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 REDHAT
cgbbrd
CGBBRD(l) ) CGBBRD(l)
NAME
CGBBRD - reduce a complex general m-by-n band matrix A to real upper bidiagonal form B by a unitary transformation
SYNOPSIS
SUBROUTINE CGBBRD( VECT, M, N, NCC, KL, KU, AB, LDAB, D, E, Q, LDQ, PT, LDPT, C, LDC, WORK, RWORK, INFO )
CHARACTER VECT
INTEGER INFO, KL, KU, LDAB, LDC, LDPT, LDQ, M, N, NCC
REAL D( * ), E( * ), RWORK( * )
COMPLEX AB( LDAB, * ), C( LDC, * ), PT( LDPT, * ), Q( LDQ, * ), WORK( * )
PURPOSE
CGBBRD reduces a complex general m-by-n band matrix A to real upper bidiagonal form B by a unitary transformation: Q' * A * P = B. The
routine computes B, and optionally forms Q or P', or computes Q'*C for a given matrix C.
ARGUMENTS
VECT (input) CHARACTER*1
Specifies whether or not the matrices Q and P' are to be formed. = 'N': do not form Q or P';
= 'Q': form Q only;
= 'P': form P' only;
= 'B': form both.
M (input) INTEGER
The number of rows of the matrix A. M >= 0.
N (input) INTEGER
The number of columns of the matrix A. N >= 0.
NCC (input) INTEGER
The number of columns of the matrix C. NCC >= 0.
KL (input) INTEGER
The number of subdiagonals of the matrix A. KL >= 0.
KU (input) INTEGER
The number of superdiagonals of the matrix A. KU >= 0.
AB (input/output) COMPLEX array, dimension (LDAB,N)
On entry, the m-by-n band matrix A, stored in rows 1 to KL+KU+1. The j-th column of A is stored in the j-th column of the array AB
as follows: AB(ku+1+i-j,j) = A(i,j) for max(1,j-ku)<=i<=min(m,j+kl). On exit, A is overwritten by values generated during the
reduction.
LDAB (input) INTEGER
The leading dimension of the array A. LDAB >= KL+KU+1.
D (output) REAL array, dimension (min(M,N))
The diagonal elements of the bidiagonal matrix B.
E (output) REAL array, dimension (min(M,N)-1)
The superdiagonal elements of the bidiagonal matrix B.
Q (output) COMPLEX array, dimension (LDQ,M)
If VECT = 'Q' or 'B', the m-by-m unitary matrix Q. If VECT = 'N' or 'P', the array Q is not referenced.
LDQ (input) INTEGER
The leading dimension of the array Q. LDQ >= max(1,M) if VECT = 'Q' or 'B'; LDQ >= 1 otherwise.
PT (output) COMPLEX array, dimension (LDPT,N)
If VECT = 'P' or 'B', the n-by-n unitary matrix P'. If VECT = 'N' or 'Q', the array PT is not referenced.
LDPT (input) INTEGER
The leading dimension of the array PT. LDPT >= max(1,N) if VECT = 'P' or 'B'; LDPT >= 1 otherwise.
C (input/output) COMPLEX array, dimension (LDC,NCC)
On entry, an m-by-ncc matrix C. On exit, C is overwritten by Q'*C. C is not referenced if NCC = 0.
LDC (input) INTEGER
The leading dimension of the array C. LDC >= max(1,M) if NCC > 0; LDC >= 1 if NCC = 0.
WORK (workspace) COMPLEX array, dimension (max(M,N))
RWORK (workspace) REAL array, dimension (max(M,N))
INFO (output) INTEGER
= 0: successful exit.
< 0: if INFO = -i, the i-th argument had an illegal value.
LAPACK version 3.0 15 June 2000 CGBBRD(l)
01-19-2019
.