Hi all, I get an issue when I want to replace multiple space by a tab in a file (in other word convert the file in a table with separator to easily import in excel). Here is the file (Basically, there are 5 columns separated by two or more spaces):
lcl|tetur19g00650 length:863 (mRNA) (E75) (Ecdysone-induced pro... 132 2e-32
lcl|tetur03g08440 length:544 (mRNA) (HR3) (Hormone Receptor 3) 85.1 5e-18
lcl|tetur04g01460 length:396 (mRNA) (SVP) (Seven Up) 66.6 1e-12
lcl|tetur07g00140 length:1063 (mRNA) (HR4) (Hormone Receptor 4) 63.5 1e-11
lcl|tetur10g04690 length:854 (mRNA) (HR38 (1)) (Hormone Recepto... 61.6 5e-11
lcl|tetur08g06490 length:645 (mRNA) (FTZ-F1) (Fushi tarazu - Fa... 61.2 6e-11
lcl|tetur01g11050 length:726 (mRNA) (n/a) (Zinc finger, nuclear... 60.8 9e-11
lcl|tetur01g11040 length:726 (mRNA) (NR2E3) (Zinc finger, nucle... 60.8 9e-11
lcl|tetur01g09240 length:431 (mRNA) (RXR (2)) (Retinoid X Recep... 60.1 1e-10
lcl|tetur10g04710 length:867 (mRNA) (HR38 (2)) (Hormone Recepto... 59.7 2e-10
lcl|tetur34g00430 length:561 (mRNA) (kni) (Hypothetical knrl) (... 57.4 1e-09
lcl|tetur03g02550 length:497 (mRNA) (PNR-like) (Photocell recep... 57.0 1e-09
lcl|tetur31g01930 length:497 (mRNA) (RXR (1)) (Retinoid X Recep... 56.6 1e-09
lcl|tetur05g04280 length:499 (mRNA) (HNF4) (Hepatocyte Nuclear ... 56.6 2e-09
lcl|tetur01g07700 length:338 (mRNA) (HR83-like) (Possibly HR83-... 52.0 4e-08
lcl|tetur01g02690 length:576 (mRNA) (dissatisfaction) (dissatis... 51.6 6e-08
lcl|tetur08g01210 length:249 (mRNA) (Tll) (Tailless) 51.2 7e-08
lcl|tetur11g04570 length:901 (mRNA) (HR39) (Hormone receptor-li... 47.4 9e-07
lcl|tetur28g00490 length:370 (mRNA) (ERR) (Estrogen-related Rec... 47.0 1e-06
lcl|tetur11g01960 length:567 (mRNA) (HR96-like g) (HR96-like nu... 45.8 2e-06
lcl|tetur01g15140 length:430 (mRNA) (EcR) (Ecdysone Receptor) 44.7 6e-06
lcl|tetur01g07820 length:564 (mRNA) (HR96-like d) (HR96-like nu... 42.7 2e-05
lcl|tetur34g00750 length:579 (mRNA) (HR96-like a) (HR96-like nu... 42.7 3e-05
lcl|tetur30g01210 length:669 (mRNA) (HR96-like b) (HR96-like nu... 39.3 2e-04
lcl|tetur36g00260 length:501 (mRNA) (HR96-like h) (HR96-like nu... 39.3 3e-04
lcl|tetur20g01820 length:499 (mRNA) (HR96-like e) (HR96-like nu... 38.9 3e-04
lcl|tetur04g03100 length:490 (mRNA) (HR96-like f) (HR96-like nu... 38.9 3e-04
lcl|tetur17g03630 length:483 (mRNA) (HR96-like c) (HR96-like nu... 38.5 4e-04
lcl|tetur07g04810 length:311 (mRNA) (E78) (Ecdysone-induced pro... 33.9 0.012
I use this command line but nothing happens (I got a new file but with the same space-separator):
sed 's/ \+ /\t/g' inputfile > outputfile
Do you have some idea? Thank you very much!
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julien-le.roy •
You're running that sed command incorrectly for what you want to do. It should just be:
sed 's/ \+/\t/g' inputfile > outputfile
Thank you, It still not working I don't know why... I'm working on mac but i'm not sure this is an issue?
On Mac, it would just be this:
sed -E $'s/[[:blank:]]+/\t/g' inputfile
However, I see your issue. Even the spaces in the gene descriptions will change.
Are you sure that using a rule whereby only 2 or more spaces combined are changed is valid?
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Thanks! It's much better!
for better readability , use
sed 's/\s\s\+/\t/g'input (for two or more spaces). However in one of the columns, i see text being separated by spaces. Make sure that you have uniform space between columns, not within column.Thank you for your reply, actually when there are 2 or more space I would like to replace them by a tab. But when there is only 1 space let it like that. I hope I'm clear