Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: awk script to extract transcript information from gff3 file
Top Forums UNIX for Beginners Questions & Answers awk script to extract transcript information from gff3 file Post 303043938 by rdrtx1 on Tuesday 11th of February 2020 11:02:45 AM
Old 02-11-2020
Code:
awk '
(! h++) {print "transcript_id", "gene_name", "description", "chromosome", "strand", "transcript_start", "transcript_end", "gene_start", "gene_end";}
$9 ~ /ID=.*Name=/ {n=$9; sub(".*Name=", "", n); sub(";.*", "", n); gs[n]=$4; ge[n]=$5;}
$3~/.RNA/ {
n=$9; sub(".*Name=", "", n); sub(";.*", "", n);
p=$9; sub(".*Parent=", "", p); sub(";.*", "", p);
print n, p, "Desc", $1, $7, $4, $5, gs[p], ge[p];
}
' FS="\t" OFS="\t" input

Last edited by RavinderSingh13; 02-28-2020 at 01:51 AM..
This User Gave Thanks to rdrtx1 For This Post:
Maduranga
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

AWK to extract information

Hi all, I am working on a shell script to extract information from a file that has output from Oracle sqlplus. The problem is that the output of a single line is spread across multiple lines and i do not know as how to extract the particular filed at ones,which spans multiple lines.... (2 Replies)
Discussion started by: harris2107
2 Replies

2. Shell Programming and Scripting

extract and format information from a file

Hi, Following is sample portion of the file; <JDBCConnectionPool DriverName="oracle.jdbc.OracleDriver" MaxCapacity="10" Name="MyApp_DevPool" PasswordEncrypted="{3DES}7tXFH69Xg1c=" Properties="user=MYAPP_ADMIN" ShrinkingEnabled="false" ... (12 Replies)
Discussion started by: sujoy101
12 Replies

3. UNIX for Dummies Questions & Answers

Write a script to extract information from a db

Hi I need to put together a script that will search certain tables in a db and send that data to a csv file. Basically I am importing data to a db and I want to write a script to check that all information was imported correctly. Thank you (1 Reply)
Discussion started by: ladyAnne
1 Replies

4. Shell Programming and Scripting

Create shell script to extract unique information from one file to a new file.

Hi to all, I got this content/pattern from file http.log.20110808.gz mail1 httpd: Account Notice: close igchung@abc.com 2011/8/7 7:37:36 0:00:03 0 0 1 mail1 httpd: Account Information: login sastria9@abc.com proxy sid=gFp4DLm5HnU mail1 httpd: Account Notice: close sastria9@abc.com... (16 Replies)
Discussion started by: Mr_47
16 Replies

5. Shell Programming and Scripting

How to extract information from a file?

Hi, i have a file like this: <Iteration> <Iteration_iter-num>3</Iteration_iter-num> <Iteration_query-ID>lcl|3_0</Iteration_query-ID> <Iteration_query-def>G383C4U01EQA0A length=197</Iteration_query-def> <Iteration_query-len>197</Iteration_query-len> ... (9 Replies)
Discussion started by: the_simpsons
9 Replies

6. Shell Programming and Scripting

Help with shell script to extract certain information

Hi, I have a file which I need to programmatically split into two files. All the information in the file before pattern "STOP HERE" is to be stripped and output into one file while everything after "STOP HERE" is to be output into a separate file. I would appreciate help on how to do... (8 Replies)
Discussion started by: PTL
8 Replies

7. Shell Programming and Scripting

awk script to parse case with information in two fields of file

The below awk parser works for most data inputs, but I am having trouble with the last one. The problem is in the below rules steps 1 and 2 come from $2 (NC_000013.10:g.20763686_20763687delinsA) and steps 3 and 4 come from $1 (NM_004004.5:c.34_35delGGinsT). Parse Rules: The header is... (0 Replies)
Discussion started by: cmccabe
0 Replies

8. Shell Programming and Scripting

Extract information from file

Gents, If is possible please help. I have a big file (example attached) which contends exactly same value in column, but from column 2 to 6 these values are diff. I will like to compile for all records all columns like the example attached in .csv format (output.rar ).. The last column in the... (11 Replies)
Discussion started by: jiam912
11 Replies

9. Shell Programming and Scripting

Extract information from file

In a particular directory, there can be 1000 files like below. filename is job901.ksh #!/bin/ksh cront -x << EOJ submit file=$PRODPATH/scripts/genReport.sh maxdelay=30 &node=xnode01 tname=job901 &pfile1=/prod/mldata/data/test1.dat ... (17 Replies)
Discussion started by: vedanta
17 Replies

10. Shell Programming and Scripting

sed / awk / grep to extract information from log

Hi all, I have a query that runs that outputs data in the following format - 01/09/12 11:43:40,ADMIN,4,77,Application Group Load: Name(TESTED) LoadId(5137-1-0-1XX-15343-15343) File(/dir/dir/File.T03.CI2.RYR.2012009.11433350806.ARD) InputSize(5344) OutputSize(1359) Rows(2) Time(1.9960)... (8 Replies)
Discussion started by: jeffs42885
8 Replies

LEARN ABOUT SUNOS

intltool-extract

intltool-extract(1)						   User Commands					       intltool-extract(1)

NAME

       intltool-extract - generate header file from XML source file

SYNOPSIS

       intltool-extract [--ini-style] [--help] [--verbose] [--version] [--xml-style] [--scheme-style] source-file

DESCRIPTION

       intltool-extract  generates header files from the strings in the specified input files which gettext can use to merge strings into the .pot
       file.

OPTIONS

       The following options are supported:

       --help	       Show usage and basic help information. You can also use -H to specify this option.

       --ini-style     Specifies that the source file is of type gettext/ini.

       --scheme-style  Specifies that the source file is of type gettext/scheme.  You can also use -O to specify this option.

       --verbose       Provide additional feedback. You can also use -X to specify this option.

       --version       Show version information. You can also use -V to specify this option.

       --xml-style     Specifies that the source file is of type gettext/xml. You can also use -O to specify this option.

OPERANDS

       The following operands are supported:

       source-file     Specifies the pathname of the XML file from which to extract translatable content.

EXAMPLES

       Example 1: Generating a Header File for a Schemas File, With Verbose Output

       example% intltool-extract -O --scheme-style foo.schemas.in

EXIT STATUS

       The following exit values are returned:

       0	Application exited successfully

       >0	Application exited with failure

FILES

       The following files are used by this application:

       /usr/bin/intltool-extracThe command-line executable for the application.

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Availability		     |SUNWgnome-common-devel	   |
       +-----------------------------+-----------------------------+
       |Interface stability	     |External			   |
       +-----------------------------+-----------------------------+

SEE ALSO

       intltool-merge(1), intltool-prepare(1), intltool-unicodify(1), intltool-update(1), intltoolize(1)

NOTES

       For more information, see the I18N-HOWTO file, which is provided with the intltool source code.

       Updated by Damien Donlon, Sun Microsystems  Inc., 2003. Written by Darin Adler, Kenneth Christiansen, Maciej Stachowiak.

SunOS 5.10							    3 Apr 2003						       intltool-extract(1)
All times are GMT -4. The time now is 01:13 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy