Split and recombine data
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 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 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 [-] [-]
2 answers
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 [-] [-]"
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 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 Autosomal recessive|-|254210 615120 616040 616330 616720 617143
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Please explain how this is relevant to bioinformatics.
This is relevant with Orphanet. I have an example data like
I want to this data, I want to remove last seperated data.
change to :
You should edit your post and add the content from your comments there.
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.