Emergency UNIX and Linux Support

The given file consists of two tags i.e., <free-energy> and <position> tag. I want the output like this. The tag <length> is not required to consider.

(General format of output)

free-energy no.

first position no – second position no
third position no – fourth position no
------
------
Free-energy no
First position no – second position no
Third position no –fourth position no.

Output for the given file is
-25.40
9 – 20
25 - 127
-24.80
2 - 13

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

<structure analysis-ids="UNAFold">
<!-- Start of folding 1 for sequence 1 ************************ -->
<model id="_1.1">
<model-info>
<free-energy>-25.40</free-energy>
</model-info>
<base-id>
<position>9</position>
</base-id>
</base-id-5p>
<base-id-3p>
<base-id>
<position>20</position>
</base-id>
</base-id-3p>
<length>4</length>
</helix>
<base-id>
<position>25</position>
</base-id>
</base-id-5p>

<position>127</position>
</base-id>
</base-id-3p>
<!-- End of folding 1 for sequence 1 ************************ -->
<!-- Start of folding 2 for sequence 1 ************************ -->
<model id="_1.2">
<model-info>
<free-energy>-24.80</free-energy>
</model-info>
<str-annotation>
<base-id>
<position>2</position>
</base-id>
</base-id-5p>
<position>13</position>



PLS. HELP ME TO WRITE A SHELL SCRIPT FOR THIS WHICH HELPS A LOT IN BIOINFORMATICS RESEARCH. THANKS IN ADVANCE.

You can make a sort of cheap xml parser of sed:

Code:

sed -n '
  s/.*<free-energy>\([^<]*\)<.*/\1/p
  t
  /<base-id>/{
    :loop
    N
    /<\/base-id-3p>/!b loop
    s/.*<position>\([^<]*\)<.*<position>\([^<]*\)<.*/\1 - \2/p
    t
    s/^/Malformed: /
    s/\n//g
    w /dev/tty
   }
 ' in_file1 in_file2 . . . .

Narrative: sed runs in no-output-but-explicit-print mode. When it finds the free-energy tag it extracts the content (everything after the tag to the next <), makes that the entire new buffer, prints it, and then, just a speedup, branches to end of script (get next line). When it finds the base-id tag, it gets the next line and loops collecting all lines to the base-id-3p end tag in the buffer, extracts the two poistions, drops them around the ' - ' as the entire new buffer, prints it, and then branches to end of script (get next line), but if there are not two position tags, it labels it as Malformed, makes it all one line, writes it to the tty (you can use a log file in batch situations).

Code:

awk -F'[<>]' '/free-energy/{print $3}/position/{printf "%s"(f?RS:"-"),$3;f=!f}' infile

Hi,

I have to insert ## at 3051th and 3085th position of a record in a file.

Sample Data:

Code:

rd    1254O3104969765S0AP     GY10KQH1413980010008    013

Let us assume that i need to insert "##" at these position : ##GY10KQH1413980010008 ##

Code I am using:

Code:

sed 's/\(.\{3051\}\)/&##/;s/\(.\{3086\}\)/&##/' newtestfile.txt > test

Output:

Code:

sed: command garbled: s/\(.\{3051\}\)/&##/;s/\(.\{3086\}\)/&##/

I guess i know the problem. the command is not accepting huge amount of data in the field ie. 3051 and 3085.
But i have no solution for this problem.
Sed command has a limitation when used on solaris machines.. where as the command works fine on red hat linux..
Please suggest me with a solution because i have to tick to Solaris OS only.

Cheers
Aviroop

@aviroops. Welcome to the forum. Please start a new thread for this.

---------- Post updated at 12:43 ---------- Previous update was at 11:05 ----------

You could try:

Code:

nawk '{$3051=$3051"##";$3086=$3086"##"}1' FS= OFS= infile

or

Code:

sed 's/\(.\{100\}\)\{30\}.\{86\}/&##/;s/\(.\{100\}\)\{30\}.\{51\}/&##/' infile

use nawk or /usr/xpg4/bin/awk and /usr/xpg4/bin/sed on Solaris

GNU sed has no field length limit, and I find it on many modern Solaris installs, but modern solaris sed goes pretty big.

Maybe stupid quuestion but how much is important to learn shell scripting ?