Sponsored Content
Full Discussion: Modifying headers
Top Forums UNIX for Dummies Questions & Answers Modifying headers Post 302547335 by Xterra on Monday 15th of August 2011 08:35:55 AM
Old 08-15-2011
Modifying headers

I have a FASTA file with thousands of sequences that looks something like this:
Quote:
>LBHCV-1-C1.seq_Contig_1_(1311)
---------TGGATATGATGATGAACTGGTCACCTACAGCAGCCCTGGTGGTGTCGCAGTTACTCCGGATCCCACAAGCCGTCGTGG-ATATGGTGGCGGGGGCCCACTGGGG-AATCCTGGC-GGGCCTTGCCTACTATTCCATGGTGGGGAACTGGGCTAAGGCCTTGATTGTGATGCTGCTATTCGCCGGCGTTGACGGGGACACCTACACAACGGGAGGA GCGGCGGGCAAGAACGCGCAGGGCCTCACGAGCCTCTTTGCAGTCGGGGCGTCTCAGAAAATCCAGCTCGTAAACACCAACGGCAGCT-GGC-ACATCAAA---------
>LBHCV-1-C10.seq_Contig_1_(1312)
--------TTGGATATGATGATGAACTGGTCACCTACAGCAGCCCTGGTGGTGTCGCAGTTACTCCGGATCCCACAAGCCGTCGTGG-ATATGGTGGCGGGGGCCCACTGGGG-AATCCTGGC-GGGACTTGCCTACTATTCCATGGTGGGGAACTGGGCTAAGGTCTTGATTGTGATGCTACTATTCGCCGGCGTTGACGGGGACACCTACACAACGGGGGGA GCGGCGGGCAAGAACGCGCAGGGCCTCACGAGCCTCTTTGCAGTCGGGGCGTCTCAGAAAATCCAGCTCGTAAACACCAACGGCAGCT-GGC-ACATCAAA---------
>LBHCV-1-C11.seq_Contig_1_(1314)
------CTTTGGATATGATGATGAACTGGTCACCTACAGCAGCCCTGGTGGTGTCGCAGTTACTCCGGATCCCACAAGCCGTCGTGG-ATATGGTGGCGGGGGCCCACTGGGG-AATCCTGGC-GGGCCTTGCCTACTATTCCATGGTGGGGAACTGGGCTAAGGTCTTGATTGTGATGCTACTATTCGCCGGCGTTGACGGGGACACCTACACAACGGGGGGA GCGGCGGGCAAGAACGCGCAGGGCCTCACGAGCCTCTTTGCAGTCGGGGCGTCTCAGAAAATCCAGCTCGTAAACACCAACGGCAGCT-GGC-ACATCAAA---------
I need to modfy the header in such way that everything after the dot is remove. Thus, I will end up with something like this:
Quote:
>LBHCV-1-C1
---------TGGATATGATGATGAACTGGTCACCTACAGCAGCCCTGGTGGTGTCGCAGTTACTCCGGATCCCACAAGCCGTCGTGG-ATATGGTGGCGGGGGCCCACTGGGG-AATCCTGGC-GGGCCTTGCCTACTATTCCATGGTGGGGAACTGGGCTAAGGCCTTGATTGTGATGCTGCTATTCGCCGGCGTTGACGGGGACACCTACACAACGGGAGGA GCGGCGGGCAAGAACGCGCAGGGCCTCACGAGCCTCTTTGCAGTCGGGGCGTCTCAGAAAATCCAGCTCGTAAACACCAACGGCAGCT-GGC-ACATCAAA---------
>LBHCV-1-C10
--------TTGGATATGATGATGAACTGGTCACCTACAGCAGCCCTGGTGGTGTCGCAGTTACTCCGGATCCCACAAGCCGTCGTGG-ATATGGTGGCGGGGGCCCACTGGGG-AATCCTGGC-GGGACTTGCCTACTATTCCATGGTGGGGAACTGGGCTAAGGTCTTGATTGTGATGCTACTATTCGCCGGCGTTGACGGGGACACCTACACAACGGGGGGA GCGGCGGGCAAGAACGCGCAGGGCCTCACGAGCCTCTTTGCAGTCGGGGCGTCTCAGAAAATCCAGCTCGTAAACACCAACGGCAGCT-GGC-ACATCAAA---------
>LBHCV-1-C11
------CTTTGGATATGATGATGAACTGGTCACCTACAGCAGCCCTGGTGGTGTCGCAGTTACTCCGGATCCCACAAGCCGTCGTGG-ATATGGTGGCGGGGGCCCACTGGGG-AATCCTGGC-GGGCCTTGCCTACTATTCCATGGTGGGGAACTGGGCTAAGGTCTTGATTGTGATGCTACTATTCGCCGGCGTTGACGGGGACACCTACACAACGGGGGGA GCGGCGGGCAAGAACGCGCAGGGCCTCACGAGCCTCTTTGCAGTCGGGGCGTCTCAGAAAATCCAGCTCGTAAACACCAACGGCAGCT-GGC-ACATCAAA---------
Thanks
 

10 More Discussions You Might Find Interesting

1. Programming

C Headers

Where can i get C/C++ headers for OS MINIX 2.0.3? (0 Replies)
Discussion started by: biosdos
0 Replies

2. Programming

headers of the query

when we are spooling query o/p to certain txt file,in that file how we can get headers in the query.(through unix shell scripting). for exmple q1="slect * from XXXXXX;"; sqlplus XXX/XXXX@XXXXX spool XXXX.txt $q1 spool off in the text file i want the headers of the query..... ... (0 Replies)
Discussion started by: bhagya.puccha
0 Replies

