05 July 2014

Pushed : makefile2graph , creating a graph of dependencies from GNU-Make.

I pushed makefile2graph at https://github.com/lindenb/makefile2graph. This is the standalone and 'C' implementation of a program I first wrote in java in 2012. The program creates a graph of dependencies from GNU-Make and its output is a graphiz-dot file or a Gexf/Gephi-XML file.

Usage

$ make -Bnd | make2graph > output.dot
$ make -Bnd | make2graph -x > gephi.gexf.xml 

Example

Here is the output of makefile2graph for Tabix:
$ cd tabix-0.2.5
$ make -Bnd |make2graph
digraph G {
n1[label="", color="green"];
n2[label="Makefile", color="green"];
n4[label="all", color="red"];
n3[label="all-recur", color="red"];
n23[label="bedidx.c", color="green"];
n22[label="bedidx.o", color="red"];
n9[label="bgzf.c", color="green"];
n10[label="bgzf.h", color="green"];
n8[label="bgzf.o", color="red"];
n27[label="bgzip", color="red"];
n29[label="bgzip.c", color="green"];
n28[label="bgzip.o", color="red"];
n18[label="index.c", color="green"];
n17[label="index.o", color="red"];
n20[label="khash.h", color="green"];
n16[label="knetfile.c", color="green"];
n11[label="knetfile.h", color="green"];
n15[label="knetfile.o", color="red"];
n24[label="kseq.h", color="green"];
n21[label="ksort.h", color="green"];
n13[label="kstring.c", color="green"];
n14[label="kstring.h", color="green"];
n12[label="kstring.o", color="red"];
n6[label="lib", color="red"];
n7[label="libtabix.a", color="red"];
n26[label="main.c", color="green"];
n25[label="main.o", color="red"];
n5[label="tabix", color="red"];
n19[label="tabix.h", color="green"];
n2 -> n1 ; 
n4 -> n1 ; 
n3 -> n1 ; 
(..)
}

That's it
Pierre

02 July 2014

Pushed today: verticalize , an everyday linux command to verticalize tab-delimited files

FYI: this morning, I pushed verticalize on github. Verticalize is an everyday simple command to 'verticalize' delimited files: https://github.com/lindenb/verticalize.

$ curl "https://raw.githubusercontent.com/ekg/vcflib/master/samples/sample.vcf" |\
  grep -vE "^##" |\
  verticalize

>>> 2
$1    #CHROM : 19
$2       POS : 111
$3        ID : .
$4       REF : A
$5       ALT : C
$6      QUAL : 9.6
$7    FILTER : .
$8      INFO : .
$9    FORMAT : GT:HQ
$10  NA00001 : 0|0:10,10
$11  NA00002 : 0|0:10,10
$12  NA00003 : 0/1:3,3
<<< 2

>>> 3
$1    #CHROM : 19
$2       POS : 112
$3        ID : .
$4       REF : A
$5       ALT : G
$6      QUAL : 10
$7    FILTER : .
$8      INFO : .
$9    FORMAT : GT:HQ
$10  NA00001 : 0|0:10,10
$11  NA00002 : 0|0:10,10
$12  NA00003 : 0/1:3,3
<<< 3



.

That's it,
Pierre

28 May 2014

Uniprot → SVG

My colleague @Solena recently asked me to write a tool that would help her to prepare a large number of figures for an article. The tool I wrote fetches an entry for a given Uniprot accession and creates a SVG diagram , editable in Inkscape. It is available at


That's it,

Pierre

22 May 2014

Breaking the " same origin security policy" with CORS. An example with @GenomeBrowser / DAS.

Jerven Bolleman recently taught me about the CORS/Cross-origin resource sharing:



"Cross-origin resource sharing (CORS) is a mechanism that allows many resources (e.g. fonts, JavaScript, etc.) on a web page to be requested from another domain outside of the domain the resource originated from. In particular, JavaScript's AJAX calls can use the XMLHttpRequest mechanism. Such "cross-domain" requests would otherwise be forbidden by web browsers, per the same origin security policy."

I've created a page testing if some bioinformatics web-service support CORS. This page is available at : http://lindenb.github.io/pages/cors/index.html

Interestingly NCBI, Uniprot and UCSC support CORS. As an example, the following <form> fetches a DNA sequence using the DAS server of the UCSC and display it:



The script:



That's it
Pierre

20 May 2014

A nodejs-based REST server for the UCSC @GenomeBrowser



Node.js provides a simple mechanism to write a REST server. As an exercise, I wrote a REST server for the mysql server of the UCSC genome bowser. The code is available on github at:


Starting the server


$ cd bionode
$ node ucsc/ucsc.js
Server running at http://localhost:8080/

METHOD: /schema/databases



Lists the available databases :e.g: http://localhost:8080/schemas/databases


[
"information_schema",
"ailMel1",
"allMis1",
"anoCar1",

(...)
"visiGene",
"xenTro1",
"xenTro2",
"xenTro3"
]


This method accepts a parameter callback for JSON-P : e.g: http://localhost:8080/schemas/databases?callback=handle


handle([
"information_schema",
"ailMel1",
"allMis1",
"anoCar1",
(...)
"visiGene",
"xenTro1",
"xenTro2",
"xenTro3"
]);


METHOD: /schema/:database/tables


Lists the available tables for a given database :e.g: http://localhost:8080/schemas/anoCar1/tables


