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legiolist
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genolist
legiolist
Commits
9052f85b
Commit
9052f85b
authored
Nov 16, 2020
by
Remi PLANEL
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remove version in project
parent
e5c21f44
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project.xml
project.xml
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project.xml
View file @
9052f85b
...
...
@@ -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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