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mkingiii
post Oct 24 2006, 04:20 AM
Post #1


Whats this Lie-nix Thing?
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I am sure this is a relatively simple problem, but I am a novice at linux and need the answer quickly as it is critical to other work. I need to find and replace the same text in multiple files. After a quick search of linux commands, I found a sight that attributed the command gawk with the ability to find and replace text. However, the sight does not give an example of the full sequence of commands to use gawk to find and replace text, only that it can be used to do it. I would greatly appreciate it if someone could provide me with an example of the full command sequence to find and replace text. Thank you for helping.
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mkingiii
post Oct 24 2006, 11:07 PM
Post #2


Whats this Lie-nix Thing?
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Group: Members
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Joined: 24-October 06
Member No.: 7,558



I am performing molecular modeling of proteins. The files contain data relevant to the protein for each amino acid in the protein, in a table format. Part of the data on the protein is the three letter designation for each amino acid in the sequence. I wanted to make the protein neutral so I had to modify a lysine residue to get rid of its positive charge. Lysine is normally given the abbreviation LYS. When I modified the lysine I called it LYSN, for lysine neutral. The program, AMBER, I use to construct the protein mandated that the amino acid code name only have three letters, so it shortened LYSN to YSN. However, I am now experiencing a problem. The analysis programs I use somehow make use of the three letter designation and are not recognizing YSN. I have gone in manually using emacs and replaced YSN with LYS in one file to confirm that this is the problem. Following the convertion to LYS I was able to use the analytical programs on the file. The analytical programs are part of a commercial package, so I can not readily alter them. So what I need to do is go into the files and change YSN to LYS. I have thousands of files to alter so I really cant do them all using emacs.

Yes, the files are compressed. They are red, although Iam not entirely sure what the color means. When I open them in emacs it says unzipping.

What I listed is the complete path from the directory I am trying to work from. However, this directory itself is a subdirectory. I actually think I tried removing the . but I believe I got an error message about something not existing, Iam not currently at the computer but I will try again later and post the exact error message.

I really appreciate your taking the time to provide assistance. Thank you.
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