[
"all_mrna",
"author",
"blastHg18KG",
"cds",
(...)
"xenoRefFlat",
"xenoRefGene",
"xenoRefSeqAli"
]

This method accepts a parameter callback for JSON-P : e.g: http://localhost:8080/schemas/anoCar1/tables?callback=handle


handle([
"all_mrna",
"author",
"blastHg18KG",
"cds",
"cell",
(...)
"xenoRefFlat",
"xenoRefGene",
"xenoRefSeqAli"
]);

METHOD: /schema/:database/:table


Returns a schema for the given database.table. E.g: http://localhost:8080/schemas/anoCar1/xenoMrna



{"database":"anoCar1","table":"xenoMrna","fields":[{"name":"bin","type":"smallint(5) unsigned","key":""},{"name":"matches","type":"int(10) unsigned","key":""},{"name":"misMatches","type":"int(10) unsigned","key":""},{"name":"repMatches","type":"int(10) unsigned","key":""},{"name":"nCount","type":"int(10) unsigned","key":""},{"name":"qNumInsert","type":"int(10) unsigned","key":""},{"name":"qBaseInsert","type":"int(10) unsigned","key":""},{"name":"tNumInsert","type":"int(10) unsigned","key":""},{"name":"tBaseInsert","type":"int(10) unsigned","key":""},{"name":"strand","type":"char(2)","key":""},{"name":"qName","type":"varchar(255)","key":"MUL"},{"name":"qSize","type":"int(10) unsigned","key":""},{"name":"qStart","type":"int(10) unsigned","key":""},{"name":"qEnd","type":"int(10) unsigned","key":""},{"name":"tName","type":"varchar(255)","key":"MUL"},{"name":"tSize","type":"int(10) unsigned","key":""},{"name":"tStart","type":"int(10) unsigned","key":""},{"name":"tEnd","type":"int(10) unsigned","key":""},{"name":"blockCount","type":"int(10) unsigned","key":""},{"name":"blockSizes","type":"longblob","key":""},{"name":"qStarts","type":"longblob","key":""},{"name":"tStarts","type":"longblob","key":""}]}


This method accepts a parameter callback for JSON-P : e.g: http://localhost:8080/schemas/anoCar1/xenoMrna?callback=handler


handler({"database":"anoCar1","table":"xenoMrna","fields":[{"name":"bin","type":"smallint(5) unsigned","key":""},{"name":"matches","type":"int(10) unsigned","key":""},{"name":"misMatches","type":"int(10) unsigned","key":""},{"name":"repMatches","type":"int(10) unsigned","key":""},{"name":"nCount","type":"int(10) unsigned","key":""},{"name":"qNumInsert","type":"int(10) unsigned","key":""},{"name":"qBaseInsert","type":"int(10) unsigned","key":""},{"name":"tNumInsert","type":"int(10) unsigned","key":""},{"name":"tBaseInsert","type":"int(10) unsigned","key":""},{"name":"strand","type":"char(2)","key":""},{"name":"qName","type":"varchar(255)","key":"MUL"},{"name":"qSize","type":"int(10) unsigned","key":""},{"name":"qStart","type":"int(10) unsigned","key":""},{"name":"qEnd","type":"int(10) unsigned","key":""},{"name":"tName","type":"varchar(255)","key":"MUL"},{"name":"tSize","type":"int(10) unsigned","key":""},{"name":"tStart","type":"int(10) unsigned","key":""},{"name":"tEnd","type":"int(10) unsigned","key":""},{"name":"blockCount","type":"int(10) unsigned","key":""},{"name":"blockSizes","type":"longblob","key":""},{"name":"qStarts","type":"longblob","key":""},{"name":"tStarts","type":"longblob","key":""}]});


METHOD: /ucsc/:database/:table/:column/:key


Fetch the rows for a given database.name having a :column==:key . The :column must be indexed. E.g: http://localhost:8080/ucsc/anoCar1/ensGene/name/ENSACAT00000004346


[
{"bin":592,"name":"ENSACAT00000004346","chrom":"scaffold_111","strand":"-","txStart":991522,"txEnd":996396,"cdsStart":991522,"cdsEnd":996396,"exonCount":3,"exonStarts":"991522,995669,995976,","exonEnds":"991954,995972,996396,","score":0,"name2":"PELO","cdsStartStat":"cmpl","cdsEndStat":"cmpl","exonFrames":"0,0,0,"}
]

This method accepts a parameter callback for JSON-P : e.g: http://localhost:8080/ucsc/anoCar1/ensGene/name/ENSACAT00000004346?callback=handler


handler([
{"bin":592,"name":"ENSACAT00000004346","chrom":"scaffold_111","strand":"-","txStart":991522,"txEnd":996396,"cdsStart":991522,"cdsEnd":996396,"exonCount":3,"exonStarts":"991522,995669,995976,","exonEnds":"991954,995972,996396,","score":0,"name2":"PELO","cdsStartStat":"cmpl","cdsEndStat":"cmpl","exonFrames":"0,0,0,"}
]);

METHOD: /ucsc/:database/:table?chrom=?&start=?&end=?




