Thanks to take time re reply me I am very grateful.
Now it's seem better ! but the third line DE I have to ignore it because my original file is very very big ! I will have repeated information in my output.
awk 'NR>1&&$3>=80{A[$1]=$1;B[A[$1]]=(B[A[$1]]?B[A[$1]]:$1)" "$2}END{for(i in A) print B[A[i]]}' test.tttt
And this is the output :
Code:
A D E
B C
D E
--> The DE is not a single group it's normally a part of the group 1 (ADE) I don't now if I'm clear
What i want to do after it's to get every group ID and using Bioperl to check the corresponding fasta files in a database. So i need just a output with two line (for this exemple).
Thanks
Moderator's Comments:
Please use code tags when posting data and code samples!
you can get all single pairs belonging to at least one group that is 80 or more with the following :
Code:
$ cat f2
ID1 ID2 Identity
A B 70
A C 50
A D 90
A E 80
B C 95
B D 66
B E 47
C D 35
C E 25
D E 98
A B 70
A C 50
A D 90
A E 40
$ awk 'NR>1&&$3>=80{i=$1" "$2;j=$2" "$1;t=i<j?i:j;C[t]}END{for(k in C) print k}' f2
A D
A E
B C
D E
$
NOTE that this code assume that an A D association is just another D A association, letters are just displayed from lower to higher :
consider the following example :
Code:
$ cat f3
A B 10
B A 80
C D 70
E D 90D B 80
A D 10
D A 93
$ awk 'NR>1&&$3>=80{i=$1" "$2;j=$2" "$1;t=i<j?i:j;C[t]}END{for(k in C) print k}' f3A B
A D
B DD E
$
---------- Post updated at 04:48 PM ---------- Previous update was at 04:24 PM ----------
you can also try the following code
Code:
$ cat f2
ID1 ID2 Identity
A B 70
A C 50
A D 90
A E 80
B C 95
B D 66
B E 47
C D 35
C E 25
D E 98
A B 70
A C 50
A D 90
A E 40
$ awk 'NR>1&&$3>=80{x=$1" "$2;for(i in A) {if (A[i]~x) next};A[$1]=(A[$1]?A[$1]:$1)" "$2}END{for(i in A) print A[i]}' f2
A D E
B C
---------- Post updated at 05:00 PM ---------- Previous update was at 04:48 PM ----------
To avoid that a same $2 appear more than once within a group you can also try :
Code:
awk 'NR>1&&$3>=80{A[$1]=(A[$1]?A[$1]:$1)(A[$1]~$2?z:" "$2)}END{for(i in A) print A[i]}' yourfile
Thanks a lot it works !! but when i use the code for my initial file that i post in the first message it don't work ): ! I never use before the awk code i must learn it. It is possible to just change the A in your code with the noun of my first column ? Other thing this code can work with a very big data ? or just adapted for this specific case ?
I do have a large matrix of the following format and it is tab delimited
ch-ab1-20 ch-bb2-23 ch-ab1-34 ch-ab1-24 er-cc1-45 bv-cc1-78
ch-ab1-20 0 2 3 4 5 6
ch-bb2-23 3 0 5 ... (6 Replies)
Hi All
I do have a matrix in the following format
a_2 a_3 s_4 t_6
b 0 0.9 0.004 0
c 0 0 1 0
d 0 0.98 0 0
e 0.0023 0.96 0 0.0034
I have thousands of rows
I would like to parse the maximum value in each of the row and out put that highest value along the column header of... (2 Replies)
Hi,
I do have couple of files in a folder. The names of each of the files have a pattern.
ahet_005678.txt
ahet_005898.txt
ahet_007678.txt
ahet_004778.txt
...
...
ahet_002378.txt
Each of the above files have the same pattern of data with 4 columns and have an header for the last 3... (4 Replies)
Hi everyone
I am very new at awk but think that that might be the best strategy for this. I have a matrix very similar to a correlation matrix and in practical terms I need to convert it into a list containing the values from the matrix (one value per line) with the first field of the line (row... (5 Replies)
Hi all,
Is there a way to convert full data matrix to linearised left data matrix?
e.g full data matrix
Bh1 Bh2 Bh3 Bh4 Bh5 Bh6 Bh7
Bh1 0 0.241058 0.236129 0.244397 0.237479 0.240767 0.245245
Bh2 0.241058 0 0.240594 0.241931 0.241975 ... (8 Replies)
Hi All
I would like to merge multiple files with the same row and column size into a matrix format
In a folder I have multiple files in the following format
vi 12.txt
a 1
b 5
c 7
d 0
vi 45.txt
a 3
b 6
c 9
d 2
vi 9.txt
a 4 (7 Replies)
Hey guys,
I have this file generated by me... i want to create some HTML output from it.
The problem is that i am really confused about how do I go about reading the file.
The file is in the following format:
TID1 Name1 ATime=xx AResult=yyy AExpected=yyy BTime=xx BResult=yyy... (8 Replies)
01-03-2012
