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# 8  
Old 10-24-2010
Oops... true !
I always mix those <() $() "" and `` just let's try them all...
One will work LoL 8)
# 9  
Old 10-24-2010
Code:
awk '
function s(a) {gsub(/[a-zA-Z()]/,"",a);return a}
/^Initial dG/ {init=$NF;t=1} 
/^Multi-loop/ { m=(m=="")?X s($(NF-1)$NF):m RS s($(NF-1)$NF)}
/^Hairpin loop/ {h=(h=="")?X s($(NF-1)$NF):h RS s($(NF-1)$NF)}
/^Structure/&&t==1 {printf "%s\nHairpin loop:\n%s\nMulti-loop:\n%s\n\n",init,h,m ; init=m=h="";t=0}
END {printf "%s\nHairpin loop:\n%s\nMulti-loop:\n%s\n",init,h,m }
' infile

-25.40
Hairpin loop:
102-110
65-71
Multi-loop:
37-115

-25.10
Hairpin loop:
79-85
Multi-loop:
37-93

# 10  
Old 11-05-2010
Shell scripting
I made corrections in the program as you suggested. It giving the output like this; It is not printing the dg number for all structures and Hairpin loop heading from the second structure.

Output given from the corrections:
Code:
Multi-loop:
37-115
Hairpin loop:
102-110
65-71
Multi-loop:
37-93
79-85

Actual output :
Code:
-25.40

Multi-loop:
37-115
Hairpin loop:
102-110
65-71

-25.10

Multi-loop:
37-93
Hairpin loop:
79-85

Quote:
Originally Posted by frans
what can be tried is to remove all spaces in the A and check for string without spaces with following changes :

Remove the quotes around $A:

line 05: case "$A" in to be replaced by case $A in

and in the 3 case statements:

line 06: "Initial dG ") to be replaced by Initial*)

line 10: "Hairpin loop") to be replaced by Hairpin*)

line 15: "Multi-loop") to be replaced by Multi-loop)

Don't forget to put the * in the first two ones
Last edited by Scott; 11-06-2010 at 08:56 AM.. Reason: Use code tags, please...
# 11  
Old 11-05-2010
I saved the code, and this one is working by me (with your sample)

bash code:
  1. #!/bin/bash
  2. PrintVal()  { C=${C#*(}; C=${C%)*}; echo $C | sed 's/).*( /-/'; } 
  3. while IFS=':=' read A B C
  4. do
  5.    case $A in
  6.       Initial*)
  7.          echo -e "\n\n$B\n"
  8.          Hairpins=0
  9.       ;;
  10.       Hairpin*)
  11.          ((Hairpins==0)) && echo "$A:"
  12.          PrintVal
  13.          ((Hairpins++))
  14.       ;;
  15.       Multi-loop)
  16.          echo "$A:"
  17.          PrintVal
  18.       ;;
  19.    esac
  20. done <$INFILE
Gives the output:
Code:
 -25.40

Multi-loop:
37-115
Hairpin loop:
102-110
65-71


 -25.10

Multi-loop:
37-93
Hairpin loop:
79-85

# 12  
Old 11-05-2010
Shell scripting
I made corrections in the program as you suggested. It giving the output like this; It is not printing the dg number for all structures and Hairpin loop heading from the second structure.

Output given from the corrections:
Code:
Multi-loop:
37-115
Hairpin loop:
102-110
65-71
Multi-loop:
37-93
79-85

Actual output :
Code:
-25.40

Multi-loop:
37-115
Hairpin loop:
102-110
65-71

-25.10

Multi-loop:
37-93
Hairpin loop:
79-85

Quote:
Originally Posted by frans
I saved the code, and this one is working by me (with your sample)

bash code:
  1. #!/bin/bash
  2. PrintVal() { C=${C#*(}; C=${C%)*}; echo $C | sed 's/).*( /-/'; } 
  3. while IFS=':=' read A B C
  4. do
  5. case $A in
  6. Initial*)
  7. echo -e "\n\n$B\n"
  8. Hairpins=0
  9. ;;
  10. Hairpin*)
  11. ((Hairpins==0)) && echo "$A:"
  12. PrintVal
  13. ((Hairpins++))
  14. ;;
  15. Multi-loop)
  16. echo "$A:"
  17. PrintVal
  18. ;;
  19. esac
  20. done <$INFILE
Gives the output:
Code:
 -25.40
 
Multi-loop:
37-115
Hairpin loop:
102-110
65-71
 
 
 -25.10
 
Multi-loop:
37-93
Hairpin loop:
79-85

Last edited by Scott; 11-06-2010 at 08:59 AM.. Reason: Code tags
# 13  
Old 11-05-2010
What's the output of this:
bash code:
  1. #!/bin/bash
  2. while IFS=':=' read A B C
  3. do
  4.    echo "A='$A' B='$B' C='$C'"
  5. done <$INFILE

---------- Post updated at 23:06 ---------- Previous update was at 21:52 ----------

Problem with leading and trailing tabs and spaces, to get rid of them, replace in line 5.
Code:
case $A in

by
Code:
case $(echo $A) in

This User Gave Thanks to frans For This Post:
kswapnadevi
# 14  
Old 11-05-2010
Shell scripting
I made modification as 'case $(echo $A) in' in script. Output is ok except '-e'. -e has to be removed. It is coming before every dG number i.e., -25.40, -25.10, etc. How it is coming I am in confusion. Thanks in advance.
Code:
-e 
-25.40
Multi-loop:
37-115
Hairpin loop:
102-110
65-71
12-17
-e 
-25.10
Multi-loop:
37-93
Hairpin loop:
79-85
57-62
-e 
-24.80
Multi-loop:
37-115
Hairpin loop:
102-110
65-71
5-10

Quote:
Originally Posted by frans
What's the output of this:
bash code:
  1. #!/bin/bash
  2. while IFS=':=' read A B C
  3. do
  4. echo "A='$A' B='$B' C='$C'"
  5. done <$INFILE

---------- Post updated at 23:06 ---------- Previous update was at 21:52 ----------

Problem with leading and trailing tabs and spaces, to get rid of them, replace in line 5.
Code:
case $A in

by
Code:
case $(echo $A) in

Last edited by Scott; 11-06-2010 at 08:59 AM.. Reason: Code tags
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