error of read.table when spaces are present in columns, (" (1 of many)" mention cases)

[sebriq]

Error of read.table in server.R; due to the presence of spaces in upstream_gene_symbol and as_gene_symbol columns; where and when " (1 of many)" mention is added.

procedure to find the error's cause.

Rscript app.R -c ~/Bureau/projets/RegenLink/2018/DiffContigsInfos.tsv -s ~/Bureau/projets/RegenLink/2018/sample_conditions_full.tsv

Listening on http://0.0.0.0:8080
Warning: Error in scan: la ligne 125 n'avait pas 57 éléments
55: scan
54: read.table
53: loadContigsfile [/home/seb/Bureau/projets/RegenLink/2018/dekupl-viewer/src/server.R#11]
52: server [/home/seb/Bureau/projets/RegenLink/2018/dekupl-viewer/src/server.R#22]
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
la ligne 125 n'avait pas 57 éléments

cat ~/Bureau/projets/RegenLink/2018/DiffContigsInfos.tsv | sed -e 's/(//' | sed -e 's/)//' > DiffContigTest.tsv # remove first double parenthesis

Warning: Error in scan: la ligne 125 n'avait pas 57 éléments
55: scan
54: read.table
53: loadContigsfile [/home/seb/Bureau/projets/RegenLink/2018/dekupl-viewer/src/server.R#11]
52: server [/home/seb/Bureau/projets/RegenLink/2018/dekupl-viewer/src/server.R#22]
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
la ligne 125 n'avait pas 57 éléments

-> Not due to the parenthesis itself

cat ~/Bureau/projets/RegenLink/2018/DiffContigsInfos.tsv | sed -e 's/ (1 of many)/_(1_of_many)/' > DiffContigTest.tsv # remove all spaces

~/Bureau/projets/RegenLink/2018/dekupl-viewer/src$ Rscript app.R -c ./DiffContigTest.tsv -s ~/Bureau/projets/RegenLink/2018/sample_conditions_full.tsv

Warning: Error in scan: la ligne 2543 n'avait pas 57 éléments
55: scan
54: read.table
53: loadContigsfile [/home/seb/Bureau/projets/RegenLink/2018/dekupl-viewer/src/server.R#11]
52: server [/home/seb/Bureau/projets/RegenLink/2018/dekupl-viewer/src/server.R#22]
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
la ligne 2543 n'avait pas 57 éléments

-> report the error to line 2543 containing the next " (1 of many)" mention.

-> so the error seems to be due to read.table which doesn't like the spaces in a tsv without quotes.

The simpler solution is to add "sep = "\t"" to the read.table function.
This correction seems to work in my case.