Split and recombine data

Question

[ersan]

I have a data like that. I want to remove last splitted part and merge them.

aa1|bb1|cc1|dd1|ee1|ff1 ~ aa2|bb2|cc2|dd2|ee2|ff2
zz1|yy1|xx1|vv1|uu1|tt1 ~ zz2|yy2|xx2|vv2|uu2|tt2

output data:

aa1,bb1,cc1,dd1,ee1 </br> aa2,bb2,cc2,dd2,ee
zz1,yy1,xx1,vv1,uu1 </br> zz2,yy2,xx2,vv2,uu2

---

Bioinformatics context - Orphanet:

Input:

590|Congenital myasthenic syndrome|1-9 / 1 000 000|Autosomal dominant<br>or&nbsp;Autosomal recessive|Infancy<br>Neonatal|254190 254210 254300 601462 603034 605809 608930 608931 610542 614198 614750 615120 616040 616227 616228 616304 616313 616314 616321 616322 616323 616324 616325 616326 616330 616720 617143~98913|Postsynaptic congenital myasthenic syndromes|-|-|-|254300 601462 605809 608930 608931 614198 615120 616304 616313 616314 616321 616322 616323 616324 616325 616326 616720~98914|Presynaptic congenital myasthenic syndromes|-|Autosomal dominant<br>or&nbsp;Autosomal recessive|-|254210 615120 616040 616330 616720 617143

Output:

https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=590" target="_blank">Congenital myasthenic syndrome [1-9 / 1 000 000] [Infancy-Neonatal]

https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=98913" target="_blank">Postsynaptic congenital myasthenic syndromes [-] [-]

https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=98914" target="_blank">Presynaptic congenital myasthenic syndromes [-] [-]

[Ram]

Side note: </br> is not a valid HTML tag, <br> is. Like <img> and <hr>, <br> does its functionality all by itself and does not need a closing tag. Even <br /> is XHTML and no longer relevant.

Answer 1

[zx8754]

Split on "~", then split on "|", and paste all bits together:

Note: This website is rendering the output wrong, the output you will see on your R console might be different. But the solution is still valid, you might want to adjust rows where I am pasting the bits together to match your exact required output.

x <- "590|Congenital myasthenic syndrome|1-9 / 1 000 000|Autosomal dominant
or Autosomal recessive|Infancy
Neonatal|254190 254210 254300 601462 603034 605809 608930 608931 610542 614198 614750 615120 616040 616227 616228 616304 616313 616314 616321 616322 616323 616324 616325 616326 616330 616720 617143~98913|Postsynaptic congenital myasthenic syndromes|-|-|-|254300 601462 605809 608930 608931 614198 615120 616304 616313 616314 616321 616322 616323 616324 616325 616326 616720~98914|Presynaptic congenital myasthenic syndromes|-|Autosomal dominant
or Autosomal recessive|-|254210 615120 616040 616330 616720 617143"


sapply(strsplit(x, "~", fixed = TRUE)[[ 1 ]], function(i){
  d <- strsplit(i, "|", fixed = TRUE)[[ 1 ]]
  paste0('https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=', d[ 1 ],
         'target="_blank">', d[ 2 ],
         ' [', d[ 3 ],
         '] [', d[ 5 ],
         ']')
}, USE.NAMES = FALSE)

[1] "https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=590target=\"_blank\">Congenital myasthenic syndrome [1-9 / 1 000 000] [Infancy
Neonatal]"
[2] "https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=98913target=\"_blank\">Postsynaptic congenital myasthenic syndromes [-] [-]"                
[3] "https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=98914target=\"_blank\">Presynaptic congenital myasthenic syndromes [-] [-]"

Answer 2

[cpad0112]

output:

$ sed 's/\(.*\)|\w\+\s~\s\(.*\)|.*/\1 \<\/br\> \2/g;s/|/,/g' test.txt 

aa1,bb1,cc1,dd1,ee1 </br> aa2,bb2,cc2,dd2,ee2
zz1,yy1,xx1,vv1,uu1 </br> zz2,yy2,xx2,vv2,uu2

input:

$ cat test.txt 

aa1|bb1|cc1|dd1|ee1|ff1 ~ aa2|bb2|cc2|dd2|ee2|ff2
zz1|yy1|xx1|vv1|uu1|tt1 ~ zz2|yy2|xx2|vv2|uu2|tt2

for URL:

output:

$ sed 's/\~/\n/g;s/|/\t/g' file.txt | cut -f1,2 | sed 's/\(.*\)\t\(.*\)/https\:\/\/www.orpha.net\/consor\/cgi-bin\/OC_Exp\.php\?lng=EN\&Expert\=\1" target="_blank">\2 \[-\]\[-\]/g'

https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=590" target="_blank">Congenital myasthenic syndrome [-][-]
https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=98913" target="_blank">Postsynaptic congenital myasthenic syndromes [-][-]
https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=98914" target="_blank">Presynaptic congenital myasthenic syndromes [-][-]

input;

$ cat file.txt 

590|Congenital myasthenic syndrome|1-9 / 1 000 000|Autosomal dominant<br>or&nbsp;Autosomal recessive|Infancy<br>Neonatal|254190 254210 254300 601462 603034 605809 608930 608931 610542 614198 614750 615120 616040 616227 616228 616304 616313 616314 616321 616322 616323 616324 616325 616326 616330 616720 617143~98913|Postsynaptic congenital myasthenic syndromes|-|-|-|254300 601462 605809 608930 608931 614198 615120 616304 616313 616314 616321 616322 616323 616324 616325 616326 616720~98914|Presynaptic congenital myasthenic syndromes|-|Autosomal dominant<br>or&nbsp;Autosomal recessive|-|254210 615120 616040 616330 616720 617143