Sponsored Content
Top Forums UNIX for Dummies Questions & Answers Find & Replace command - Fasta file Post 302580319 by Cevin21 on Thursday 8th of December 2011 06:29:55 AM
Old 12-08-2011
Thank you so much for your help !

I see the spirit of your approach.

But I didn't explain myself very well.

In reality my file looks like that:

>Sequence1
RTYIPLCASQHKLCPITFLAVK
>Sequence2
ERCCVASTWQCIPLKMCI
>Sequence3
TYIPLKCRYTWSCCPLVAQCYTR

And I would like to obtain:
>Sequence1
------C------C--------
>Sequence2
--CC------C-----C-
>Sequence3
------C-----CC-----C---

By "only the second line" I meant the second line of the pair of lines (or only the line with even number)
Cevin21
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Find & Replace

I get a text file with 70+ columns (seperated by Tab) and about 10000 rows. The 58th Column is all numbers. But sometimes 58th columns has "/xxx=##" after the numeric data. I want to truncate this string using the script. Any Ideas...:confused: (3 Replies)
Discussion started by: gagansharma
3 Replies

2. UNIX for Dummies Questions & Answers

how to use sed or perl command to find and replace a directory in a file

how to use sed command to find and replace a directory i have a file.. which contains lot of paths ... for eg.. file contains.. /usr/kk/rr/12345/1 /usr/kk/rr/12345/2 /usr/kk/rr/12345/3 /usr/kk/rr/12345/4 /usr/kk/rr/12345/5 /usr/kk/rr/12345/6 /usr/kk/rr/12345/7... (1 Reply)
Discussion started by: wip_vasikaran
1 Replies

3. Shell Programming and Scripting

Find & Replace string in multiple files & folders using perl

find . -type f -name "*.sql" -print|xargs perl -i -pe 's/pattern/replaced/g' this is simple logic to find and replace in multiple files & folders Hope this helps. Thanks Zaheer (0 Replies)
Discussion started by: Zaheer.mic
0 Replies

4. Shell Programming and Scripting

find & replace comma in a .csv file.

HI, Please find the text below. I receive a .csv file on server. I need the comma(,) in the second column to be replaced by a semi-colon( ; ). How to do it. Please help. Sample text: "1","lastname1,firstname1","xxxxxx","19/10/2009","23/10/2009","0","N","Leave"... (2 Replies)
Discussion started by: libin4u2000
2 Replies

5. Shell Programming and Scripting

How to use grep & find command to find references to a particular file

Hi all , I'm new to unix I have a checked project , there exists a file called xxx.config . now my task is to find all the files in the checked out project which references to this xxx.config file. how do i use grep or find command . (2 Replies)
Discussion started by: Gangam
2 Replies

6. Shell Programming and Scripting

Find & replace --> create a new file

Hi All, I have a unix shell script file as below. My task is a)to replace 248 to 350 and need to create a new file as BW3_350.sh b)to replace 248 to 380 and need to create a new file as BW3_380.sh c)to replace 248 to 320 and need to create a new file as BW3_320.sh there is no... (6 Replies)
Discussion started by: karthi_mrkg
6 Replies

7. Solaris

Monitoring log file for entries - Find command & sorting

hi, I would like to monitor a log file, which rolls over, everytime a server is restarted. I would like to grep for a string, and to be more efficient i'd like to grep only newly appended data. so something like a 'tail -f' would do, however, as the log rolls over i think a 'tail -F' is... (2 Replies)
Discussion started by: horhif
2 Replies

8. UNIX for Dummies Questions & Answers

Find & Replace

Hi I am looking to rename the contents of this dir, each one with a new timestamp, interval of a second for each so it the existing format is on lhs and what I want is to rename each of these to what is on rhs..hopefully it nake sense CDR.20060505.150006.gb CDR.20121211.191500.gb... (3 Replies)
Discussion started by: rob171171
3 Replies

9. Shell Programming and Scripting

Command Line Perl for parsing fasta file

I would like to take a fasta file formated like >0001 agttcgaggtcagaatt >0002 agttcgag >0003 ggtaacctga and use command line perl to move the all sample gt 8 in length to a new file. the result would be >0001 agttcgaggtcagaatt >0003 ggtaacctga cat ${sample}.fasta | perl -lane... (2 Replies)
Discussion started by: jdilts
2 Replies

10. UNIX for Beginners Questions & Answers

How to find a specific sequence pattern in a fasta file?