3. Shell Programming and Scripting

Remove text between headers while leaving headers intact

Hi, I'm trying to strip all lines between two headers in a file: ### BEGIN ### Text to remove, contains all kinds of characters ... Antispyware-Downloadserver.com (Germany)=http://www.antispyware-downloadserver.c om/updates/ Antispyware-Downloadserver.com #2... (3 Replies)
Discussion started by: Trones
3 Replies

4. Shell Programming and Scripting

Merging of files with different headers to make combined headers file

Hi , I have a typical situation. I have 4 files and with different headers (number of headers is varible ). I need to make such a merged file which will have headers combined from all files (comman coluns should appear once only). For example - File 1 H1|H2|H3|H4 11|12|13|14 21|22|23|23... (1 Reply)
Discussion started by: marut_ashu
1 Replies

5. UNIX for Dummies Questions & Answers

Grep Headers

Hi! Trying to find string and then put the above Headers of corresponding fist line. After executing a Property command a get this output: SP/CH-CH Span Name Type TG Idle InUse OffHk OnHk Ring -------- ------------------------------ ------ ---- ----- ----- ----- 02/01-24 CARRIERSS7... (6 Replies)
Discussion started by: Joel_john
6 Replies

6. IP Networking

Modifying IPv4 headers

Hi, My query is: I need to set the IPv4 header fields(like TOS, TTL, Precedence and Flags) in the linux kernel using the system calls. I tried setting the fields using the setsockopt() call using sockets but it is not reflecting the actual IPv4 header fields. Is it possible to modify these... (0 Replies)
Discussion started by: kiran_4u
0 Replies

7. Programming

c - problem with headers?

I have a simple program to create a poker deck, shuffle it and deal cards. Here it is: #include <stdio.h> #include <stdlib.h> #include <time.h> struct Card { char *face, *suit; }; void fillDeck (Card *deck, char *face, char *suit); void shuffle (Card *deck); void... (4 Replies)
Discussion started by: Luke Bonham
4 Replies

8. Shell Programming and Scripting

Editing headers

Hi, I have a folder that contains many (multiple) files 1.fasta 2.fasta 3.fasta 4.fasta 5.fasta . . 100's of files Each such file have data in the following format for example: vi 1.fasta >AB_1 200bp MLKKPIIIGVTGGSGGGKTSVSRAILDSFPNARIAMIQHDSYYKDQSHMSFEERVKTNYDHPLAFDTDFM... (4 Replies)
Discussion started by: Lucky Ali
4 Replies

9. Shell Programming and Scripting

editing headers

Hi, I have a folder that contains many (multiple) files 1.fasta 2.fasta 3.fasta 4.fasta 5.fasta . . 100's of files Each such file have data in the following format for example: vi 1.fasta 58 390 A GTATACATTATTGATGAAGTCCACATGCTTTCTATGGGTGCCTTCAATGCGCTTTTAAAA (7 Replies)
Discussion started by: Lucky Ali
7 Replies

10. UNIX for Dummies Questions & Answers

Email Headers

I'm trying to pick up some Unix SysAdmin skills on my own outside of work through the use of the "Unix and Linux System Administrators Handbook." I've found the exercises to be very beneficial, until I came to this.... "What path did the email take? To Whom was it addressed, and to whom was it... (0 Replies)
Discussion started by: ksmarine1980
0 Replies
SHELL-QUOTE(1p) 					User Contributed Perl Documentation					   SHELL-QUOTE(1p)

NAME
shell-quote - quote arguments for safe use, unmodified in a shell command SYNOPSIS
shell-quote [switch]... arg... DESCRIPTION
shell-quote lets you pass arbitrary strings through the shell so that they won't be changed by the shell. This lets you process commands or files with embedded white space or shell globbing characters safely. Here are a few examples. EXAMPLES
ssh preserving args When running a remote command with ssh, ssh doesn't preserve the separate arguments it receives. It just joins them with spaces and passes them to "$SHELL -c". This doesn't work as intended: ssh host touch 'hi there' # fails It creates 2 files, hi and there. Instead, do this: cmd=`shell-quote touch 'hi there'` ssh host "$cmd" This gives you just 1 file, hi there. process find output It's not ordinarily possible to process an arbitrary list of files output by find with a shell script. Anything you put in $IFS to split up the output could legitimately be in a file's name. Here's how you can do it using shell-quote: eval set -- `find -type f -print0 | xargs -0 shell-quote --` debug shell scripts shell-quote is better than echo for debugging shell scripts. debug() { [ -z "$debug" ] || shell-quote "debug:" "$@" } With echo you can't tell the difference between "debug 'foo bar'" and "debug foo bar", but with shell-quote you can. save a command for later shell-quote can be used to build up a shell command to run later. Say you want the user to be able to give you switches for a command you're going to run. If you don't want the switches to be re-evaluated by the shell (which is usually a good idea, else there are things the user can't pass through), you can do something like this: user_switches= while [ $# != 0 ] do case x$1 in x--pass-through) [ $# -gt 1 ] || die "need an argument for $1" user_switches="$user_switches "`shell-quote -- "$2"` shift;; # process other switches esac shift done # later eval "shell-quote some-command $user_switches my args" OPTIONS
--debug Turn debugging on. --help Show the usage message and die. --version Show the version number and exit. AVAILABILITY
The code is licensed under the GNU GPL. Check http://www.argon.org/~roderick/ or CPAN for updated versions. AUTHOR
Roderick Schertler <roderick@argon.org> perl v5.8.4 2005-05-03 SHELL-QUOTE(1p)
All times are GMT -4. The time now is 02:08 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy