Thank you! Your answer is very much appreciated
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Changing file name with sed command
Hi all. I need a little bit of help. I have a list of files in a folder, they look like this:
H3K4me1/Cell-Line=S2-DRSC#Developmental-Stage=Late-Embryonic-stage#Tissue=Embryo-derived-cell-line/ChIP-chip/Rep-1//Dmel_r5.32/modENCODE_304.gff3
H3K4me2/Cell-Line=S2-DRSC#Developmental-Stage=Late-Embryonic-stage#Tissue=Embryo-derived-cell-line/ChIP-chip/Rep-1//Dmel_r5.32/modENCODE_965.gff3
H3K4me3/Cell-Line=S2-DRSC#Developmental-Stage=Late-Embryonic-stage#Tissue=Embryo-derived-cell-line/ChIP-chip/Rep-1//Dmel_r5.32/modENCODE_3761.gff3
H3K9ac/Cell-Line=S2-DRSC#Developmental-Stage=Late-Embryonic-stage#Tissue=Embryo-derived-cell-line/ChIP-chip/Rep-1//Dmel_r5.32/modENCODE_3765.gff3
I would like to change their name with sed command, so the final name would be like this:
H3K4me1_modENCODE_304.gff3
H3K4me2_modENCODE_965.gff3
H3K4me3_modENCODE_3761.gff3
H3K9ac_modENCODE_3765.gff3
I know i can play with sed s and the / but I don't manage to get it to work. I would extremely appreciate if you explain a bit the code you give as an answer.
Thank you in advance! Best wishes,
Jordi
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1 answer
This is all you need in terms of an expression:
sed 's|/.*/|_|gi'
e.g.
$ echo "H3K4me1/Cell-Line=S2-DRSC#Developmental-Stage=Late-Embryonic-stage#Tissue=Embryo-derived-cell-line/ChIP-chip/Rep-1//Dmel_r5.32/modENCODE_304.gff3" | sed 's|/.*/|_|gi'
H3K4me1_modENCODE_304.gff3
Pro tip, use that regular expression with the rename program.
Explained:
s = substitute
| = sed delimiter so as to avoid confusion with the more traditional /
/ = Match the first forward slash you find
.* = followed by any character, any number of times
/ = until you meet another /.
|_| = replace all the previously matched stuff with an underscore.
gi = globally, and case insensitive (you don't strictly need these, I include them as force of habit).
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every time you put a '#' or a '=' in a filename, god kills a kitten.
got them named like this from modENCODE page, but thanks for the information, never will dare to do it (poor kittens!)
Just be a little cautious with all the
/'s in those names. That'll look like a directory structure to bash.e.g.
touch 'H3K4me1/Cell-Line=S2-DRSC#Developmental-Stage=Late-Embryonic-stage#Tissue=Embryo-derived-cell-line/ChIP-chip/Rep-1//Dmel_r5.32/modENCODE_304.gff3'fails miserably, even when hard quoted.+1 Pierre
Then we have the culprit for wars and famines: spaces in filenames.