Fetch the rows for a given genomic database.name overlapping the given range. This method uses the UCSC-bin index if it is available; E.g: http://localhost:8080/ucsc/anoCar1/ensGene?chrom=scaffold_111&start=600000&end=900000


[
{"bin":589,"name":"ENSACAT00000003906","chrom":"scaffold_111","strand":"-","txStart":594783,"txEnd":614216,"cdsStart":595000,"cdsEnd":614201,"exonCount":9,"exonStarts":"594783,601291,601744,603640,604745,604865,609139,611740,614097,","exonEnds":"595105,601406,601813,603736,604771,604942,609173,611840,614216,","score":0,"name2":"DPM1","cdsStartStat":"cmpl","cdsEndStat":"cmpl","exonFrames":"0,2,2,2,0,1,0,2,0,"},
{"bin":589,"name":"ENSACAT00000003908","chrom":"scaffold_111","strand":"+","txStart":614382,"txEnd":615600,"cdsStart":614382,"cdsEnd":615600,"exonCount":1,"exonStarts":"614382,","exonEnds":"615600,","score":0,"name2":"MOCS3","cdsStartStat":"incmpl","cdsEndStat":"cmpl","exonFrames":"0,"},
{"bin":589,"name":"ENSACAT00000003918","chrom":"scaffold_111","strand":"-","txStart":638920,"txEnd":642127,"cdsStart":638920,"cdsEnd":642127,"exonCount":2,"exonStarts":"638920,641368,","exonEnds":"639691,642127,","score":0,"name2":"KCNG1","cdsStartStat":"cmpl","cdsEndStat":"cmpl","exonFrames":"0,0,"},
{"bin":591,"name":"ENSACAT00000003920","chrom":"scaffold_111","strand":"+","txStart":814576,"txEnd":826972,"cdsStart":814576,"cdsEnd":826972,"exonCount":3,"exonStarts":"814576,825125,826845,","exonEnds":"814594,825247,826972,","score":0,"name2":"ENSACAG00000003945","cdsStartStat":"incmpl","cdsEndStat":"cmpl","exonFrames":"0,0,2,"},
{"bin":591,"name":"ENSACAT00000004042","chrom":"scaffold_111","strand":"-","txStart":849731,"txEnd":881887,"cdsStart":849731,"cdsEnd":881887,"exonCount":24,"exonStarts":"849731,851343,855421,856165,857842,858090,861054,861943,862949,863773,865029,865639,867414,868216,872220,873601,874396,876850,877105,877711,878919,879681,881320,881738,","exonEnds":"849809,851460,855511,856279,857947,858201,861157,862027,863026,863866,865171,865722,867525,868368,872360,873738,874600,876994,877263,877850,878993,879847,881471,881887,","score":0,"name2":"ITGA2","cdsStartStat":"incmpl","cdsEndStat":"incmpl","exonFrames":"0,0,0,0,0,0,2,2,0,0,2,0,0,1,2,0,0,0,1,0,1,0,2,0,"},
{"bin":591,"name":"ENSACAT00000004050","chrom":"scaffold_111","strand":"-","txStart":883724,"txEnd":897808,"cdsStart":883724,"cdsEnd":897808,"exonCount":5,"exonStarts":"883724,885433,889264,889742,897701,","exonEnds":"883858,885548,889356,889852,897808,","score":0,"name2":"ENSACAG00000004086","cdsStartStat":"incmpl","cdsEndStat":"incmpl","exonFrames":"1,0,1,2,0,"}
]

This method accepts a parameter callback for JSON-P : e.g: http://localhost:8080/ucsc/anoCar1/ensGene?chrom=scaffold_111&start=600000&end=900000&callback=handler


handler([
{"bin":589,"name":"ENSACAT00000003906","chrom":"scaffold_111","strand":"-","txStart":594783,"txEnd":614216,"cdsStart":595000,"cdsEnd":614201,"exonCount":9,"exonStarts":"594783,601291,601744,603640,604745,604865,609139,611740,614097,","exonEnds":"595105,601406,601813,603736,604771,604942,609173,611840,614216,","score":0,"name2":"DPM1","cdsStartStat":"cmpl","cdsEndStat":"cmpl","exonFrames":"0,2,2,2,0,1,0,2,0,"},
{"bin":589,"name":"ENSACAT00000003908","chrom":"scaffold_111","strand":"+","txStart":614382,"txEnd":615600,"cdsStart":614382,"cdsEnd":615600,"exonCount":1,"exonStarts":"614382,","exonEnds":"615600,","score":0,"name2":"MOCS3","cdsStartStat":"incmpl","cdsEndStat":"cmpl","exonFrames":"0,"},
{"bin":589,"name":"ENSACAT00000003918","chrom":"scaffold_111","strand":"-","txStart":638920,"txEnd":642127,"cdsStart":638920,"cdsEnd":642127,"exonCount":2,"exonStarts":"638920,641368,","exonEnds":"639691,642127,","score":0,"name2":"KCNG1","cdsStartStat":"cmpl","cdsEndStat":"cmpl","exonFrames":"0,0,"},
{"bin":591,"name":"ENSACAT00000003920","chrom":"scaffold_111","strand":"+","txStart":814576,"txEnd":826972,"cdsStart":814576,"cdsEnd":826972,"exonCount":3,"exonStarts":"814576,825125,826845,","exonEnds":"814594,825247,826972,","score":0,"name2":"ENSACAG00000003945","cdsStartStat":"incmpl","cdsEndStat":"cmpl","exonFrames":"0,0,2,"},
{"bin":591,"name":"ENSACAT00000004042","chrom":"scaffold_111","strand":"-","txStart":849731,"txEnd":881887,"cdsStart":849731,"cdsEnd":881887,"exonCount":24,"exonStarts":"849731,851343,855421,856165,857842,858090,861054,861943,862949,863773,865029,865639,867414,868216,872220,873601,874396,876850,877105,877711,878919,879681,881320,881738,","exonEnds":"849809,851460,855511,856279,857947,858201,861157,862027,863026,863866,865171,865722,867525,868368,872360,873738,874600,876994,877263,877850,878993,879847,881471,881887,","score":0,"name2":"ITGA2","cdsStartStat":"incmpl","cdsEndStat":"incmpl","exonFrames":"0,0,0,0,0,0,2,2,0,0,2,0,0,1,2,0,0,0,1,0,1,0,2,0,"},
{"bin":591,"name":"ENSACAT00000004050","chrom":"scaffold_111","strand":"-","txStart":883724,"txEnd":897808,"cdsStart":883724,"cdsEnd":897808,"exonCount":5,"exonStarts":"883724,885433,889264,889742,897701,","exonEnds":"883858,885548,889356,889852,897808,","score":0,"name2":"ENSACAG00000004086","cdsStartStat":"incmpl","cdsEndStat":"incmpl","exonFrames":"1,0,1,2,0,"}
]);


