What is the correct syntax to pipe or run three awk commands? Basically, using the output of the first awk as input in the second. Then using the output of the second awk in the third. Thank you .
Code:
awk 'FNR==NR {E[$1]; next }$3 in E {print $3, $5}' panel_genes.txt RefSeqGene.txt > update.txt | awk 'NR==FNR { X[toupper($1)]++ ; next } ; toupper($13) in X' update.txt hg19_annovar_refGene.txt > match.txt | awk -v OFS="\t" '{ sub(/\r/, "") } ; NR==FNR { N=$2 ; sub(/\..*/, "", $2); A[$2]=N; next } ; $2 in A { $2=A[$2] } 1' update.txt match.txt > hg19_refgene.txt
How i can combine output of two commands in one file.......i tried this but it is not working although each command is working good seperately.....
head -1 filename | tail -1 filename
i think there is problem with command concatenator? (16 Replies)
This script is supposed to find out if tomcat is running or not.
#!/bin/sh
if netstat -a | grep `grep ${1}: /tomcat/bases | awk -F: '{print $3}'` > /dev/null
then
echo Tomcat for $1 running
else
echo Tomcat for $1 NOT running
fi
the /tomcat/bases is a file that... (2 Replies)
Hi All. Thanks for your help in advance.
I have a requirement to examine the number of delimiters in each record of a file. If the record has the expected number of delimiters it should be passed into a 'good' file. If it does not, the record should be passed into a 'bad' file. I have been able... (8 Replies)
Hi Friends,
I am using a command that prints certain lines from a file.
For ex:
cat input
abc chr1 456
def chr1 789
ghi chr1 999
jjj chr1 777
jhk chr7 914
My command
awk '{if($2=="chr1" && $3>=456 && $3<=999) {print $0}}' OFS="\t" input
Output being printed is
abc chr1 456 (7 Replies)
Dear friends,
I am just trying write one script using 2 files
one file will contain details like below
#X SERVER X LOCATION
URL="http://www.abcd.com"
FILENAME="abc.txt"
ID_NAME="myabc_xyz"
SERVER_PATH="/usr/local/dummy/html/....."
#Y SERVER Y LOCATION
URL="http://www.xyz.com"... (10 Replies)
my code:
gawk 'NR>'"${LASTLINENUM}"' && NR<='"${LINEENDNUM}"'' ${LOGFILE} | gawk '{l=$0;} /'"${STRING1}"'/ && /'"${STRING2}"'/ {for (i=NR-'"${BEFOREGLAF}"'; i<=NR+'"${AFTERGLAF}"'; i++) o=i; t++;} END { for(i=1; i<=NR; i++) if (o) print l; print t+=0;}'
i would like to combine this into one... (5 Replies)
Hi,
Can someone please guide me how to combine the following two awk calls in one?
I noticed that it is very often situation for me, and I think that it can be replaced with one awk call.
The question is more general, not the exact one.
echo "A B C/D" | awk '{print $3}' | awk -F/ '{print... (4 Replies)
Hi,
I have identified how to use command chaining as per below on a file, to capture the header of a file, as well as the line containing the C: drive.
$ cat test.txt
Filesystem Size Used Avail Use% Mounted on
rootfs 237G 153G 84G 65% /
none 237G 153G 84G ... (6 Replies)
Discussion started by: sand1234
6 Replies
LEARN ABOUT DEBIAN
pyp
PYP(1) General Commands Manual PYP(1)NAME
pyp - The Pyed Piper: A Modern Python Alternative to awk, sed and Other Unix Text Manipulation Utilities
SYNOPSIS
pyp [options] files ...
DESCRIPTION
pyp, the Pyed Piper, is a command line tool for text manipulation. It is similar to awk and sed in functionality, but its subcommands are
Python based, and thus more familiar to many programmers.
It can operate both on a per-line base and on the complete input stream. Different features can be pipelined in a single command by using
the pipe character familiar from shell commands.
pyp backs up its input for reruns with modified commands, and can save commands as macros. On the downside, the rerun feature makes it
unsuitable for continuous pipe operation.
OPTIONS
These programs follow the usual GNU command line syntax, with long options starting with two dashes (`-'). A summary of options is
included below. For a complete description, use --manual.
-h, --help
Show this help message and exit.
-m, --manual
Prints out extended help.
-l, --macro_list
Lists all available macros.
-s MACRO_SAVE_NAME, --macro_save=MACRO_SAVE_NAME
Saves current command as macro. use "#" for adding
comments EXAMPLE:
pyp -s "great_macro # prints first letter" "p[1]".
-f MACRO_FIND_NAME, --macro_find=MACRO_FIND_NAME
Searches for macros with keyword or user name.
-d MACRO_DELETE_NAME, --macro_delete=MACRO_DELETE_NAME
Deletes specified public macro.
-g, --macro_group
Specify group macros for save and delete; default is user.
-t TEXT_FILE, --text_file=TEXT_FILE
Specify text file to load. For advanced users,
you should typically cat a file into pyp.
-x, --execute
Execute all commands.
-c, --turn_off_color
Prints raw, uncolored output.
-u, --unmodified_config
Prints out generic PypCustom.py config file.
-b BLANK_INPUTS, --blank_inputs=BLANK_INPUTS
Generate this number of blank input lines; useful for
generating numbered lists with variable 'n'.
-n, --no_input
Use with command that generates output with no input;
same as --dummy_input 1.
-k, --keep_false
Print blank lines for lines that test as False.
default is to filter out False lines from the output.
-r, --rerun
Rerun based on automatically cached data from the last run.
Use this after executing "pyp", pasting input into the shell,
and hitting CTRL-D.
SEE ALSO awk(1), grep(1), sed(1).
AUTHOR
pyp was written by Toby Rosen <tobyrosen@gmail.com>.
This manual page was written by Khalid El Fathi <khalid@elfathi.fr>, for the Debian project (and may be used by others).
March 19, 2012 PYP(1)
01-08-2016
.