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Find & Replace command - Fasta file

 
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# 1  
Old 12-08-2011
Find & Replace command - Fasta file
Hi all !

I have a fasta file that looks like that:

>Sequence1
RTYIPLCASQHKLCPITFLAVK

(it's just an example, obviously in reality I have several pairs of lines like that)

Using UNIX command(s), would it be possible to replace all the characters except the "C" of the second line only by a dash. So without modifying the first line.
To be able to obtain this:

>Sequence1
------C------C--------

Or at least which command would you use? (grep, awk, perl, sed...)

Thank you very much for your help !!!
Cevin21
# 2  
Old 12-08-2011
Code:
 
$ cat test.txt
>Sequence1
RTYIPLCASQHKLCPITFLAVK
>Sequence1
RTYIPLCASQHKLCPITFLAVK
>Sequence1
RTYIPLCASQHKLCPITFLAVK
 
$ sed '2 s/[A-BD-Z]/\-/g' test.txt
>Sequence1
------C------C--------
>Sequence1
RTYIPLCASQHKLCPITFLAVK
>Sequence1
RTYIPLCASQHKLCPITFLAVK

# 3  
Old 12-08-2011
Thank you so much for your help !

I see the spirit of your approach.

But I didn't explain myself very well.

In reality my file looks like that:

>Sequence1
RTYIPLCASQHKLCPITFLAVK
>Sequence2
ERCCVASTWQCIPLKMCI
>Sequence3
TYIPLKCRYTWSCCPLVAQCYTR

And I would like to obtain:
>Sequence1
------C------C--------
>Sequence2
--CC------C-----C-
>Sequence3
------C-----CC-----C---

By "only the second line" I meant the second line of the pair of lines (or only the line with even number)
Cevin21
# 4  
Old 12-08-2011
No doubt posssible in "awk" or "sed" or whatever.

Open logic Shell approach. Too slow for large files.

Code:
cat filename.txt | while read line
do
        echo "${line}"
        read line
        echo "${line}"|fold -w 1|while read char
        do
                if [ ! "${char}" = "C" ]
                then
                        char="-"
                fi
                echo "${char}\c"
        done
        echo ""
done

>Sequence1
------C------C--------
>Sequence2
--CC------C-----C-
>Sequence3
------C-----CC-----C---

# 5  
Old 12-08-2011
Code:
awk '/^[^>]/ { gsub(/[^C]/, "-"); }' < infile > outfile

if awk doesn't work, try nawk or gawk.
# 6  
Old 12-09-2011
Thank you methyl and Corona !

Unfortunately none of the propositions work.

---------- Post updated at 02:41 PM ---------- Previous update was at 02:19 PM ----------

I was thinking about something like that:

awk '{if ($1 ~/>/) print $0; else (sed 's/[^C]/-/g') print $0}' file.fasta

but it doesn't work.
Syntax error probably !
Cevin21
# 7  
Old 12-09-2011
Code:
perl -npe '!/^>Sequence/&&s/[ABD-Z]/-/g' inputfile.dat

 
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