That's it,

Pierre

15 May 2014

How I start a bioinformatics project

Phil Ashton tweeted a link to a paper about how to set up a bioinformatics project file hierarchy: " A Quick Guide to Organizing Computational Biology Projects ".

Nick Loman posted his version yesterday : "How I start a bioinformatics project" on http://nickloman.github.io/2014/05/14/how-i-start-a-bioinformatics-project/.

Here is mine (simplified):

  • I start by creating a directory managed by git
  • I create a JSON-based description of my data, including the path to the softwares, to the references
  • I create a git submodule for a project hosting an Apache-velocity template transforming a Makefile from config.json :
  • The Makefile is generated using jsvelocity :It produces the following Makefile:
  • The Makefile is invoked with option -j N(Allow N jobs at once) using GNU-Make or QMake(distributed parallel make, scheduled by Sun Grid Engine)

That's it,

Pierre

12 May 2014

Generating wikipedia semantic links from a pubmed-id

In "Building a biomedical semantic network in Wikipedia with Semantic Wiki Links" (Database . 2012 Mar 20;2012) Benjamin Good & al. introduced the Semantic Wiki Link (SWL):

An SWL is a hyperlink on Wikipedia that allows the editor to explicitly specify the type of relationship between the concept described on the page being edited and the concept that is being linked to (http://en.wikipedia.org/wiki/Template:SWL). These SWLs are implemented using MediaWiki templates.
(...)
any programmer can now write computer programs to parse Wikipedia content for SWLs and import them into third-party tools (e.g. triplestores, etc.)
Example: Phospholamban:
The protein encoded by this gene is found as a pentamer and is a major substrate for the cAMP-dependent protein kinase ({{SWL|type=substrate_for|target=protein kinase A|label=PKA}}) in cardiac muscle.




Using Entrez-Ajax (Loman & al.) and the Wikipedia API, I wrote a HTML+JS interface to accelerate the creation of a semantic SWL wiki-text from a PUBMED-id:


and.. well, that's it,

Pierre

30 January 2014

Parallelizing #RStats using #make

In the current post, I'll show how to use R as the main SHELL of GNU-Make instead of using a classical linux shell like 'bash'. Why would you do this ?

  • awesomeness
  • Make-based workflow management
  • Make-based execution with --jobs. GNU make knows how to execute several recipes at once. Normally, make will execute only one recipe at a time, waiting for it to finish before executing the next. However, the '-j' or '--jobs' option tells make to execute many recipes simultaneously.
The following recipe has been tested with GNU-Make 4.0 and I'm not sure it would world with '<=3.81'.

The only problem is that R doesn't accept a multiline-argument on the command line (see http://stackoverflow.com/questions/21442674) so I created a wrapper 'mockR' that save the argument '-e "code"' into a file and pipe it into R:

(Edit1: A comment from madscientist : Re your script; you can save yourself some wear-and-tear on your disk and avoid the need for temp files and cleanup by just piping the input directly: echo "$R" | R --vanilla --no-readline --quiet . Just a thought. ")

(Edit2: the exit value of 'R' should also be returned by 'mockR'.)

This file is set as executable:
$ chmod u+x ./mockR
In the makefile, we tell 'make' to use 'mockR' instead of '/usr/bin/sh':
SHELL = ./mockR
The R code will be passed to 'mockR' using the argument '-e "code"'
.SHELLFLAGS= -e
We also set 'ONESHELL': "If .ONESHELL is mentioned as a target, then when a target is built all lines of the recipe will be given to a single invocation of the shell rather than each line being invoked separately"
.ONESHELL:

Example 1

We download the table 'knownGene' from the UCSC and we plot a pdf file 'countExons=f(txStart)'. Please, note that the targets are created using some R statements, NOT bash statements:

Now Invoke make


Example 2

Using a the eval and the call function we can make the previous 'Makefile' applicable for all the chromosomes:

Now Invoke make USING TRHEE PARALLEL JOBS





You can now watch the final pdf files:




That's it,
Pierre

Mapping the UCSC/Web-Sequences to a world map.

