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awk code to reconstruct sequence from alignment

 
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# 1  
Old 07-22-2013
awk code to reconstruct sequence from alignment
Hi Everyone,

I need some help to construct a long 'Sbjct' string from the following input using incremental order of 'Sbjct' starting number (e.g. 26325115,33716368,33769033,34869860 etc.)
Different 'Sbject' string will be separated by 'NNNN's as:

(Sbjct:26325115-26325094)NNNN(Sbjct:33716368-33716347)NNNN(Sbjct:33769033-33769073)NNNN(Sbjct:34869860-34869889)

The output expected is shown in 'Example Output'.

--------- Example Input (just a small segment of the whole file)-----------

Score = 44.1 bits (22), Expect = 0.30
Identities = 28/30 (93%)
Strand = Plus / Plus

Query: 1684 atcaaaatgaccaaaatatttcattaaaaa 1713
|||||||||| |||||| ||||||||||||
Sbjct: 34869860 atcaaaatgaacaaaatgtttcattaaaaa 34869889

Score = 44.1 bits (22), Expect = 0.30
Identities = 22/22 (100%)
Strand = Plus / Minus


Query: 1758 ttagggtttagagttaaggggt 1779
||||||||||||||||||||||
Sbjct: 26325115 ttagggtttagagttaaggggt 26325094


Score = 44.1 bits (22), Expect = 0.30
Identities = 22/22 (100%)
Strand = Plus / Minus


Query: 1687 aaaatgaccaaaatatttcatt 1708
||||||||||||||||||||||
Sbjct: 33716368 aaaatgaccaaaatatttcatt 33716347


Score = 44.1 bits (22), Expect = 0.30
Identities = 38/42 (90%), Gaps = 1/42 (2%)
Strand = Plus / Plus


Query: 1734 ccctagggttaactaattcaaaccttagggtttagagttaag 1775
||||||| ||||||||| |||| ||||||||||||||||||
Sbjct: 33769033 ccctaggattaactaatctaaac-ttagggtttagagttaag 33769073

----------------------

---------------------- Example Output -----------
Whole Sbjct string
ttagggtttagagttaaggggtNNNNaaaatgaccaaaatatttcattNNNNccctaggattaactaatctaaac-ttagggtttagagttaagNNNNatcaaaatgaacaaaatgtttcattaaaaa

Thanks for your help.
# 2  
Old 07-22-2013
Could you please put some code tag ?
# 3  
Old 07-22-2013
I need some help to construct a long 'Sbjct' string from the following input using incremental order of 'Sbjct' starting number (e.g. 26325115,33716368,33769033,34869860 etc.)
Different 'Sbject' string will be separated by 'NNNN's as:
Code:
(Sbjct:26325115-26325094)NNNN(Sbjct:33716368-33716347)NNNN(Sbjct:33769033-33769073)NNNN(Sbjct:34869860-34869889)

The output expected is shown in 'Example Output'.
Code:
--------- Example Input (just a small segment of the whole file)-----------

Score = 44.1 bits (22), Expect = 0.30
Identities = 28/30 (93%)
Strand = Plus / Plus

Query: 1684 atcaaaatgaccaaaatatttcattaaaaa 1713
|||||||||| |||||| ||||||||||||
Sbjct: 34869860 atcaaaatgaacaaaatgtttcattaaaaa 34869889

Score = 44.1 bits (22), Expect = 0.30
Identities = 22/22 (100%)
Strand = Plus / Minus


Query: 1758 ttagggtttagagttaaggggt 1779
||||||||||||||||||||||
Sbjct: 26325115 ttagggtttagagttaaggggt 26325094


Score = 44.1 bits (22), Expect = 0.30
Identities = 22/22 (100%)
Strand = Plus / Minus


Query: 1687 aaaatgaccaaaatatttcatt 1708
||||||||||||||||||||||
Sbjct: 33716368 aaaatgaccaaaatatttcatt 33716347


Score = 44.1 bits (22), Expect = 0.30
Identities = 38/42 (90%), Gaps = 1/42 (2%)
Strand = Plus / Plus


Query: 1734 ccctagggttaactaattcaaaccttagggtttagagttaag 1775
||||||| ||||||||| |||| ||||||||||||||||||
Sbjct: 33769033 ccctaggattaactaatctaaac-ttagggtttagagttaag 33769073

Code:
---------------------- Example Output -----------
Whole Sbjct string
ttagggtttagagttaaggggtNNNNaaaatgaccaaaatatttcattNNNNccctaggattaactaatctaaac-ttagggtttagagttaagNNNNatcaaaatgaacaaaatgtttcattaaaaa

Thanks for your help.
# 4  
Old 07-22-2013
Fahmida, for future reference, note that you could have edited the 1st message in this thread to add CODE tags instead of duplicating it in a new message. Smilie
# 5  
Old 07-22-2013
If you have gawk:
Code:
gawk '
        /Sbjct/ {
                A[$2] = $3
        }
        END {
                n = asorti ( A, D )
                for ( i = 1; i <= n; i++ )
                        s = s ? s "NNNN" A[D[i]] : A[D[i]]
                print s
        }
' file

