资源说明：My xslt sandbox

# my XSLT sandbox.


## Examples

Saving a github-wiki page so I can use it in a blog:

```bash
$ curl -s "https://github.com/lindenb/jvarkit/wiki/Illuminadir" |\
  xsltproc --html ./github2html.xsl  -   >  file.html
  
```

Saving a github-wiki page to **LaTex**:

```bash
$ curl -s "https://github.com/lindenb/jvarkit/wiki/Illuminadir" |\
  xsltproc --html ./github2html.xsl  -   >  file.html
  
```


Transforming (X)html to **LaTex**

```bash
$ curl -s "https://github.com/lindenb/jvarkit/wiki/Illuminadir" |\
  xsltproc --html ./stylesheets/github/github2tex.xsl  -  > tmp.tex && \
  pdflatex tmp.tex && \
  evince tmp.pdf
```

Insert **Blast** results in **sqlite3**:
```bash
$ xsltproc --novalid blast2sqlite.xsl blast.xml | sqlite3 blast.sqlite3
```

Convert blast to HTML (see also http://www.biostars.org/p/6635/ )

```bash
$ xsltproc --novalid blast2html.xsl blast.xml > result.html
```


Convert kegg-xml (kgml) to GEXF (see also http://www.biostars.org/p/85763/ )

```bash
$ xsltproc --novalid kgml2gexf.xsl "http://kgmlreader.googlecode.com/svn/trunk/KGMLReader/testData/kgml/non-metabolic/organisms/hsa/hsa04060.xml" > result.gexf
```

Insert **Pubmed** into a **sqlite3** database.

```bash
$ xsltproc --novalid stylesheets/bio/ncbi/pubmed2sqlite.xsl pubmed_result.xml | sqlite3 jeter.db
```

convert **Pubmed** to **JSON**

```bash
$ xsltproc --novalid stylesheets/bio/ncbi/pubmed2json.xsl pubmed_result.xml  | python -mjson.tool

```


Create a simple Blast dot plot (see  http://www.biostars.org/p/85258/ "Make a dotplot from blast alignment" ) 

```bash
$ xsltproc --novalid stylesheets/bio/ncbi/pubmed2sqlite.xsl pubmed_result.xml | sqlite3 jeter.db
```


Transforms a **NCBI taxonomy** to **Graphiz dot**:
```bash
 xsltproc taxon2dot.xsl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=9606,9913,30521,562,2157" |\
 	dot -oout.png -Tpng 
```

Get the number of children for each term in gene-ontology (see  https://www.biostars.org/p/102699/ "How to determine the terminal GO terms within GO DAG" ) 

```bash
curl  "http://archive.geneontology.org/latest-termdb/go_daily-termdb.rdf-xml.gz" |\
	gunzip -c |\
	xsltproc --novalid go2countchildren.xsl go.rdf - > count.tsv
```

Extract **HTML** form:
```bash
$ curl -L google.com | xsltproc --html  stylesheets/html/html2curl.xsl -
'&ie=ISO-8859-1&hl=fr&source=hp&q=&btnG=Recherche%20Google&btnI=J'ai%20de%20la%20chance&gbv=1'
```

convert **NCBI/EInfo** to **HTML**

```
xsltproc --novalid \
	stylesheets/bio/ncbi/einfo2html.xsl \
	http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi  > index.html
```

convert **Blast/XML** to a **HTML** matrix

```
xsltproc --novalid \
	stylesheets/bio/ncbi/blast2matrix.xsl \
	blastn.xml  > blast.html
```

convert **NCBI Taxonomy** to **newick**

```
$ xsltproc stylesheets/bio/ncbi/taxon2newick.xsl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=9606,10090,9031,7227,562" 

(((((((((((((((((((((((((((((((Homo_sapiens)Homo)Homininae)Hominidae)Hominoidea)Catarrhini)Simiiform
es)Haplorrhini)Primates,((((((((Mus_musculus)Mus)Mus)Murinae)Muridae)Muroidea)Sciurognathi)Rodentia)
Glires)Euarchontoglires)Boreoeutheria)Eutheria)Theria)Mammalia,(((((((((((((((Gallus_gallus)Gallus)P
hasianinae)Phasianidae)Galliformes)Galloanserae)Neognathae)Aves)Coelurosauria)Theropoda)Saurischia)D
inosauria)Archosauria)Archelosauria)Sauria)Sauropsida)Amniota)Tetrapoda)Dipnotetrapodomorpha)Sarcopt
erygii)Euteleostomi)Teleostomi)Gnathostomata)Vertebrata)Craniata)Chordata)Deuterostomia,((((((((((((
(((((((((((((((((Drosophila_melanogaster)melanogaster_subgroup)melanogaster_group)Sophophora)Drosoph
ila)Drosophiliti)Drosophilina)Drosophilini)Drosophilinae)Drosophilidae)Ephydroidea)Acalyptratae)Schi
zophora)Cyclorrhapha)Eremoneura)Muscomorpha)Brachycera)Diptera)Endopterygota)Neoptera)Pterygota)Dico
ndylia)Insecta)Hexapoda)Pancrustacea)Mandibulata)Arthropoda)Panarthropoda)Ecdysozoa)Protostomia)Bila
teria)Eumetazoa)Metazoa)Opisthokonta)Eukaryota,((((((Escherichia_coli)Escherichia)Enterobacteriaceae
)Enterobacteriales)Gammaproteobacteria)Proteobacteria)Bacteria)cellular_organisms);