People at the UCSC have recently released a new track for the GenomeBrowser


"We're pleased to announce the release of the Web Sequences track on the UCSC Genome Browser. This track, produced in collaboration with Microsoft Research, contains the results of a 30-day scan for DNA sequences from over 40 billion different webpages. The sequences were then mapped with Blat to the human genome (...) The data were extracted from a variety of sources including patents, online textbooks, help forums, and any other webpages that contain DNA sequence. In essence, this track displays the Blat alignments of nearly every DNA sequence on the internet!"

I've mapped each genomic location from this track to a country and generated the following (unreadable) picture:

How this picture was generated

  • I've downloaded the data from the UCSC using the Table browser. The data look like this:
    #bin    chrom   chromStart      chromEnd        name    score   strand  thickStart      thickEnd        reserved        blockCount      blockSizes      chromStarts     tSeqTypes     seqIds  seqRanges       publisher       pmid    doi     issn    journal title   firstAuthor     year    impact  classes locus
    585     chr1    14789   15004   3500336380      75              14789   15004   8421504 2       40,35   0,180   g       350033638000000000      0-75                          Tophat, Cufflinks and replicates - Page 2 - SEQanswers  seqanswers.com  0       0               WASH2P,WASH7P
    585     chr1    15017   15590   3500327042      381             15017   15590   8421504 2       326,55  0,518   g       350032704200000008      0-747                        Research Technologies at Indiana University      biomedapp.iu.edu        0       0               WASH7P
    585     chr1    68858   68895   3500020489      37              68858   68895   8421504 1       37      0       g       350002048900000000,350002048900000001   0-36,0-36    Genome mapability - Musings from a PhD candidate davetang.org    0       0               OR4F5
    585     chr1    69170   69479   3500359797      142             69170   69479   8421504 2       76,66   0,243   c       350035979700000000,350035979700000002   0-76,10-76    CRAM compression and TLEN SAM's field - SEQanswers      seqanswers.com  0       0               OR4F5
    585     chr1    70013   70230   3500427570      150             70013   70230   8421504 2       75,75   0,142   g       350042757000000000,350042757000000001   0-75,0-75     Inconsistency with SAM flag output? - SEQanswers        seqanswers.com  0       0               OR4F5
    585     chr1    98860   98888   3500207083      26              98860   98888   8421504 3       5,7,14  0,6,14  g       350020708300000108,350020708300000060,350020708300000239      0-24,0-21,0-21                                          Method For The Simultaneous Determination Of Blood Group And Platelet Antigen Genotypes         .freshpatents.com     0       0               OR4F5
    586     chr1    137603  138008  3500170315      405             137603  138008  8421504 1       405     0       p       350017031500015076,350017031500015074   0-135,0-270  Balding D. (2007) Handbook of Statistical Genetics       www.scribd.com  0       0               OR4F5
    586     chr1    139485  143008  3500419332      1794            139485  143008  8421504 2       65,1729 0,1794  g       350041933200000004,350041933200000000,350041933200000001,350041933200000002,350041933200000003        0-1263,0-1859,0-1852,0-1860,0-576                                               PPT  Evolution by Genome Duplication PowerPoint presentation | free to view   www.powershow.com       0       0               OR4F5
    586     chr1    141535  143008  3500270480      1372            141535  143008  8421504 24      57,60,58,59,61,59,60,59,59,62,61,58,60,58,16,59,59,59,59,57,57,59,58,58 0,61,125,187,250,314,377,441,503,566,631,695,756,819,881,919,981,1044,1107,1170,1230,1291,1353,1415   g       350027048000000003,350027048000000002   0-902,0-525                  Chen-Kung Chou 3-22-2004 www.dls.ym.edu.tw       0       0               OR4F5
  • I want to generate BED file: 'chrom/start/end/country'. The 23rd column contains the URL of the web-sequence. I use the domain of the URL to try to guess the country. The following awk script was used to generate the file:
    BEGIN   {
            FS="[\t]";
            }
    
            {
            country=$23;
            for(;;)
                    {
                    slash=index(country,"/");
                    if(slash==0) break;
                    country=substr(country,1,slash-1);
                    }
            for(;;)
                    {
                    colon=index(country,":");
                    if(colon==0) break;
                    country=substr(country,1,colon-1);
                    }
            if( country ~ /\.$/ ) next;
            if( country ~ /\.com$/ ) next;
            if( country ~ /\.org$/ ) next;
            if( country ~ /\.cat$/ ) next;
            if( country ~ /\.net$/ ) next;
            if( country ~ /\.gov$/ ) next;
            if( country ~ /\.edu$/ ) next;
            if( country ~ /\.name$/ ) next;
            if( country ~ /\.info$/ ) next;
            if( country ~ /\.biz$/ ) next;
            if( country ~ /\.[0-9]+$/ ) next;
            if( index(country,".")==0) next;
            if( index(country," ")!=0) next;
            for(;;)
                    {
                    dot=index(country,".");
                    if(dot==0) break;
                    country=substr(country,dot+1);
                    }
    
