 @@
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
<source name="Long_Mage-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<source name="Long_Mage-protein-gene" type="legiolist-gene-prot" >
<property name="legiolist.taxid" value="661367"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir.includes" value="Long_Mage-prot-gene.tsv"/>
</source>
<source name="Long_Mage-protein-fasta" type="fasta" version="4.1.1">
<source name="Long_Mage-protein-fasta" type="fasta" >
<property name="fasta.taxonId" value="661367"/>
<property name="fasta.dataSetTitle" value="Legiolist protein sequence"/>
<property name="fasta.className" value="org.intermine.model.bio.Protein"/>
......@@ -202,7 +202,7 @@
<source name="Lorraine-gff" type="legiolist-gff" version="4.1.1">
<source name="Lorraine-gff" type="legiolist-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"/>
......@@ -210,7 +210,7 @@
<property name="gff3.dataSetTitle" value="Legionella pneumophila subsp. pneumophila str. Lorraine genome annotation"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/Lorraine"/>
</source>
<source name="lorraine-chromosome-fasta" type="fasta" version="4.1.1">
<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"/>
......@@ -220,7 +220,7 @@
</source>
<source name="Lorraine-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<source name="Lorraine-protein-gene" type="legiolist-gene-prot" >
<property name="legiolist.taxid" value="1046632"/>
<property name="legiolist-gene-prot.dataSetTitle" value="LegioList Lorraine proteins"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
......@@ -228,7 +228,7 @@
</source>
<source name="Lorraine-protein-fasta" type="fasta" version="4.1.1">
<source name="Lorraine-protein-fasta" type="fasta" >
<property name="fasta.taxonId" value="1046632"/>
<property name="fasta.dataSetTitle" value="Legiolist Lorraine protein sequence"/>
<property name="fasta.className" value="org.intermine.model.bio.Protein"/>
......@@ -246,7 +246,7 @@
<source name="LpAlcoy-gff" type="legiolist-gff" version="4.1.1">
<source name="LpAlcoy-gff" type="legiolist-gff" >
<property name="gff3.taxonId" value="423212"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila 2300/99 Alcoy"/>
<property name="gff3.dataSourceName" value="LegioList"/>
......@@ -254,7 +254,7 @@
<property name="gff3.dataSetTitle" value="Legionella pneumophila 2300/99 Alcoy genome annotation"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/LpAlcoy"/>
</source>
<source name="LpAlcoy-chromosome-fasta" type="fasta" version="4.1.1">
<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"/>
......@@ -264,14 +264,14 @@
</source>
<source name="LpAlcoy-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<source name="LpAlcoy-protein-gene" type="legiolist-gene-prot" >
<property name="legiolist.taxid" value="423212"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir.includes" value="LpAlcoy-prot-gene.tsv"/>
</source>
<source name="LpAlcoy-protein-fasta" type="fasta" version="4.1.1">
<source name="LpAlcoy-protein-fasta" type="fasta" >
<property name="fasta.taxonId" value="423212"/>
<property name="fasta.dataSetTitle" value="Legiolist protein sequence"/>
<property name="fasta.className" value="org.intermine.model.bio.Protein"/>
......@@ -289,7 +289,7 @@
<source name="LpCorby-gff" type="legiolist-gff" version="4.1.1">
<source name="LpCorby-gff" type="legiolist-gff" >
<property name="gff3.taxonId" value="400673"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila str. Corby"/>
<property name="gff3.dataSourceName" value="LegioList"/>
......@@ -297,7 +297,7 @@
<property name="gff3.dataSetTitle" value="Legionella pneumophila str. Corby genome annotation"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/LpCorby"/>
</source>
<source name="LpCorby-chromosome-fasta" type="fasta" version="4.1.1">
<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"/>
......@@ -307,14 +307,14 @@
</source>
<source name="LpCorby-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<source name="LpCorby-protein-gene" type="legiolist-gene-prot" >
<property name="legiolist.taxid" value="400673"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir.includes" value="LpCorby-prot-gene.tsv"/>
</source>
<source name="LpCorby-protein-fasta" type="fasta" version="4.1.1">
<source name="LpCorby-protein-fasta" type="fasta" >
<property name="fasta.taxonId" value="400673"/>
<property name="fasta.dataSetTitle" value="Legiolist protein sequence"/>
<property name="fasta.className" value="org.intermine.model.bio.Protein"/>
......@@ -332,7 +332,7 @@
<source name="LpLens-gff" type="legiolist-gff" version="4.1.1">
<source name="LpLens-gff" type="legiolist-gff" >
<property name="gff3.taxonId" value="297245"/>
<property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila str. Lens"/>
<property name="gff3.dataSourceName" value="LegioList"/>
......@@ -340,7 +340,7 @@
<property name="gff3.dataSetTitle" value="Legionella pneumophila str. Lens genome annotation"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/LpLens"/>
</source>
<source name="LpLens-chromosome-fasta" type="fasta" version="4.1.1">
<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"/>
......@@ -349,14 +349,14 @@
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
</source>
<source name="LpLens-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<source name="LpLens-protein-gene" type="legiolist-gene-prot" >
<property name="legiolist.taxid" value="297245"/>
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
<property name="src.data.dir.includes" value="LpLens-prot-gene.tsv"/>
</source>
<source name="LpLens-protein-fasta" type="fasta" version="4.1.1">
<source name="LpLens-protein-fasta" type="fasta" >
<property name="fasta.taxonId" value="297245"/>
<property name="fasta.dataSetTitle" value="Legiolist protein sequence"/>
<property name="fasta.className" value="org.intermine.model.bio.Protein"/>
......@@ -370,7 +370,7 @@
-->
<source name="LpPhila-gff" type="legiolist-gff" version="4.1.1">
<source name="LpPhila-gff" type="legiolist-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" />
......@@ -378,7 +378,7 @@
<property name="gff3.dataSetTitle" value="Legionella pneumophila subsp. pneumophila str. Philadelphia 1 genome annotation" />
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/LpPhila" />
</source>
<source name="LpPhila-chromosome-fasta" type="fasta" version="4.1.1">
<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" />
......@@ -387,14 +387,14 @@
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta" />
</source>
<source name="LpPhila-protein-gene" type="legiolist-gene-prot" version="4.1.1">
<source name="LpPhila-protein-gene" type="legiolist-gene-prot">
<property name="legiolist.taxid" value="272624" />
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein" />
<property name="src.data.dir.includes" value="LpPhila-prot-gene.tsv" />
</source>
<source name="LpPhila-protein-fasta" type="fasta" version="4.1.1">
<source name="LpPhila-protein-fasta" type="fasta">
<property name="fasta.taxonId" value="272624" />
<property name="fasta.dataSetTitle" value="Legiolist protein sequence" />
<property name="fasta.className" value="org.intermine.model.bio.Protein" />
......@@ -417,7 +417,7 @@
<property name="loadtrembl" value="true"/>
</source> -->
<source name="legiolist-homology" type="legiolist-homology" version="4.1.1">
<source name="legiolist-homology" type="legiolist-homology">
<property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/" />
<property name="src.data.dir.includes" value="table_orthos_sample.txt" />
<property name="legiolistTaxids" value="272624 297246" />
......
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