Search Results

Hi Xterra,
Maybe something like:
awk -v genes="gene-a gene-b" \
-v lengths="3 6" \
-v strings="GCATGAAAACATACA TTTCCAGAAATTGT" '
BEGIN { nString = split(strings, String)
split(lengths,...

It was interesting to try to implement this algorithm on the sed
#!/bin/sed -nrf
2~4 h
4~4 {
H;x
s/(.*GCATGAAAACATACA.{3})(.*)/\1\r\2/
}
/\r/ {
:1
s/^.(.{2}[^\r].*)/\1/
T2...

Making a few wild guesses... If the output you're trying to produce is:
Codon: AAC Quality Score: ,ED
Codon: TCCAAG Quality Score: G7DCGG
Codon: AAC Quality Score: GCC
Codon: TCCAAG Quality...

This is probably easier to read and produces the same output:
awk '
BEGIN { String = "GCATGAAAACATACA"
StringLen = length(String)
}
/^@/ { getline CodonLine
getline
getline QualityLine...

There are more efficient ways to do this, but this seems to do what you want:
awk '
BEGIN { String = "GCATGAAAACATACA"
StringLen = length(String)
}
/^@/ { matchline = NR + 1
qualityline = NR...

It might be worthwhile to mention that this code should be run with
- the -r flag removed
- the -n flag set
- the -fscriptname option added:


sed -nfscriptname datafile

Yes, true - but this works only with GNU-grep, not with a standard-(POSIX-) grep because "-B" is not a POSIX-switch.

It is a hard lesson one learns in administrating very diverse large datacenters...

grep -x -B1 '^[^>]\{,15\}'
grep -x -B1 '^[^>]\{15,\}'

Note that the following awk code produces both output files you want in one invocation (with pairs with 2nd lines longer than 15 characters in a file name long and pairs with 2nd lines shorter than...

Let us first examine why your script doesn't do what you want it to do. As a scientist you surely know that finding out why something doesn't work is as well a publishable result as is finding out...

Can't tell. Although man awk says , it might be it doesn't like the caret for begin-of-line. When I modified your code snippet like in post#3, it seems to work.

Always four lines per record? Try
awk '{for (i=1; i<=3; i++) {getline X; $0 = $0 "\n" X}} !x[$2]++' file
@Muestra-1
agctgcgagctgcgacccgggttatataggaagagacacacacaccccc
+
...

I have no way to test it, since I have no Windows, but could you give this a try:
C:\cygwin64\bin\gawk -F, "NR == 1{print \"Source,Well_Source,Volume,Destination_Well,Destination\"; OFS = \",\";...

This is probably a quoting issue, which works differently in Windows. Try putting the script itself in a script file :

BEGIN {
FS=","
}

NR == 1 {
print...

Try:

GNU sed:
sed ':a /^>/!N;s/\r\?\n\([^>]\)/\1/;ta' file
sed ':a /^>/!N;s/\r\{0,1\}\n\([^>]\)/\1/;ta' file
sed -r ':a 1!N;s/\r?\n([^>])/\1/;ta' file




---
Note:
The above approaches...

There you are:awk -F, ' # set field separator to comma
FNR == 1 {FLNR++ ...

OK, now that everthing is more or less clear, let's try
awk -F, '
FNR == 1 {FLNR++
FN[FLNR] = FILENAME
next
}

{V[FLNR,...

It means
IF LAST2 has a value which means we're at least in input line 2 (remember variables are unset thus "empty" thus FALSE at the beginning of the script; minor risk that $2 will be 0 or empty...

Unfortunately I'm not at my own *nix system but on a - hrrrrgh - windows machine, so I can't test what I'm proposing here. It might still be a pointer in a desireable direction. Read and apply to...

Slightly shorter:
ls *.txt | sed -r 's/^(.*_)S([0-9]{1,2}_)(.*)/mv & MID-0\2\1\3/; s/-0([0-9]{2})/-\1/'

Another solution.
The substitution for the two digit is straight forward;
a second substitution cares about the one digit.
ls *.txt | sed '
s/\(.*_\)S\([0-9][0-9]_\)\(.*\)/mv & MID-\2\1\3/...

The following was written and tested using a Korn shell, but will work with any POSIX-conforming shell. It does, however, depend on the version of awk that you are using allowing multi-character...

Hi Xterra,
I think you don't understand what is being suggested. If you have a file containing a million records, each of those records has a 1st line that is one of four values, and you want to...

Did you even consider what Jim McNamara said and what I tried to cast into some sample code? Reading AND WRITING a large file multiple times - even slightly reduced in size - is unnecessary a task...

The latter has the print S within the loop, needs to be after the loop
awk ' NR==FNR { POS[++P]=$1+0; next } /^>/ { print; next } { S=sep=""; for (N=1; N in POS; N++) { S=S sep substr($0, POS[N],...