                    if( country== "af") {country="afghanistan";}
                    else if( country== "ax") {country="Ålandislands";}
                    else if( country== "al") {country="albania";}
                    else if( country== "dz") {country="algeria";}
                    else if( country== "as") {country="americansamoa";}
                    else if( country== "ad") {country="andorra";}
                    else if( country== "ao") {country="angola";}
                    else if( country== "ai") {country="anguilla";}
                    else if( country== "aq") {country="antarctica";}
                    else if( country== "ag") {country="antiguaandbarbuda";}
                    else if( country== "ar") {country="argentina";}
                    else if( country== "am") {country="armenia";}
                    else if( country== "aw") {country="aruba";}
                    else if( country== "au") {country="australia";}
                    else if( country== "at") {country="austria";}
                    else if( country== "az") {country="azerbaijan";}
                    else if( country== "bs") {country="bahamas";}
                    else if( country== "bh") {country="bahrain";}
                    else if( country== "bd") {country="bangladesh";}
                    else if( country== "bb") {country="barbados";}
                    else if( country== "by") {country="belarus";}
                    else if( country== "be") {country="belgium";}
                    else if( country== "bz") {country="belize";}
                    else if( country== "bj") {country="benin";}
                    else if( country== "bm") {country="bermuda";}
                    else if( country== "bt") {country="bhutan";}
                    else if( country== "bo") {country="bolivia,plurinationalstateof";}
                    else if( country== "bq") {country="bonaire,sinteustatiusandsaba";}
                    else if( country== "ba") {country="bosniaandherzegovina";}
                    else if( country== "bw") {country="botswana";}
                    else if( country== "bv") {country="bouvetisland";}
                    else if( country== "br") {country="brazil";}
                    else if( country== "io") {country="britishindianoceanterritory";}
                    else if( country== "bn") {country="bruneidarussalam";}
                    else if( country== "bg") {country="bulgaria";}
                    else if( country== "bf") {country="burkinafaso";}
                    else if( country== "bi") {country="burundi";}
                    else if( country== "kh") {country="cambodia";}
                    else if( country== "cm") {country="cameroon";}
                    else if( country== "ca") {country="canada";}
                    else if( country== "cv") {country="capeverde";}
                    else if( country== "ky") {country="caymanislands";}
                    else if( country== "cf") {country="centralafricanrepublic";}
                    else if( country== "td") {country="chad";}
                    else if( country== "cl") {country="chile";}
                    else if( country== "cn") {country="china";}
                    else if( country== "cx") {country="christmasisland";}
                    else if( country== "cc") {country="cocos(keeling)islands";}
                    else if( country== "co") {country="colombia";}
                    else if( country== "km") {country="comoros";}
                    else if( country== "cg") {country="congo";}
                    else if( country== "cd") {country="congo,thedemocraticrepublicofthe";}
                    else if( country== "ck") {country="cookislands";}
                    else if( country== "cr") {country="costarica";}
                    else if( country== "ci") {country="cÔted'ivoire";}
                    else if( country== "hr") {country="croatia";}
                    else if( country== "cu") {country="cuba";}
                    else if( country== "cw") {country="curaÇao";}
                    else if( country== "cy") {country="cyprus";}
                    else if( country== "cz") {country="czechrepublic";}
                    else if( country== "dk") {country="denmark";}
                    else if( country== "dj") {country="djibouti";}
                    else if( country== "dm") {country="dominica";}
                    else if( country== "do") {country="dominicanrepublic";}
                    else if( country== "ec") {country="ecuador";}
                    else if( country== "eg") {country="egypt";}
                    else if( country== "sv") {country="elsalvador";}
                    else if( country== "gq") {country="equatorialguinea";}
                    else if( country== "er") {country="eritrea";}
                    else if( country== "ee") {country="estonia";}
                    else if( country== "et") {country="ethiopia";}
                    else if( country== "fk") {country="falklandislands(malvinas)";}
                    else if( country== "fo") {country="faroeislands";}
                    else if( country== "fj") {country="fiji";}
                    else if( country== "fi") {country="finland";}
                    else if( country== "fr") {country="france";}
                    else if( country== "gf") {country="frenchguiana";}
                    else if( country== "pf") {country="frenchpolynesia";}
                    else if( country== "tf") {country="frenchsouthernterritories";}
                    else if( country== "ga") {country="gabon";}
                    else if( country== "gm") {country="gambia";}
                    else if( country== "ge") {country="georgia";}
                    else if( country== "de") {country="germany";}
                    else if( country== "gh") {country="ghana";}
                    else if( country== "gi") {country="gibraltar";}
                    else if( country== "gr") {country="greece";}
                    else if( country== "gl") {country="greenland";}
                    else if( country== "gd") {country="grenada";}
                    else if( country== "gp") {country="guadeloupe";}
                    else if( country== "gu") {country="guam";}
                    else if( country== "gt") {country="guatemala";}
                    else if( country== "gg") {country="guernsey";}
                    else if( country== "gn") {country="guinea";}
                    else if( country== "gw") {country="guinea-bissau";}
                    else if( country== "gy") {country="guyana";}
                    else if( country== "ht") {country="haiti";}
                    else if( country== "hm") {country="heardislandandmcdonaldislands";}
                    else if( country== "va") {country="holysee(vaticancitystate)";}
                    else if( country== "hn") {country="honduras";}
                    else if( country== "hk") {country="china";}
                    else if( country== "hu") {country="hungary";}
                    else if( country== "is") {country="iceland";}
                    else if( country== "in") {country="india";}
                    else if( country== "id") {country="indonesia";}
                    else if( country== "ir") {country="iran";}
                    else if( country== "iq") {country="iraq";}
                    else if( country== "ie") {country="ireland";}
                    else if( country== "im") {country="isleofman";}
                    else if( country== "il") {country="israel";}
                    else if( country== "it") {country="italy";}
                    else if( country== "jm") {country="jamaica";}
                    else if( country== "jp") {country="japan";}
                    else if( country== "je") {country="jersey";}
                    else if( country== "jo") {country="jordan";}
                    else if( country== "kz") {country="kazakhstan";}
                    else if( country== "ke") {country="kenya";}
                    else if( country== "ki") {country="kiribati";}
                    else if( country== "kp") {country="northkorea";}
                    else if( country== "kr") {country="southkorea";}
                    else if( country== "kw") {country="kuwait";}
                    else if( country== "kg") {country="kyrgyzstan";}
                    else if( country== "la") {country="laopeople'sdemocraticrepublic";}
                    else if( country== "lv") {country="latvia";}
                    else if( country== "lb") {country="lebanon";}
                    else if( country== "ls") {country="lesotho";}
                    else if( country== "lr") {country="liberia";}
