Concatenate lines between lines starting with a specific pattern
Hi,
I have a file such as:
---
>contig00001 length=35524 numreads=2944
gACGCCGCGCGCCGCGGCCAGGGCTGGCCCA
CAGGCCGCGCGGCGTCGGCTGGCTGAG
>contig00002 length=4242 numreads=43423
ATGCCGAAGGTCCGCCTGGGGCTGG
CGCCGGGAGCATGTAGCG
---
I would like to concatenate the lines not starting with ">" (concatenate any lines between lines starting with ">"). My wanted output is:
---
>contig00001 length=35524 numreads=2944
gACGCCGCGCGCCGCGGCCAGGGCTGGCCCACAGGCCGCGCGGCGTCGGCTGGCTGAG
>contig00002 length=4242 numreads=43423
ATGCCGAAGGTCCGCCTGGGGCTGGCGCCGGGAGCATGTAGCG
---
Thanks
---------- Post updated at 01:54 PM ---------- Previous update was at 01:48 PM ----------
I have tried like this:
% awk '{if(substr($0,1)==">") print $0"\n";else printf("%s",$0);}' test2.fna | fold -w60
But my output looks like:
Instead of what I want which is like this:
hi,,
i hav a file with many lines.i need to remove all lines before a line begginning with a specific pattern from the file because these lines are not required.
Can u help me out with either a perl script or shell script
example:-
if file initially contains lines:
a
b
c
d
.1.2
d
e
f... (2 Replies)
i have a file sample.txt containing
i want to delete lines starting with 123 neglecting spaces and tabs.
but not lines containing 123. i.e.
i want files sample.txt as
help me
thanxx (4 Replies)
Hi, just tried some script, awk, sed for the last 2 hours and now need help.
Let's say I have a huge file of 800,000 lines like this :
It's a tedious job to look through it, I'd like to remove those useless lines in it as there's a few thousands :
Or to be even more precise :
if line1 =... (6 Replies)
Input:
09:43:46,538 INFO first text
10:45:46,538 INFO second
text
11:00:46,538 INFO third
more
text
Output:
09:43:46,538 INFO first text
10:45:46,538 INFO second text
11:00:46,538 INFO third more text
The rule is to append all lines so each line contains this format... (7 Replies)
I have a file that looks like this:
John Smith
http://www.profile1.com
http://www.profile2.com
http://www.profile3.com
Marc Olsen
http://www.profile4.com
http://www.profile5.com
http://www.profile6.com
http://www.profile7.com
Lynne Doe
http://www.profile8.com
http://www.profile9.com... (3 Replies)
How to concatenate lines with specific pattern?
I have data dumped from a table into text file. In some occurrence the data row is split into two rows.
Example:
12345678|Global Test|Global Test Task|My Request|Date|Date|Date|1|1|
12345679|Global Test2|Global Test Task2|My... (8 Replies)
Hi ,
I want to insert data into a new file after grepping specific pattern . for more info please read following
for example:
abc=12345678902222
def=45678904444
-------
-------
INAVLID ABC
I want to "INAVLID ABC" grep above pattern from multiple files and want to write abc value and ... (3 Replies)
Hi,
I need to delete all lines in the file using vi editor which start with word aternqaco.
Please assist.
aternqaco.__oracle_base='/amdbqa01/app/oracle'#ORACLE_BASE set from environment
aternqa.__oracle_base='/amdbqa01/app/oracle'#ORACLE_BASE set from environment... (3 Replies)
Dear all,
I would like to delete even lines starting with "N" together with their respective titles which are actually odd lines.
Below is the example of input file. I would like to remove line 8 and 12 together with its title line, i.e., line 7 and 11, respectively.... (2 Replies)
Hi all!
Thanks for taking the time to view this!
I want to grep out all lines of a file that starts with pattern 1 but also does not match with the second pattern.
Example:
Drink a soda
Eat a banana
Eat multiple bananas
Drink an apple juice
Eat an apple
Eat multiple apples
I... (8 Replies)
Discussion started by: demmel
8 Replies
LEARN ABOUT REDHAT
split
SPLIT(1) FSF SPLIT(1)NAME
split - split a file into pieces
SYNOPSIS
split [OPTION] [INPUT [PREFIX]]
DESCRIPTION
Output fixed-size pieces of INPUT to PREFIXaa, PREFIXab, ...; default PREFIX is `x'. With no INPUT, or when INPUT is -, read standard
input.
Mandatory arguments to long options are mandatory for short options too.
-a, --suffix-length=N
use suffixes of length N (default 2)
-b, --bytes=SIZE
put SIZE bytes per output file
-C, --line-bytes=SIZE
put at most SIZE bytes of lines per output file
-l, --lines=NUMBER
put NUMBER lines per output file
--verbose
print a diagnostic to standard error just before each output file is opened
--help display this help and exit
--version
output version information and exit
SIZE may have a multiplier suffix: b for 512, k for 1K, m for 1 Meg.
AUTHOR
Written by Torbjorn Granlund and Richard M. Stallman.
REPORTING BUGS
Report bugs to <bug-coreutils@gnu.org>.
COPYRIGHT
Copyright (C) 2002 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICU-
LAR PURPOSE.
SEE ALSO
The full documentation for split is maintained as a Texinfo manual. If the info and split programs are properly installed at your site,
the command
info split
should give you access to the complete manual.
split (coreutils) 4.5.3 February 2003 SPLIT(1)