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.pdfInsert Blast results in sqlite3:
$ xsltproc --novalid blast2sqlite.xsl blast.xml | sqlite3 blast.sqlite3Convert blast to HTML (see also http://www.biostars.org/p/6635/ )
$ xsltproc --novalid blast2html.xsl blast.xml > result.htmlConvert 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.gexfInsert Pubmed into a sqlite3 database.
$ xsltproc --novalid stylesheets/bio/ncbi/pubmed2sqlite.xsl pubmed_result.xml | sqlite3 jeter.dbconvert 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.dbTransforms 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.tsvExtract 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
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
Pubmed Trending Articles as a RSS feed.
see https://github.com/lindenb/xslt-sandbox/wiki/PubmedTrending
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.xmlPSI/Biogrid to SQL
xsltproc -o tmp.sql psi2sql.xslt BIOGRID-ALL-3.4.129.psi.xml
sqlite3 db.sqlite3 < tmp.sqlfind 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|SNCAIPGet the coverage of a blast query.
$ xsltproc stylesheets/bio/ncbi/blast2coverage.xsl blastn.xmloutput:
#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.gtfContribute
- 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