UNIX for Dummies Questions & Answers

$ head infile.txt | od -x -c
0000000 413e 756c 6159 0935 4953 454e 2f31 5337
> A l u Y a 5 \t S I N E 1 / 7 S
0000020 094c 6f48 6f6d 7320 7061 6569 736e 670a
L \t H o m o s a p i e n s \n g
0000040 6367 6763 6767 6763 6763 7467 6767 7463
g c c g g g c g c g g t g g c t
0000060 6163 6763 6363 6774 6174 7461 6363 6163
c a c g c c t g t a a t c c c a
0000100 6367 6361 7474 6774 6767 6761 6367 6763
g c a c t t t g g g a g g c c g
0000120 6761 6367 6767 6367 6767 7461 6163 6763
a g g c g g g c g g a t c a c g
0000140 6761 7467 0a63 6761 6167 6167 6374 6167
a g g t c \n a g g a g a t c g a
0000160 6167 6363 7461 6363 6763 6367 6174 6161
g a c c a t c c c g g c t a a a
0000200 6361 6767 6774 6161 6361 6363 6763 6374
a c g g t g a a a c c c c g t c
0000220 6374 6174 7463 6161 6161 7461 6361 6161
t c t a c t a a a a a t a c a a
0000240 6161 6161 7474 6761 6363 6767 3e0a 6c41
a a a a t t a g c c g g \n > A l
0000260 5975 3862 5309 4e49 3145 372f 4c53 4809
u Y b 8 \t S I N E 1 / 7 S L \t H
0000300 6d6f 206f 6173 6970 6e65 0a73 6767 6363
o m o s a p i e n s \n g g c c
0000320 6767 6367 6367 6767 6774 6367 6374 6361
g g g c g c g g t g g c t c a c
0000340 6367 7463 7467 6161 6374 6363 6761 6163
g c c t g t a a t c c c a g c a
0000360 7463 7474 6767 6167 6767 6363 6167 6767
c t t t g g g a g g c c g a g g
0000400 6763 6767 6774 6167 6374 7461 6167 6767
c g g g t g g a t c a t g a g g
0000420 6374 740a 6363 7467 7463 6163 3e0a 6c41
t c \n t c c g t c t c a \n > A l
0000440 5975 3962 5309 4e49 3145 372f 4c53 4809
u Y b 9 \t S I N E 1 / 7 S L \t H
0000460 6d6f 206f 6173 6970 6e65 0a73 6767 6363
o m o s a p i e n s \n g g c c
0000500 6767 6367 6367 6767 6774 6367 6374 6361
g g g c g c g g t g g c t c a c
0000520 6367 7463 7467 6161 6374 6363 6761 6163
g c c t g t a a t c c c a g c a
0000540 7463 7474 6767 6167 6767 6363 6167 6767
c t t t g g g a g g c c g a g g
0000560 6763 6767 6774 6167 6374 7461 6167 6767
c g g g t g g a t c a t g a g g
0000600 6374 000a
t c \n
0000603

Thanks for posting the bit of data. Base on the original output of what did/didn't get replaced, the sed is not replacing the tabs. The whitespace in the file is just tabs and spaces (nothing that might have been suppressed during printing etc.)

The problem lies with how the command is being interpreted, which seems odd since it works for me and apparently several other people.

Rather than sed, try this command:

Code:

awk  '/^>/ { gsub( "[ \t]", "_", $0 ); } { print; }' your-file-name

Maybe it's the implementation of sed in your environment. If this doesn't work Im out of guesses.

it is much better now; I need to replace '/' by '_' also:

Code:

$awk  '/^>/ { gsub( "[ \t]", "_", $0 ); } { print; }' infile.txt 
>AluYa5_SINE1/7SL_Homo_sapiens
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggcggatcacgaggtc
aggagatcgagaccatcccggctaaaacggtgaaaccccgtctctactaaaaatacaaaaaattagccgg
>AluYb8_SINE1/7SL_Homo_sapiens
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtc
tccgtctca
>AluYb9_SINE1/7SL_Homo_sapiens
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtc

thank you very much

I think you've probably figured it out, but for the sake of completeness, to also replace the / with '_' just add a slant (/) to the class of characters:

Code:

awk '  /^>/ { gsub( "[ /\t]", "_", $0 ); } { print; }

Glad it worked.

Code:

awk '/>/{gsub(/ +/,"_");gsub(/\t+/,"_");gsub(/\//,"_");gsub(/_+/,"_")}1' infile