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Removing columns with dashes

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# 8  
Old 07-07-2010
Quote:
Originally Posted by Xterra
Thank you very much -I own you many at this stage Smilie
I tried your code
Code:
$ perl -nla -F"" -e 'if (!/^>/){$n++;for ($i=0;$i<=$#F;$i++){$a{$i}{$F[$i]}++}}END{for ($i=0;$i<=$#F;$i++){if ($a{$i}{"-"}/$n>0.5)\
> {print $i}}}' Input.txt | awk -vFS="" -vOFS="" 'NR==FNR{a[$0+1]++}{for (i=1;i<=NF;i++) if (i in a) $i=""}1' - Input.txt > Output.txt

and this is what I got
Code:
Backslash found where operator expected at -e line 1, near ")\"
(Missing operator before \?)
syntax error at -e line 1, near ")\"
syntax error at -e line 2, near ";}"
Execution of -e aborted due to compilation errors.
awk: cmd. line:1: fatal: cannot open file `Input.txt' for reading (No such file or directory)

Am I missing something?
Remove marked(red) backslash.
# 9  
Old 07-07-2010
bartus
It worked! I was just wondering why am I getting 2 different number at the very top of the file
Quote:
38
45
>GHL8OVD01BNNCA Freq 4
TAGATGTGCCCGTGGGTTTCCCGTCAACACCGGATAGTGCAGCATA
>GHL8OVD01CMQVT Freq 15
TTGATGTCGTGGGTTTCCCGTCAACACCGGCAAATAGTGCAGCATA
>GHL8OVD01CMQVT Freq 50
TTGATGTGCCAGTTTCCCGTCTAGCAGCACTACCAGGACTTCGCTA
>GHL8OVD01CMQVW Freq 700
TTGATGTGTCCCGTCGACACCGGCAAATAGCAGCAGCATACCAGAC
>GHL8OVD01A45V3 Freq 9
TTGATTCCCGTCGACACCGGCAAATAGCAGCAGCACTAAGGACCTC
>GHL8OVD01AV2U9 Freq 17
TTGATGTGCCAGCTTTCGCGTCGACACCGGCAAATAGTGCAGCGTA
I ran it in Cygwin, could that be the problem? I will try on my Linux (red hat) box.
# 10  
Old 07-07-2010
Right. My fault Smilie. Replace "1" at the end of AWK statement with "FNR!=NR", so it looks like:
Code:
$ perl -nla -F"" -e 'if (!/^>/){$n++;for ($i=0;$i<=$#F;$i++){$a{$i}{$F[$i]}++}}END{for ($i=0;$i<=$#F;$i++){if ($a{$i}{"-"}/$n>0.5)
> {print $i}}}' Input.txt | awk -vFS="" -vOFS="" 'NR==FNR{a[$0+1]++}{for (i=1;i<=NF;i++) if (i in a) $i=""}FNR!=NR' - Input.txt > Output.txt

# 11  
Old 07-07-2010
Syntax error
I got the following error
Code:
syntax error at -e line 2, near ")
>"
syntax error at -e line 2, near ";}"
Execution of -e aborted due to compilation errors.

# 12  
Old 07-07-2010
The ">" character was from your output, and it isn't part of the code:
Code:
perl -nla -F"" -e 'if (!/^>/){$n++;for ($i=0;$i<=$#F;$i++){$a{$i}{$F[$i]}++}}END{for ($i=0;$i<=$#F;$i++){if ($a{$i}{"-"}/$n>0.5)
 {print $i}}}' Input.txt | awk -vFS="" -vOFS="" 'NR==FNR{a[$0+1]++}{for (i=1;i<=NF;i++) if (i in a) $i=""}FNR!=NR' - Input.txt > Output.txt

# 13  
Old 07-07-2010
I got it!
It is working great on CygWin.
The Output file is empty when I run it on Red Hat though.
# 14  
Old 07-07-2010
I tested it on Oracle Enterprise Linux, which is based on Red Hat, so it should work..
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