I have to mine the following sequence pattern from a large fasta file namely gene.fasta (contains multiple fasta sequences) along with the flanking sequences of 5 bases at starting position and ending position, AAGCZ-N16-AAGCZ Z represents A, C or G (Except T) N16 represents any of the four... (3 Replies)
Discussion started by: dineshkumarsrk
3 Replies
scotty(1)							 Tnm Tcl Extension							 scotty(1)

__________________________________________________________________________________________________________________________________________________

NAME
scotty - A Tcl shell including the Tnm extensions. SYNOPSIS
scotty ?fileName arg arg ...? _________________________________________________________________ DESCRIPTION
scotty is a Tcl interpreter with extensions to obtain status and configuration information about TCP/IP networks. After startup, scotty evaluates the commands stored in .scottyrc and .tclshrc in the home directory of the user. SCRIPT FILES
If scotty is invoked with arguments then the first argument is the name of a script file and any additional arguments are made available to the script as variables (see below). Instead of reading commands from standard input scotty will read Tcl commands from the named file; scotty will exit when it reaches the end of the file. If you create a Tcl script in a file whose first line is #!/usr/local/bin/scotty2.1.11 then you can invoke the script file directly from your shell if you mark the file as executable. This assumes that scotty has been installed in the default location in /usr/local/bin; if it's installed somewhere else then you'll have to modify the above line to match. Many UNIX systems do not allow the #! line to exceed about 30 characters in length, so be sure that the scotty executable can be accessed with a short file name. An even better approach is to start your script files with the following three lines: #!/bin/sh # the next line restarts using scotty exec scotty2.1.11 "$0" "$@" This approach has three advantages over the approach in the previous paragraph. First, the location of the scotty binary doesn't have to be hard-wired into the script: it can be anywhere in your shell search path. Second, it gets around the 30-character file name limit in the previous approach. Third, this approach will work even if scotty is itself a shell script (this is done on some systems in order to handle multiple architectures or operating systems: the scotty script selects one of several binaries to run). The three lines cause both sh and scotty to process the script, but the exec is only executed by sh. sh processes the script first; it treats the second line as a comment and executes the third line. The exec statement cause the shell to stop processing and instead to start up scotty to reprocess the entire script. When scotty starts up, it treats all three lines as comments, since the backslash at the end of the second line causes the third line to be treated as part of the comment on the second line. VARIABLES
Scotty sets the following Tcl variables: argc Contains a count of the number of arg arguments (0 if none), not including the name of the script file. argv Contains a Tcl list whose elements are the arg arguments, in order, or an empty string if there are no arg arguments. argv0 Contains fileName if it was specified. Otherwise, contains the name by which scotty was invoked. tcl_interactive Contains 1 if scotty is running interactively (no fileName was specified and standard input is a terminal-like device), 0 otherwise. PROMPTS
When scotty is invoked interactively it normally prompts for each command with ``% ''. You can change the prompt by setting the variables tcl_prompt1 and tcl_prompt2. If variable tcl_prompt1 exists then it must consist of a Tcl script to output a prompt; instead of out- putting a prompt scotty will evaluate the script in tcl_prompt1. The variable tcl_prompt2 is used in a similar way when a newline is typed but the current command isn't yet complete; if tcl_prompt2 isn't set then no prompt is output for incomplete commands. SEE ALSO
Tnm(n), Tcl(n) AUTHORS
Juergen Schoenwaelder <schoenw@cs.utwente.nl> Tnm scotty(1)
All times are GMT -4. The time now is 01:35 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy