jvarkit

PubmedCodingLanguages

Last commit

Programming language use distribution from recent programs / articles

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar pubmedcodinglang  [options] Files

Usage: pubmedcodinglang [options] Files
  Options:
    -c, --common
      [20180302] only common languages. What is a 'common' language ? well .. 
      it's subjective...
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

pubmed
xml
code
programming

Creation Date

20170404

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/pubmed/PubmedCodingLanguages.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/pubmed/PubmedCodingLanguagesTest.java

Contribute

Issue Tracker: http://github.com/lindenb/jvarkit/issues
Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite pubmedcodinglang ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Example

$ java -jar dist/pubmeddump.jar 'Bioinformatics 2017' | java -jar dist/pubmedcodinglang.jar

(...)
28464826	java	microTaboo: a general and practical solution to the k-disjoint problem.	2017	, running [java] 7 and hig
28453684	python	MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform.	2017	eloped in [python], using r 
28453672	python	Primerize-2D: automated primer design for RNA multidimensional chemical mapping.	2017	and-alone [python] package f
28449031	python	RNAblueprint: Flexible multiple target nucleic acid sequence design.	2017	ritten in [python] to demons
28444126	ruby	CImbinator: A web-based tool for drug synergy analysis in small- and large-scale datasets.	2017	ritten in [ruby] and r. it
28437135	python	D3GB: An Interactive Genome Browser for R, Python, and WordPress.	2017	ackage, a [python] module, a
28431529	python	HirBin: high-resolution identification of differentially abundant functions in metagenomes.	2017	nted as a [python] package a
28430977	java	Deep Mining Heterogeneous Networks of Biomedical Linked Data to Predict Novel Drug-Target Associations.	2017	eloped in [java] and it is
28415074	python	NaviCom: a web application to create interactive molecular network portraits using multi-level omics data.	2017	avicom, a [python] package a

Plotting:

cut -f2,4 output.txt  | sort | uniq -c |\
awk '{printf("%s\t%s\t%s\n",$3,$2,$1);}' | ./yxv2table -n 0 | grep -v '^null' | grep -v '^     ' | sed 's/^#/Year/' > table.txt && \
gnuplot script.gnuplot

set terminal png size 2000,1500;
set output "output.png"
set title "Bioinformatics/language"
set key invert reverse Left outside
set key autotitle columnheader
set yrange [0:]
set auto x
unset xtics
set xlabel "Year"
set ylabel "Count"
set xtics nomirror rotate by -45 scale 0
set style data histogram
set style histogram rowstacked
set style fill solid border -1
set boxwidth 0.75
N=`awk 'NR==1 {print NF}' table.txt`
plot 'table.txt' using 2:xtic(1), for [i=3:N] '' using i;