```

Get all the child terms in **Disease ontology** under **DOID:2914** ( immune system disease ) http://disease-ontology.org/ .


```bash
$ curl "http://www.berkeleybop.org/ontologies/doid.owl" |\
    xsltproc --stringparam ID "DOID:2914" do_children.xsl -
```

```tsv
#ID	LABEL	URI	DESCRIPTION
DOID:2914	immune system disease	http://purl.obolibrary.org/obo/DOID_7	A disease of anatomical entity that is located_in the immune system.
DOID:0060056	hypersensitivity reaction disease	http://purl.obolibrary.org/obo/DOID_2914	
DOID:1205	hypersensitivity reaction type I disease	http://purl.obolibrary.org/obo/DOID_0060056	An immune system disease that is an exaggerated immune response to allergens, such as insect venom, dust mites, pollen, pet dander, drugs or some foods.
DOID:3044	food allergy	http://purl.obolibrary.org/obo/DOID_1205	A hypersensitivity reaction type I disease that is an abnormal response to a food, triggered by the body's immune system.
DOID:0060057	gluten allergic reaction	http://purl.obolibrary.org/obo/DOID_3044	
DOID:3660	wheat allergic reaction	http://purl.obolibrary.org/obo/DOID_3044	
DOID:4376	milk allergic reaction	http://purl.obolibrary.org/obo/DOID_3044	A food allergy that results in adverse immune reaction to one or more of the proteins in cow's milk and/or the milk of other animals, which are normally harmless to the non-allergic individual.
DOID:4377	egg allergy	http://purl.obolibrary.org/obo/DOID_3044	A food allergy that is an allergy or hypersensitivity to dietary substances from the yolk or whites of eggs, causing an overreaction of the immune system which may lead to severe physical symptoms.
DOID:4378	peanut allergic reaction	http://purl.obolibrary.org/obo/DOID_3044	A food allergy that is an allergy or hypersensitivity to dietary substances from peanuts causing an overreaction of the immune system which in a small percentage of people may lead to severe physical symptoms.
(...)
```

### Generation of new java __KNIME__ nodes

see https://github.com/lindenb/xslt-sandbox/wiki/Knime2java

### Draw a [Manhattan plot](https://en.wikipedia.org/wiki/Manhattan_plot) in SVG

see https://github.com/lindenb/xslt-sandbox/wiki/ManhattanPlot

![Plot](http://i.imgur.com/HrGjouY.jpg)

## Create a Makefile from an apache-maven pom.xml to download the required jars:

```
$ xsltproc pom2make.xsl "http://central.maven.org/maven2/org/eclipse/jetty/jetty-server/9.3.0.M2/jetty-server-9.3.0.M2.pom"  2> /dev/null 
```

```make
lib.dir=lib
all.jars = $(addprefix ${lib.dir}/,$(sort  org/eclipse/jetty/jetty-server/9.3.0.M2/jetty-server-9.3.0.M2.jar javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar org/eclipse/jetty/jetty-http/9.3.0.M2/jetty-http-9.3.0.M2.jar org/eclipse/jetty/jetty-util/9.3.0.M2/jetty-util-9.3.0.M2.jar javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar org/slf4j/slf4j-api/1.7.10/slf4j-api-1.7.10.jar org/eclipse/jetty/jetty-io/9.3.0.M2/jetty-io-9.3.0.M2.jar org/eclipse/jetty/jetty-util/9.3.0.M2/jetty-util-9.3.0.M2.jar javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar org/slf4j/slf4j-api/1.7.10/slf4j-api-1.7.10.jar org/eclipse/jetty/jetty-jmx/9.3.0.M2/jetty-jmx-9.3.0.M2.jar org/eclipse/jetty/jetty-util/9.3.0.M2/jetty-util-9.3.0.M2.jar javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar org/slf4j/slf4j-api/1.7.10/slf4j-api-1.7.10.jar))

.PHONY:all

all: ${all.jars}
${all.jars} : 
	mkdir -p $(dir $@) && curl -o $@ "http://central.maven.org/maven2/$(patsubst ${lib.dir}/%,%,$@)"
```
see https://github.com/lindenb/xslt-sandbox/wiki/Maven2Make


