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lindenb / xslt-sandbox

My xslt sandbox

Home Page:http://plindenbaum.blogspot.com

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xmlxsltbioinformaticsformatting

my XSLT sandbox.

Examples

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

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

Saving a github-wiki page to LaTex:

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

Transforming (X)html to LaTex

$ 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:

$ xsltproc --novalid blast2sqlite.xsl blast.xml | sqlite3 blast.sqlite3

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

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

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

$ 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.

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

convert Pubmed to JSON

$ 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" )

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

Transforms a NCBI taxonomy to Graphiz dot:

 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" )

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:

$ 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/ .

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

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

Plot

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 

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

Pubmed Trending Articles as a RSS feed.

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

http://i.imgur.com/a1VAdCa

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  - 

digraph G
	{
	idp0 [label="<ROOT>"];
	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/

xsltproc --novalid blast2fasta.xsl blastn.xml

PSI/Biogrid to SQL

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 )

$ 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.

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

output:

#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)

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

Contribute

License

The project is licensed under the MIT license.

Author

Pierre Lindenbaum PhD @yokofakun

About

My xslt sandbox

http://plindenbaum.blogspot.com

xmlxsltbioinformaticsformatting

Languages

Language:XSLT 97.9%Language:Java 1.5%Language:Makefile 0.4%Language:Awk 0.2%