                    else if( country== "ly") {country="libya";}
                    else if( country== "li") {country="liechtenstein";}
                    else if( country== "lt") {country="lithuania";}
                    else if( country== "lu") {country="luxembourg";}
                    else if( country== "mo") {country="macao";}
                    else if( country== "mk") {country="macedonia,theformeryugoslavrepublicof";}
                    else if( country== "mg") {country="madagascar";}
                    else if( country== "mw") {country="malawi";}
                    else if( country== "my") {country="malaysia";}
                    else if( country== "mv") {country="maldives";}
                    else if( country== "ml") {country="mali";}
                    else if( country== "mt") {country="malta";}
                    else if( country== "mh") {country="marshallislands";}
                    else if( country== "mq") {country="martinique";}
                    else if( country== "mr") {country="mauritania";}
                    else if( country== "mu") {country="mauritius";}
                    else if( country== "yt") {country="mayotte";}
                    else if( country== "mx") {country="mexico";}
                    else if( country== "fm") {country="micronesia,federatedstatesof";}
                    else if( country== "md") {country="moldova,republicof";}
                    else if( country== "mc") {country="monaco";}
                    else if( country== "mn") {country="mongolia";}
                    else if( country== "me") {country="montenegro";}
                    else if( country== "ms") {country="montserrat";}
                    else if( country== "ma") {country="morocco";}
                    else if( country== "mz") {country="mozambique";}
                    else if( country== "mm") {country="myanmar";}
                    else if( country== "na") {country="namibia";}
                    else if( country== "nr") {country="nauru";}
                    else if( country== "np") {country="nepal";}
                    else if( country== "nl") {country="netherlands";}
                    else if( country== "nc") {country="newcaledonia";}
                    else if( country== "nz") {country="newzealand";}
                    else if( country== "ni") {country="nicaragua";}
                    else if( country== "ne") {country="niger";}
                    else if( country== "ng") {country="nigeria";}
                    else if( country== "nu") {country="niue";}
                    else if( country== "nf") {country="norfolkisland";}
                    else if( country== "mp") {country="northernmarianaislands";}
                    else if( country== "no") {country="norway";}
                    else if( country== "om") {country="oman";}
                    else if( country== "pk") {country="pakistan";}
                    else if( country== "pw") {country="palau";}
                    else if( country== "ps") {country="palestine,stateof";}
                    else if( country== "pa") {country="panama";}
                    else if( country== "pg") {country="papuanewguinea";}
                    else if( country== "py") {country="paraguay";}
                    else if( country== "pe") {country="peru";}
                    else if( country== "ph") {country="philippines";}
                    else if( country== "pn") {country="pitcairn";}
                    else if( country== "pl") {country="poland";}
                    else if( country== "pt") {country="portugal";}
                    else if( country== "pr") {country="puertorico";}
                    else if( country== "qa") {country="qatar";}
                    else if( country== "re") {country="france";}
                    else if( country== "ro") {country="romania";}
                    else if( country== "ru") {country="russia";}
                    else if( country== "rw") {country="rwanda";}
                    else if( country== "bl") {country="saintbarthÉlemy";}
                    else if( country== "sh") {country="sainthelena,ascensionandtristandacunha";}
                    else if( country== "kn") {country="saintkittsandnevis";}
                    else if( country== "lc") {country="saintlucia";}
                    else if( country== "mf") {country="saintmartin(frenchpart)";}
                    else if( country== "pm") {country="saintpierreandmiquelon";}
                    else if( country== "vc") {country="saintvincentandthegrenadines";}
                    else if( country== "ws") {country="samoa";}
                    else if( country== "sm") {country="sanmarino";}
                    else if( country== "st") {country="saotomeandprincipe";}
                    else if( country== "sa") {country="saudiarabia";}
                    else if( country== "sn") {country="senegal";}
                    else if( country== "rs") {country="serbia";}
                    else if( country== "sc") {country="seychelles";}
                    else if( country== "sl") {country="sierraleone";}
                    else if( country== "sg") {country="singapore";}
                    else if( country== "sx") {country="sintmaarten(dutchpart)";}
                    else if( country== "sk") {country="slovakia";}
                    else if( country== "si") {country="slovenia";}
                    else if( country== "sb") {country="solomonislands";}
                    else if( country== "so") {country="somalia";}
                    else if( country== "za") {country="southafrica";}
                    else if( country== "gs") {country="southgeorgiaandthesouthsandwichislands";}
                    else if( country== "ss") {country="southsudan";}
                    else if( country== "es") {country="spain";}
                    else if( country== "lk") {country="srilanka";}
                    else if( country== "sd") {country="sudan";}
                    else if( country== "sr") {country="suriname";}
                    else if( country== "sj") {country="svalbardandjanmayen";}
                    else if( country== "sz") {country="swaziland";}
                    else if( country== "se") {country="sweden";}
                    else if( country== "ch") {country="switzerland";}
                    else if( country== "sy") {country="syrianarabrepublic";}
                    else if( country== "tw") {country="taiwan";}
                    else if( country== "tj") {country="tajikistan";}
                    else if( country== "tz") {country="tanzania";}
                    else if( country== "th") {country="thailand";}
                    else if( country== "tl") {country="timor-leste";}
                    else if( country== "tg") {country="togo";}
                    else if( country== "tk") {country="tokelau";}
                    else if( country== "to") {country="tonga";}
                    else if( country== "tt") {country="trinidadandtobago";}
                    else if( country== "tn") {country="tunisia";}
                    else if( country== "tr") {country="turkey";}
                    else if( country== "tm") {country="turkmenistan";}
                    else if( country== "tc") {country="turksandcaicosislands";}
                    else if( country== "tv") {country="tuvalu";}
                    else if( country== "ug") {country="uganda";}
                    else if( country== "ua") {country="ukraine";}
                    else if( country== "ae") {country="unitedarabemirates";}
                    else if( country== "gb") {country="unitedkingdom";}
                    else if( country== "uk") {country="unitedkingdom";}
                    else if( country== "us") {country="USA";}
                    else if( country== "um") {country="unitedstatesminoroutlyingislands";}
                    else if( country== "uy") {country="uruguay";}
                    else if( country== "uz") {country="uzbekistan";}
                    else if( country== "vu") {country="vanuatu";}
                    else if( country== "ve") {country="venezuela";}
                    else if( country== "vn") {country="vietnam";}
                    else if( country== "vg") {country="virginislands,british";}
                    else if( country== "vi") {country="virginislands,u.s.";}
                    else if( country== "wf") {country="wallisandfutuna";}
                    else if( country== "eh") {country="westernsahara";}
                    else if( country== "ye") {country="yemen";}
                    else if( country== "zm") {country="zambia";}
                    else if( country== "zw") {country="zimbabwe";}
                    else { next;}
    