Output:
Code:
ttagggtttagagttaaggggtNNNNaaaatgaccaaaatatttcattNNNNccctaggattaactaatctaaac-ttagggtttagagttaagNNNNatcaaaatgaacaaaatgtttcattaaaaa

# 6  
Old 07-22-2013
With regular awk, try:
Code:
awk '
  NR==FNR{
    if(/Sbjct/)A[$2 "-" $4]=$3
    next
  }
  { 
    for(i=2; i<=NF; i+=2) $i=A[$i]
  }
  1
' file2 FS='\\(Sbjct:|\\)' OFS= file1

Code:
$ cat file1
(Sbjct:26325115-26325094)NNNN(Sbjct:33716368-33716347)NNNN(Sbjct:33769033-33769073)NNNN(Sbjct:34869860-34869889)

Output:
Code:
ttagggtttagagttaaggggtNNNNaaaatgaccaaaatatttcattNNNNccctaggattaactaatctaaac-ttagggtttagagttaagNNNNatcaaaatgaacaaaatgtttcattaaaaa

# 7  
Old 07-23-2013
Dear Yoda,

Thanks for your reply. Your code is working, it adds the 'NNNN's after each subject line, it would be great if code is modified to add 'NNNN's at the end of the Sbjct of a whole block (each block starts with 'Score =...' and may contain many Sbjct lines).
For example there are three segments below. If we look at the starting point of 'Sbjcts' at each segment: 11561582, 3294707, 11140709,.

Code:
Score =  139 bits (70), Expect = 7e-30
 Identities = 103/114 (90%)
 Strand = Plus / Plus
Query: 2040     atctagagtattatggtctttttacatattaaatgaaacattttgatcattttcctactt 2099
                |||||| |||||| |||| |||||| ||||||||||||||||||| |||||||||| |||
Sbjct: 11561582 atctagggtattagggtccttttacctattaaatgaaacattttggtcattttcctcctt 11561641
                                                                     
Query: 2100     gtggtatatttttgtgatcaaaatttgaaaatagtatatttaggagaattgccc 2153
                ||||| |||||||||||||||||  ||||||| || ||||||||||||||||||
Sbjct: 11561642 gtggtctatttttgtgatcaaaacatgaaaatggtctatttaggagaattgccc 11561695

Score =  139 bits (70), Expect = 7e-30
 Identities = 103/114 (90%)
 Strand = Plus / Minus
                                                                         
Query: 2040    atctagagtattatggtctttttacatattaaatgaaacattttgatcattttcctactt 2099
               |||||| |||||| |||| |||||| ||||||||||||||||||| ||||||| || || 
Sbjct: 3294707 atctagggtattagggtcattttacctattaaatgaaacattttggtcatttttctcctc 3294648
                                                                
Query: 2100    gtggtatatttttgtgatcaaaatttgaaaatagtatatttaggagaattgccc 2153
               ||||||||||||||||||||||| |||||||| || ||||||||||||||||||
Sbjct: 3294647 gtggtatatttttgtgatcaaaacttgaaaattgtctatttaggagaattgccc 3294594

 Score =  139 bits (70), Expect = 7e-30
 Identities = 103/114 (90%)
 Strand = Plus / Minus
                                                                       
Query: 2040     atctagagtattatggtctttttacatattaaatgaaacattttgatcattttcctactt 2099
                |||||| |||||| | ||||||||  ||||||||||||||||||| |||||||||| |||
Sbjct: 11140709 atctagggtattaggatctttttagctattaaatgaaacattttggtcattttcctcctt 11140650
                                                                  
Query: 2100     gtggtatatttttgtgatcaaaatttgaaaatagtatatttaggagaattgccc 2153
                ||||| ||||||||||| ||||| || |||||||||||||||||||||||||||
Sbjct: 11140649 gtggtttatttttgtgaccaaaacttaaaaatagtatatttaggagaattgccc 11140596

So,
1) Sort the Sbjct based on their starting points in each block i.e 3294707, 11140709, 11561582,
2) Add Sbjcts strings of each block in the order of (1) separated by 'NNNN'.

Expected Output is:
Code:
gtggtatatttttgtgatcaaaacttgaaaattgtctatttaggagaattgccc
atctagggtattagggtcattttacctattaaatgaaacattttggtcatttttctcctcNNNN
gtggtttatttttgtgaccaaaacttaaaaatagtatatttaggagaattgcccatctagggta
ttaggatctttttagctattaaatgaaacattttggtcattttcctccttNNNNatctagggtatt
agggtccttttacctattaaatgaaacattttggtcattttcctccttgtggtctatttttgtgatca
aaacatgaaaatggtctatttaggagaattgccc

 
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