Thank you for the hint, I made two adjustments to the script and commented them. The output is the same but maybe I have the idea just not implementing it correctly? Thank you .
Code:
awk '
BEGIN{
SUBSEP=","
}
FNR==NR{
max[$1,$NF,++count[$1,$NF]]=$3 # read with count each line of f1max
min[$1,$NF,count[$1,$NF]]=$2
next
}
{ for (i in count) # start a loop with setting each line in id to i
split($4,array,"_")
}
(($1,array[1],i++) in max){ # search each matching id line in f2
if(($2>min[array[5],array[1]] && $2<max[array[5],array[1]]) || ($3>max[array[5],array[1]] && $3<max[array[5],array[1]])){
print array[5],array[1],min[array[5],array[1]],max[array[5],array[1]],"exon"
next
}
}
{
print $0,"intron"}' f1 f2
chr7 94024333 94024423 COL1A2_cds_0_0_chr7_94024344_f 0 + intron
chr7 94027049 94027080 COL1A2_cds_1_0_chr7_94027060_f 0 + intron
chr7 94027683 94027718 COL1A2_cds_2_0_chr7_94027694_f 0 + intron
hello experts,
I have a file: File1 Sample Test1
This is a Test
Sample Test2
Another Test
Final Test3
A final Test
I can use sed to delete the line with specific text
ie: sed '/Test2/d' File1.txt > File2.txt
How can I delete the line with the matching text and the line immediately... (6 Replies)
Hi,
I wish to use a column, as inputted by a user from command line, for pattern matching.
awk file:
{
if($1 ~ /^8/)
{
print $0> "temp2.csv"
}
}
something like this, but i want '$1' to be any column as selected by the user from command line.
... (1 Reply)
Dear All,
I would like to add values of a field, if the lines match in a certain field. Then I would like to divide the sum though the number of lines that have a matched field. This is the Input:
Input:
Test1 5
Test1 10
Test2 2
Test2 5
Test2 13
Test3 4
Output:
Test1 7.5
Test1 7.5... (6 Replies)
Sample file:
This is line one,
this is another line,
this is the PRIMARY INDEX line
l ;
This is another line
The command should find the line with “PRIMARY INDEX” and remove the last character from the line preceding it (in this case , comma) and remove the first character from the line... (5 Replies)
Hi,
I want to achieve something similar to what described in another post:
The difference is I want to add the line if the pattern is not found.
File 1:
A123, valueA, valueB
B234, valueA, valueB
C345, valueA, valueB
D456, valueA, valueB
E567, valueA, valueB
F678, valueA, valueB
... (11 Replies)
Hi there,
I'm trying to use awk to print out the entire line that contains a match to a certain regex and then append some text,plus the match to the end of the line.
So far I have:
awk -F: '{print "RG:Z:" $2}' file
Which prints out the match I want plus the additional text, but I'm stuck... (3 Replies)
Hello Help,
2356798 7689867 999 000
123678 20385907 9797 666
17978975 87468976 968978 98798
I am trying to have out put which actually look for the third column value of 9797 and then it insert line there after with first, second column value exactly as the previous line and replace the third... (3 Replies)
The bash bash below extracts the oldest folder from a directory and stores it in filename
That result will match a line in bold in input. In the matching line there is an_xxx digit in italics that
(once the leading zero is removed) will match a line in link. That is the lint to print in output.... (2 Replies)
In the awk I am trying to add :p.=? to the end of each $9 that matches the pattern NM_. The below executes andis close but I can not seem to figure out why the :p.=? repeats in the split as in the green in the current output. I have added comments as well. Thank you :).
file
... (4 Replies)
In the awk below I am trying to cp and paste each matching line in f2 to $3 in f1 if $2 of f1 is in the line in f2 somewhere. There will always be a match (usually more then 1) and my actual data is much larger (several hundreds of lines) in both f1 and f2. When the line in f2 is pasted to $3 in... (4 Replies)
Discussion started by: cmccabe
4 Replies
LEARN ABOUT PHP
count
COUNT(3) 1 COUNT(3)count - Count all elements in an array, or something in an objectSYNOPSIS
int count (mixed $array_or_countable, [int $mode = COUNT_NORMAL])
DESCRIPTION
Counts all elements in an array, or something in an object.
For objects, if you have SPL installed, you can hook into count(3) by implementing interface Countable. The interface has exactly one
method, Countable::count, which returns the return value for the count(3) function.
Please see the Array section of the manual for a detailed explanation of how arrays are implemented and used in PHP.
PARAMETERS
o $array_or_countable
- An array or Countable object.
o $mode
- If the optional $mode parameter is set to COUNT_RECURSIVE (or 1), count(3) will recursively count the array. This is particu-
larly useful for counting all the elements of a multidimensional array.
Caution
count(3) can detect recursion to avoid an infinite loop, but will emit an E_WARNING every time it does (in case the array
contains itself more than once) and return a count higher than may be expected.
RETURN VALUES
Returns the number of elements in $array_or_countable. If the parameter is not an array or not an object with implemented Countable inter-
face, 1 will be returned. There is one exception, if $array_or_countable is NULL, 0 will be returned.
Caution
count(3) may return 0 for a variable that isn't set, but it may also return 0 for a variable that has been initialized with an empty
array. Use isset(3) to test if a variable is set.
EXAMPLES
Example #1
count(3) example
<?php
$a[0] = 1;
$a[1] = 3;
$a[2] = 5;
$result = count($a);
// $result == 3
$b[0] = 7;
$b[5] = 9;
$b[10] = 11;
$result = count($b);
// $result == 3
$result = count(null);
// $result == 0
$result = count(false);
// $result == 1
?>
Example #2
Recursive count(3) example
<?php
$food = array('fruits' => array('orange', 'banana', 'apple'),
'veggie' => array('carrot', 'collard', 'pea'));
// recursive count
echo count($food, COUNT_RECURSIVE); // output 8
// normal count
echo count($food); // output 2
?>
SEE ALSO is_array(3), isset(3), strlen(3).
PHP Documentation Group COUNT(3)
01-19-2019
.