Little problem with AWK


 
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# 1  
Old 10-26-2011
Little problem with AWK

I thought I had solved this problem but after testing the script I came to realize that it is not doing what I need. So, here it goes again. This is the code:

Code:
awk '/\>/{F=$2; N=$3; split(FILENAME, A, "."); getline; x = ">"}{print ">" A[1]"-" x++" "F" " N"\n" $0}'

This is the input file:

06.fas:
Quote:
>HBGKACG01A208Q Freq 5
ACGAGTGCGTGGATATGATGATGAACTGGTCCCCTACGACGGCA
>HBGKACG01ASP9W Freq 2
ACGAGTGCGTGGATATGATGATGAACTGGTCCCCTACGACGGCA
>HBGKACG01B0MS7 Freq 5
ACGAGTGCGTGGATATGATGATGAACTGGTCCCCTACGACGGCA
>HBGKACG01BSGGM Freq 2
ACGAGTGCGTGGATATGATGATGAACTGGTCCCCCACGACGGCA
And this is the expected outfile:

Quote:
>06-1 Freq 5
ACGAGTGCGTGGATATGATGATGAACTGGTCCCCTACGACGGCA
>06-2 Freq 2
ACGAGTGCGTGGATATGATGATGAACTGGTCCCCTACGACGGCA
>06-3 Freq 5
ACGAGTGCGTGGATATGATGATGAACTGGTCCCCTACGACGGCA
>06-4 Freq 2
ACGAGTGCGTGGATATGATGATGAACTGGTCCCCCACGACGGCA
I am almost there I just need some help numbering the id with consecutive numbers.
Any help will be greatly appreciated!
# 2  
Old 10-26-2011
What's this x = ">"?
# 3  
Old 10-26-2011
tukuyomi

">" is the identifier for each sequence. If you see in my example, each seqeunce has a name (>HBGKACG01A208Q Freq 5). So, ">" inidcates the name of the DNA sequence.
I have also tried this code:
Code:
awk '/\>/{F=$2; N=$3; split(FILENAME, A, "."); getline; RS = ">"}{print ">" A[1]"-" RS++" "F" " N"\n" $0}'

but ther results is pretty much the same.
# 4  
Old 10-26-2011
something along these lines:
Code:
nawk 'FNR==1{n=substr(FILENAME,1,index(FILENAME,".")-1)} /^>/ {print n "-" ++c, $2, $3;next}1' 06.txt

This User Gave Thanks to vgersh99 For This Post:
# 5  
Old 10-27-2011
vgersh99

This worked like a charm!
Code:
awk 'FNR==1{n=substr(FILENAME,1,index(FILENAME,".")-1)} /^>/ {print ">" n "-" ++c, $2, $3;next}1' 06.txt

Would you mind explaining the following parts of your script?

Code:
'FNR==1{n=substr(FILENAME,1,index(FILENAME,".")-1)}

Thanks a bunch!
# 6  
Old 10-27-2011
Code:
FNR==1{n=substr(FILENAME,1,index(FILENAME,".")-1)}

FNR==1 - if current record in the current file is 1, execute the following action in '{}'
index(FILENAME,".") - position of the first '.' in variable FILENAME.
n=substr(FILENAME,1,index(FILENAME,".")-1) - substring of variable FILENAME starting at position 1 up to the first '.', e.g. foo.txt -> foo, blah.blah.txt -> blah
 
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