### Plotting project Tycho data:

see https://github.com/lindenb/xslt-sandbox/wiki/Tycho

![http://i.imgur.com/gBZCVTX.png](http://i.imgur.com/gBZCVTX.png)

### Pubmed Trending Articles as a RSS feed.

see https://github.com/lindenb/xslt-sandbox/wiki/PubmedTrending

![http://i.imgur.com/a1VAdCa](http://i.imgur.com/a1VAdCa.jpg)


### XML to dot

show a XML tree as graphviz dot

```
$ curl -s  "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=25&retmode=xml&rettype=fasta" |\
 xsltproc xml2dot.xsl  - 
````

```dot
digraph G
	{
	idp0 [label=""];
	idp5184 [label="TSeqSet",shape=oval]
idp5120 [label="TSeq",shape=oval]
idp228784 [label="TSeq_seqtype",shape=oval]
idp234608 [label="@value=nucleotide",shape=box]
idp234608 -> idp228784;
idp228784 -> idp5120;
(...)
```


### Blast to fasta

see https://www.biostars.org/p/14913/

```bash
xsltproc --novalid blast2fasta.xsl blastn.xml
```

### PSI/Biogrid to SQL

```bash
xsltproc -o tmp.sql psi2sql.xslt BIOGRID-ALL-3.4.129.psi.xml
sqlite3 db.sqlite3 < tmp.sql
```

find the interactions for B4DG32  (http://www.uniprot.org/uniprot/B4DG32 )

```bash
$ sqlite3 -header db.sqlite3  'select distinct I1.shortLabel,I2.shortLabel from interaction as L,interaction2interactor as I2I1, interaction2interactor as I2I2, interactor as I1 ,interactor as I2, xref as X1 where X1.pk="B4DG32" and X1.interactor_pk=I1.pk and I2I1.interaction_pk = L.pk and I2I1.interactor_pk = I1.pk and I2I2.interaction_pk = L.pk and I2I2.interactor_pk = I2.pk'

shortLabel|shortLabel
SH2D3C|BCAR1
SH2D3C|EFS
SH2D3C|EGFR
SH2D3C|LYN
SH2D3C|NEDD9
SH2D3C|SH2D3C
SH2D3C|SNCAIP
```

### Get the coverage of a blast query.

```bash
$ xsltproc stylesheets/bio/ncbi/blast2coverage.xsl blastn.xml
```

output:
```tsv
#ID	DEF	POS	LENGTH	CONSENSUS	DEPTH
gi|9626372|ref|NC_001422.1|	Enterobacteria phage phiX174 sensu lato, complete genome	1	5386	GGGGGGGGGGGGGGGGGG	18
gi|9626372|ref|NC_001422.1|	Enterobacteria phage phiX174 sensu lato, complete genome	2	5386	AAAAAAAAAAAAAAAAAA	18
gi|9626372|ref|NC_001422.1|	Enterobacteria phage phiX174 sensu lato, complete genome	3	5386	GGGGGGGGGGGGGGGGGG	18
gi|9626372|ref|NC_001422.1|	Enterobacteria phage phiX174 sensu lato, complete genome	4	5386	TTTTTTTTTTTTTTTTTT	18
gi|9626372|ref|NC_001422.1|	Enterobacteria phage phiX174 sensu lato, complete genome	5	5386	TTTTTTTTTTTTTTTTTT	18
gi|9626372|ref|NC_001422.1|	Enterobacteria phage phiX174 sensu lato, complete genome	6	5386	TTTTTTTTTTTTTTTTTT	18
gi|9626372|ref|NC_001422.1|	Enterobacteria phage phiX174 sensu lato, complete genome	7	5386	TTTTTTTTTTTTTTTTTT	18
gi|9626372|ref|NC_001422.1|	Enterobacteria phage phiX174 sensu lato, complete genome	8	5386	AAAAAAAAAAAAAAAAAA	18
gi|9626372|ref|NC_001422.1|	Enterobacteria phage phiX174 sensu lato, complete genome	9	5386	TTTTTTTTTTTTTTTTTT	18
(...)
```

### convert genbank gbc to gtf
should work with simple genbank files (tested with a simple virus)

```bash
xsltproc --novalid stylesheets/bio/ncbi/gb2gtf.xsl input.gbc.xml | sort -t '  ' -k4,4n > out.gtf
```

## Contribute

- Issue Tracker: http://github.com/lindenb/xslt-sandbox/issues`
- Source Code: http://github.com/lindenb/xslt-sandbox

## License

The project is licensed under the MIT license.

## Author

Pierre Lindenbaum PhD @yokofakun

联系我们：verysource_com

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