Sponsored Content
Top Forums UNIX for Dummies Questions & Answers Find & Replace command - Fasta file Post 302580353 by methyl on Thursday 8th of December 2011 08:21:14 AM
Old 12-08-2011
No doubt posssible in "awk" or "sed" or whatever.

Open logic Shell approach. Too slow for large files.

Code:
cat filename.txt | while read line
do
        echo "${line}"
        read line
        echo "${line}"|fold -w 1|while read char
        do
                if [ ! "${char}" = "C" ]
                then
                        char="-"
                fi
                echo "${char}\c"
        done
        echo ""
done

>Sequence1
------C------C--------
>Sequence2
--CC------C-----C-
>Sequence3
------C-----CC-----C---

 

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
ED(1)							      General Commands Manual							     ED(1)

NAME
ed - editor SYNOPSIS
ed file OPTIONS
- Suppress line/byte count messages (for in scripts) EXAMPLES
ed prog.c # Edit prog.c echo '1,$p' | ed - file # Odd way to write 'cat file' DESCRIPTION
Ed is functionally equivalent to the standard V7 editor, ed. It supports the following commands: (.) a: append (.,.)c: change (.,.)d: delete e: edit new file" f: print name of edited file" (1,$)g: global command (.) i: insert (.,.+1)j: join lines together (.) k: mark (.) l: print with special characters in octal (.,.)m: move (.,.)p: print q: quit editor" (.) r: read in new file (.,.)s: substitute (1,$)v: like g, except select lines that do not match (1,$)w: write out edited file Many of the commands can take one or two addresses, as indicated above. The defaults are shown in parentheses. Thus a appends to the cur- rent line, and g works on the whole file as default. The dot refers to the current line. Below is a sample editing session with comments given following the # symbol. ed prog.c # Edit prog.c 3,20p # Print lines 3 through 20 /whole/ # Find next occurence of whole s/whole/while/ # Replace whole by while g/Buf/s//BUF/g # Replace Buf by BUF everywhere w # Write the file back q # Exit the editor Ed is provided for its sentimental value. If you want a line-oriented editor, try ex. If you want a good editor, use elle, elvis, or mined. SEE ALSO
elvis(1), elle(9), mined(9). ED(1)
All times are GMT -4. The time now is 05:08 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy