After a bash function is run the below file is produced:
out_name.txt tab-delimeted
I am trying to add a condition that will suppress the warning message produced if $2 is (variantchecker): Intronic position given for a non-genomic reference sequence.,
In addition, that the $1 string "is an intronic variant" is displayed instead of the waring. My 2nd attempt to incorporate these changes is below,
which executes but nothing results. Thank you .
desired result
awk
Last edited by cmccabe; 03-09-2017 at 01:11 PM..
Reason: fixed format
Does anyone know how I can supress the "Killed" message that's produced when I kill a process? I've got a script that performs a "tail -f" on a database error log and pipes the output into an awk script which looks for certain error messages and forwards any that qualify to my pager. The problem... (2 Replies)
Hi All
this is a simple script
#! /bin/bash
FileCnt=`ls -lrt $DIR/* | wc -l`
echo $FileCnt
how could i escape the error msg if there are no files in $DIR
ls: /home/sayantan/test/files/cnt/*: No such file or directory
0
Looking forward for a quick reply
Regards, Newbie (2 Replies)
How can I modify my awk code to get rid of the divion by zero error message? If I run the script without an input file, it should return error message "Input file missing" but not divison by zero.
Code:
#!/bin/nawk -f
BEGIN {
if (NR == 0)
{print "Input file... (4 Replies)
Hi
I have a script which connects to oracle using sqlplus
if ! check_sqlplus "$ORACLE_SID" ; then
echo "Unable to use sqlplus for sid $ORACLE_SID"
return 1
else
echo "attempting to connect to database"
echo $ORACLE_HOME
echo $ORACLE_SID
echo "Status before entering... (2 Replies)
Hi Friends,
I am using the below code in my script:
elif
then
NEW_LINE=`echo $Line | awk '{sub ($4, "2010\\\/04\\\/07"); printf "# %s %9s %18s\n", $2,$3,$4}'`
sed $n" s/.*/$NEW_LINE/" kfile > tmp
mv tmp kfile
fi
Around 30 lines are replaced by this code... (2 Replies)
Hi,
I am trying to run a script using awk and sed a few times.
The script itself seems to work fine but in a final awk statement it throws up a warning:
awk: warning: escape sequence `\.' treated as plain `.'
script:
... (3 Replies)
Hi,
I was looking for a simple code to suppress the text between 2 characters. the characters can be of same kind like "*" or "(" and ")". The number of characters are not consistent and could vary.
How can I suppress the text between 2 characters?
Example:
Input : Hello (Within Bracket)... (8 Replies)
Hello,
I know this isn't exactly a shell script question but I'm not sure where else to post it.
I am running a java program out of a shell script. There are times when I get an error like,
"java.lang.ArrayIndexOutOfBoundsException: 22
at blah, blah
at blah, blah
... (3 Replies)
Hello :
I want to make a netfilter conntrack module for myself. So I copy all the source code about netfilter conntrack from kernel source tree to my external directory. It can be insmod after compiled. Then I add some members to the struct nf_conn, and it 's compiled successfully. However, it... (1 Reply)
Discussion started by: 915086731
1 Replies
LEARN ABOUT DEBIAN
dotter
DOTTER:(1) General Commands Manual DOTTER:(1)NAME
dotter - Sequence dotplots with image enhancement tools.
SYNOPSIS
dotter [options] <horizontal_sequence> <vertical_sequence> [X options]
DESCRIPTION
Reference: Sonnhammer ELL & Durbin R (1995). A dot-matrix program with dynamic threshold control suited for genomic DNA and protein
sequence analysis. Gene 167(2):GC1-10.
Allowed types:
Protein - Protein DNA - DNA DNA - Protein
Options:
-b <file>
Batch mode, write dotplot to <file>
-l <file>
Load dotplot from <file>
-m <float>
Memory usage limit in Mb (default 0.5)
-z <int>
Set zoom (compression) factor
-p <int>
Set pixel factor manually (ratio pixelvalue/score)
-W <int>
Set sliding window size. (K => Karlin/Altschul estimate)
-M <file>
Read in score matrix from <file> (Blast format; Default: Blosum62).
-F <file>
Read in sequences and data from <file> (replaces sequencefiles).
-f <file>
Read feature segments from <file>
-H Do not calculate dotplot at startup.
-R Reversed Greyramp tool at start.
-r Reverse and complement horizontal_sequence (DNA vs Protein)
-D Don't display mirror image in self comparisons
-w For DNA: horizontal_sequence top strand only (Watson)
-c For DNA: horizontal_sequence bottom strand only (Crick)
-q <int>
Horizontal_sequence offset
-s <int>
Vertical_sequence offset
Some X options: -acefont <font> Main font. -font <font> Menu font.
SEE ALSO
http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html for more info.
AUTHOR
Erik.Sonnhammer@cgb.ki.se Version 3.1, compiled Jul 10 2010
July 2010 DOTTER:(1)