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Problem with AWK and OFS

 
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# 1  
Old 10-20-2011
Problem with AWK and OFS
I have a file that looks like this:

Infile.seq
Quote:
"Contig 1" (1,314)
Contig Length: 314 bases
Average Length/Sequence: 257 bases
Total Sequence Length: 515 bases
Top Strand: 1 sequences
Bottom Strand: 1 sequences
Total: 2 sequences
FEATURES Location/Qualifiers
coverage_once 1..56
/Note="Only_once"
coverage_below 57..257
/Note="Below threshold"
coverage_once 258..314
/Note="Only_once"
^^
TTTGGATATGATGATGAACTGGTCACCTACAACGGCCCTGGTGGTATCGCAGTTACTCCGGATCCCACAAGCTGTCGTGGATATGGTGGCGGGGGCCC
I want to output the DNA sequence and add the filename as the identifier. The output file should look like this:

Quote:
>Infile.seq
TTTGGATATGATGATGAACTGGTCACCTACAACGGCCCTGGTGGTATCGCAGTTACTCCGGATCCCACAAGCTGTCGTGGATATGGTGGCGGGGGCCC
I am using the following code but I do not understand why the sequence is not in the output:

Code:
awk 'BEGIN { RS = "^^"; FS="\n"; OFS ="\n" }{print ">"FILENAME OFS}' Infile.seq

Any help will be greatly appreciated!
Last edited by Xterra; 10-20-2011 at 04:05 PM..
# 2  
Old 10-20-2011
Is that a complete file or just one record? Could you post a more representative sample if you have one?
Code:
nawk '/^\^\^/ {$0=">" FILENAME}1' myFile

# 3  
Old 10-20-2011
If sequence is always last line in the file:
Code:
awk 'END{print ">"FILENAME"\n"$0}' Infile.seq

This User Gave Thanks to bartus11 For This Post:
Xterra
# 4  
Old 10-20-2011
bartus
As usual you are right on the money! For my education, why "END"?

vgersh99,

I am not getting the expected output with your code
Quote:
"Contig 1" (1,314)
Contig Length: 314 bases
Average Length/Sequence: 257 bases
Total Sequence Length: 515 bases
Top Strand: 1 sequences
Bottom Strand: 1 sequences
Total: 2 sequences
FEATURES Location/Qualifiers
coverage_once 1..56
/Note="Only_once"
coverage_below 57..257
/Note="Below threshold"
coverage_once 258..314
/Note="Only_once"
>Prueba.seq
TTTGGATATGATGATGAACTGGTCACCTACAACGGCCCTGGTGGTATCGCAGTTACTCCGGATCCCACAAGCTGTCGTGGATATGGTGGCGGGGGCCC
How can I modify it to get the sequence only?
# 5  
Old 10-20-2011
"END" is a clause that is executed after whole file is processed. All the variables that were created during processing of the file are accessible there, so when AWK reads last line into $0, it is still there when executing "END" Smilie
This User Gave Thanks to bartus11 For This Post:
Xterra
# 6  
Old 10-20-2011
I see! But it wouldn't work with the following file, right?
Quote:
"Contig 1" (1,314)
Contig Length: 314 bases
Average Length/Sequence: 257 bases
Total Sequence Length: 515 bases
Top Strand: 1 sequences
Bottom Strand: 1 sequences
Total: 2 sequences
FEATURES Location/Qualifiers
coverage_once 1..56
/Note="Only_once"
coverage_below 57..257
/Note="Below threshold"
coverage_once 258..314
/Note="Only_once"
^^
TTTGGATATGATGATGAACTGGTCACCTACAACGGCCCTGGTGGTATCGCAGTTACTCCGGATCCCACAAGCTGTCGTGGATATGGTGGCGGGGGCCC
'Contig'
123
What would be the best way to look for the DNA sequence below "^^"?
# 7  
Old 10-20-2011
Code:
awk '/\^\^/{getline;print ">"FILENAME"\n"$0}' Infile.seq

This User Gave Thanks to bartus11 For This Post:
Xterra
 
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