            printf("%s\t%s\t%s\t%s\n",$2,$3,$4,country);
            }
    
  • For the world map, I've used a SVG-vectorial map from wikipedia: https://commons.wikimedia.org/wiki/File:World_V2.0.svg.

    The coordinates of the boundaries of each country are defined in a SVG 'path' element:
    <?xml version="1.0" encoding="UTF-8" standalone="no"?>
    <!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 20010904//EN" "http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/
    <svg xmlns="http://www.w3.org/2000/svg" width="8.88889in" height="4.44444in" viewBox="0 0 800 400">
      <path id="Taiwan" fill="none" stroke="black" stroke-width="1" d="M 668.85,151.22  C 668.98,150.71 ...
      <path id="Estonia" fill="none" stroke="black" stroke-width="1" d="M 460.75,68.26  C 459.95,68.11 4 ...
      <path id="Latvia" fill="none" stroke="black" stroke-width="1" d="M 461.23,72.27  C 460.75,72.20 46 ...
      <path id="Lithuania" fill="none" stroke="black" stroke-width="1" d="M 452.39,79.42  C 452.67,79.72 ...
      <path id="Byelarus" fill="none" stroke="black" stroke-width="1" d="M 453.57,81.92  C 453.87,82.37  ...
      <path id="Ukraine" fill="none" stroke="black" stroke-width="1" d="M 453.09,85.95  C 453.43,86.30 4 ...
      <path id="Moldova" fill="none" stroke="black" stroke-width="1" d="M 460.57,93.00  C 461.00,93.70 4 ...
      <path id="Syria" fill="none" stroke="black" stroke-width="1" d="M 480.33,127.61  C 481.03,127.90 4 ...
      <path id="Turkey" fill="none" stroke="black" stroke-width="1" d="M 499.47,116.91  C 499.31,116.32  ...
      <path id="Kuwait" fill="none" stroke="black" stroke-width="1" d="M 505.26,133.84  C 504.97,134.56  ...
      <path id="Saudi Arabia" fill="none" stroke="black" stroke-width="1" d="M 495.83,163.75  C 496.31,1 ...
      <path id="United Arab Emirates" fill="none" stroke="black" stroke-width="1" d="M 516.03,150.12  C  ...
      <path id="Yemen" fill="none" stroke="black" stroke-width="1" d="M 517.68,161.79  C 517.01,160.50 5 ...
      <path id="Slovenia" fill="none" stroke="black" stroke-width="1" d="M 430.55,97.07  C 429.62,97.36  ...
      <path id="Croatia" fill="none" stroke="black" stroke-width="1" d="M 439.09,103.97  C 439.01,103.46 ...
      <path id="Bosnia and Herzegovina" fill="none" stroke="black" stroke-width="1" d="M 440.44,105.02   ...
    (...)
  • I've joined the data using a custom java program (available on github at: https://github.com/lindenb/jvarkit/wiki/WorldMapGenome ). The program transforms the 'path' elements to a GeneralPath
    $  cat map.bed |\
         java -jar dist/worldmapgenome.jar \
         -u World_V2.0.svg \
         -w 2000 -o ~/ouput.jpg \
         -R hg19.fasta
That's it,
Pierre