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 PHP
substr
SUBSTR(3) 1 SUBSTR(3)substr - Return part of a stringSYNOPSIS
string substr (string $string, int $start, [int $length])
DESCRIPTION
Returns the portion of $string specified by the $start and $length parameters.
PARAMETERS
o $string
- The input string. Must be one character or longer.
o $start
- If $start is non-negative, the returned string will start at the $start'th position in $string, counting from zero. For
instance, in the string ' abcdef', the character at position 0 is ' a', the character at position 2 is ' c', and so forth. If
$start is negative, the returned string will start at the $start'th character from the end of $string. If $string is less than or
equal to $start characters long, FALSE will be returned.
Example #1
Using a negative $start
<?php
$rest = substr("abcdef", -1); // returns "f"
$rest = substr("abcdef", -2); // returns "ef"
$rest = substr("abcdef", -3, 1); // returns "d"
?>
o $length
- If $length is given and is positive, the string returned will contain at most $length characters beginning from $start (depend-
ing on the length of $string). If $length is given and is negative, then that many characters will be omitted from the end of
$string (after the start position has been calculated when a $start is negative). If $start denotes the position of this trunca-
tion or beyond, false will be returned. If $length is given and is 0, FALSE or NULL, an empty string will be returned. If
$length is omitted, the substring starting from $start until the end of the string will be returned.
Example #2
Using a negative $length
<?php
$rest = substr("abcdef", 0, -1); // returns "abcde"
$rest = substr("abcdef", 2, -1); // returns "cde"
$rest = substr("abcdef", 4, -4); // returns false
$rest = substr("abcdef", -3, -1); // returns "de"
?>
RETURN VALUES
Returns the extracted part of $string; or FALSE on failure, or an empty string.
CHANGELOG
+--------------+---------------------------------------------------+
| Version | |
| | |
| | Description |
| | |
+--------------+---------------------------------------------------+
|5.2.2 - 5.2.6 | |
| | |
| | If the $start parameter indicates the position |
| | of a negative truncation or beyond, false is |
| | returned. Other versions get the string from |
| | start. |
| | |
+--------------+---------------------------------------------------+
EXAMPLES
Example #3
Basic substr(3) usage
<?php
echo substr('abcdef', 1); // bcdef
echo substr('abcdef', 1, 3); // bcd
echo substr('abcdef', 0, 4); // abcd
echo substr('abcdef', 0, 8); // abcdef
echo substr('abcdef', -1, 1); // f
// Accessing single characters in a string
// can also be achieved using "square brackets"
$string = 'abcdef';
echo $string[0]; // a
echo $string[3]; // d
echo $string[strlen($string)-1]; // f
?>
Example #4
substr(3) casting behaviour
<?php
class apple {
public function __toString() {
return "green";
}
}
echo "1) ".var_export(substr("pear", 0, 2), true).PHP_EOL;
echo "2) ".var_export(substr(54321, 0, 2), true).PHP_EOL;
echo "3) ".var_export(substr(new apple(), 0, 2), true).PHP_EOL;
echo "4) ".var_export(substr(true, 0, 1), true).PHP_EOL;
echo "5) ".var_export(substr(false, 0, 1), true).PHP_EOL;
echo "6) ".var_export(substr("", 0, 1), true).PHP_EOL;
echo "7) ".var_export(substr(1.2e3, 0, 4), true).PHP_EOL;
?>
The above example will output:
1) 'pe'
2) '54'
3) 'gr'
4) '1'
5) false
6) false
7) '1200'
ERRORS /EXCEPTIONS
Returns FALSE on error.
Example #5
<?php
var_dump(substr('a', 1)); // bool(false)
?>
SEE ALSO strrchr(3), substr_replace(3), preg_match(3), trim(3), mb_substr(3), wordwrap(3), String access and modification by character.
PHP Documentation Group SUBSTR(3)