Sponsored Content
Top Forums UNIX for Dummies Questions & Answers Help parsing and replacing text with file name Post 302341388 by mycoguy on Wednesday 5th of August 2009 08:06:34 PM
Old 08-05-2009
Help parsing and replacing text with file name

Hi everyone,

I'm having trouble figuring this one out. I have ~100 *.fa files with multiple lines of fasta sequences like this: file1.fa

>xyzsequence
atcatgcacac......
ataccgagagg.....
atataccagag.....
>abcsequence
atgagatatat.....
acacacggd.....
atcgaacac....
agttccagat....

The name of each sequence is delimited by a ">" and followed by a newline. I'm trying to figure out how iterate through all of my files with a ".fa" extension and create a single tab-delimited table with the name of the sequence (tab) and the name of the file it came from. Like so:
xyzsequence file1
abcsequence file1
somsequence file2
etc...

Can anyone point me in the right direction?
Many thanks,
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Text File Parsing

Hey Guys.I am a newbie on Bash Shell Scripting and Perl.And I have a question about file parsing. I have a log file which contains reports about a communication device.I need to take some of the reports from the log file.Its hard to explain the issue.but shortly I can say that, the reports has a... (2 Replies)
Discussion started by: Djlethal
2 Replies

2. Shell Programming and Scripting

replacing strings with text from other file

Hi, Im trying to update some properties files with text from another file: file1 user=xyz file2 user= after script file2 user=xyz Im using this reading the $QUARTZURL,ETC... from quartz.properties: echo... (1 Reply)
Discussion started by: mc1392
1 Replies

3. Shell Programming and Scripting

Parsing text from file

Any ideas? 1)loop through text file 2)extract everything between SOL and EOL 3)output files, for example: 123.txt and 124.txt for the file below So far I have: sed -n "/SOL/,/EOL/{p;/EOL/q;}" file Here is an example of my text file. SOL-123.go something goes here something goes... (0 Replies)
Discussion started by: ndnkyd
0 Replies

4. Shell Programming and Scripting

Replacing Text in Text file

Hi Guys, I am needing some help writing a shell script to replace the following in a text file /opt/was/apps/was61 with some other path eg /usr/blan/blah/blah. I know that i can do it using sed or perl but just having difficulty writing the escape characters for it All Help... (3 Replies)
Discussion started by: cgilchrist
3 Replies

5. Shell Programming and Scripting

replacing text in a file, but...

Hi all, Very first post on this forums, hope you can help me with this scripting task. I have a big text file with over 3000 lines, some of those lines contain some text that I need to replace, lets say for simplicity the text to be replaced in those lines is "aaa" and I need it to replace it... (2 Replies)
Discussion started by: Angelseph
2 Replies

6. Shell Programming and Scripting

replacing text with contents from another file

I'm trying to change the ramfs size in kernel .config automatically. I have a ramfs_size file generated with du -s cat ramfs_size 64512 I want to replace the linux .config's ramdisk size with the above value CONFIG_BLK_DEV_RAM_SIZE=73728 Right now I'm doing something dumb like: ... (3 Replies)
Discussion started by: amoeba
3 Replies

7. Shell Programming and Scripting

Need help parsing a text file

I have a text file: router1#sh ip blah blah | incl --- Gi2/8 10.60.4.181 --- 10.60.123.175 11 0000 0000 355K Gi2/8 10.60.83.28 --- 224.10.10.26 11 F9FF 3840 154K Gi2/8 10.60.83.198 --- ... (1 Reply)
Discussion started by: streetfighter2
1 Replies

8. Programming

Parsing a Text file using C++

I was trying to parse the text file, which will looks like this ###XYZABC#### ############ int = 4 char = 1 float = 1 . . ############ like this my text file will contains lots of entries and I need to store these entries in the map eg. map.first = int and map.second = 4 same way I... (5 Replies)
Discussion started by: agupta2
5 Replies

9. Shell Programming and Scripting

Parsing text file

I'm totally stumped with how to handle this huge text file I'm trying to deal with. I really need some help! Here is what is looks like: ab1ba67c331a3d731396322fad8dd71a3b627f89359827697645c806091c40b9 0.2 812a3c3684310045f1cb3157bf5eebc4379804e98c82b56f3944564e7bf5dab5 0.6 0.6... (3 Replies)
Discussion started by: comp8765
3 Replies

10. Shell Programming and Scripting

Parsing text file

Hi Friends, I am back for the second round today - :D My input text file is this way Home friends friendship meter Tools Mirrors Downloads My Data About Us Help My own results BLAT Search Results ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND ... (7 Replies)
Discussion started by: jacobs.smith
7 Replies
merge(1)																  merge(1)

NAME
merge - three-way file merge SYNOPSIS
merge [-Llabel1 [-Llabel3]] [-p] [-q] file1 file2 file3 DESCRIPTION
merge incorporates all changes that lead from file2 to file3 into file1. The result goes to standard output if -p is present, into file1 otherwise. merge is useful for combining separate changes to an original. Suppose file2 is the original, and both file1 and file3 are modifications of file2. Then merge combines both changes. An overlap occurs if both file1 and file3 have changes in a common segment of lines. On a few older hosts where diff3 does not support the -E option, merge does not detect overlaps, and merely supplies the changed lines from file3. On most hosts, if overlaps occur, merge out- puts a message (unless the -q option is given), and includes both alternatives in the result. The alternatives are delimited as follows: <<<<<<< file1 lines in file1 ======= lines in file3 >>>>>>> file3 If there are overlaps, the user should edit the result and delete one of the alternatives. If the -L label1 and -L label3 options are given, the labels are output in place of the names file1 and file3 in overlap reports. DIAGNOSTICS
Exit status is 0 for no overlaps, 1 for some overlaps, 2 for trouble. IDENTIFICATION
Author: Walter F. Tichy. Revision Number: 1.1.6.2; Release Date: 1993/10/07. Copyright (C) 1982, 1988, 1989 by Walter F. Tichy. Copyright (C) 1990, 1991 by Paul Eggert. SEE ALSO
diff3(1), diff(1), rcsmerge(1), co(1) merge(1)
All times are GMT -4. The time now is 07:43 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy