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[Solved] Editing the alphabet's based on position information

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Top Forums Shell Programming and Scripting [Solved] Editing the alphabet's based on position information
# 8  
Old 06-16-2013
So - how do you count <newline> chars?
# 9  
Old 06-16-2013
That is where i am not able to proceed. On thing in the real file that I am using to edit has exactly 60 alphabet in each line.
# 10  
Old 06-16-2013
Try this
Code:
awk     'NR==FNR        {F[$1]=$2; R[$1]=$3; next}
                        {for (i=1; i<=NF; i++) if ($i == F[++CNT]) $i=R[CNT]}
         1
        ' file2 FS="" OFS="" file1
ATGTTCCTTCGCTACGTAACAAGTAGAAAAAA
AGCGCTAGCATTGAAGCGGAGGAGAGGAAGA
TGCGATGATGACCCAGTATAAAGAGTGATGAT

# 11  
Old 06-16-2013
I am getting the same file1 as output with out the edits. Am I missing some thing
# 12  
Old 06-16-2013
Strange. I used your file1 and file2, and you see the result above being what you requested as an output.
# 13  
Old 06-16-2013
This what I get (i have diferent names for file1 and file 2)

Code:
awk     'NR==FNR        {F[$1]=$2; R[$1]=$3; next}
                        {for (i=1; i<=NF; i++) if ($i == F[++CNT]) $i=R[CNT]}
         1
        ' list.txt FS="" OFS="" sam.fasta
>SAM
ATGCTCCTTAGCTACGTAGCAAGTAGAAAAAA
ATCGCGAGCATTGAAGCGGAGGAGAGGAGGA
TGAGATGATGACCCAGTATAAAGAGTGATGAT

# 14  
Old 06-16-2013
So you have ">SAM" in the file? I read it as being a prompt and a command... In your spec, you didn't count it nor took it into account! Should have mentioned that.
Add FNR > 1 to the second line...
Last edited by RudiC; 06-16-2013 at 04:21 PM.. Reason: typo
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