How to extract some parts of a file to create some outfile


 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting How to extract some parts of a file to create some outfile
# 22  
Old 05-11-2009
Dear All,
I was trying like below to get rid off the space in front of the line(see the previous post).
It will be very nice if anybody can correct this code below.
Code:
#!/usr/bin/perl -w

$#ARGV==0 or die "Usage: 2ndprocess-megan-script 1st-output-file-as-inputfile\n";

$i=1;
while (<>){
chomp;
   
 if (/Taxonomy:/ ) { 
     $x = $1; $x =~ s/^\s+|\s+$//g; ##for this line there is the error
     open(OUT,">>","output_".$i++) or die "Cannot open for writing:$!\n";
     $f=1; next;
 }
 
 if (/\+*End of summary for file/ ){
    $f=0;close(OUT);next;
 }
 if ($f) { print OUT $_."\n";}
}

But its not working.

Can anybody please help me to have the out put in the form:
Gammaproteobacteria: 2767
Alphaproteobacteria: 4123
Deltaproteobacteria: 1343
Epsilonproteobacteria: 26
Betaproteobacteria: 397
unclassified Proteobacteria: 48
Elusimicrobium: 2
candidate division WWE1: 9
Flavobacteria: 2358
Sphingobacteria: 136
Bacteroidia: 162
environmental samples: 21
Chlorobia: 77
Planctomycetacia: 40
Spirochaetes (class): 15
Nitrospira (class): 1
Bacilli: 25
Not assigned: 1445
No hits: 220253

Thanks a lot.
Best,
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. UNIX for Beginners Questions & Answers

TCL script to extract the file name and then create two independent list

I am having one problem as stated below Problem Description I am having some "sv" extension files , I am using "glob" to extract the matching files , Now in these matching files , I need to split them and extract the elements and create different lists. For example set files This... (1 Reply)
Discussion started by: kshitij
1 Replies

2. Shell Programming and Scripting

Extract parts of the line

I have a long list of lines in a txt file which i'm only interested to extract the list of domains like the colored ones. domain.com domain.com/page codes $.09 domain.org domain.org/page2/ codes $0.10 domain.net domain.net/page03 codes $0.05 domain.info ... (3 Replies)
Discussion started by: garfish
3 Replies

3. Solaris

Solaris 10 error "-sh: /tmp/outfile: cannot create"

Hello, Each time a user log on to host, they receive below error: -sh: /tmp/outfile: cannot create Example: $ ssh host user@host's password: Last login: Fri Dec 4 08:17:28 2015 from client.ref |-----------------------------------------------------------------| -sh:... (2 Replies)
Discussion started by: feroccimx
2 Replies

4. Shell Programming and Scripting

Incrementing parts of ten digits number by parts

I have number in file which contains date and serial number: 2013101000. The last two digits are serial number (00). So maximum of serial number is 100. After reaching 100 it becomes 00 with incrementing 10 which is day with max 31. after reaching 31 it becomes 00 and increments 10... (31 Replies)
Discussion started by: Natalie
31 Replies

5. Shell Programming and Scripting

Extract Parts of File

Hello All, I have a file like this Define schema flat_file_schema ( a varchar(20) ,b varchar(30) ,c varchar(40) ); (Insert into table ( a ,b ,c ) values ( 1 ,2 ,3 ); (4 Replies)
Discussion started by: nnani
4 Replies

6. Shell Programming and Scripting

extract certain parts from a file

I have a logfile from which i need to extract certain pattern based on the time but the problem here is the time is not same for all days. Input file: Mon 12:34:56 abvjingjgg Mon 12:34:57 ofjhjgjhgh . . . Mon 22:30:00 kkfng . . . Mon 23:12:23 kjgsdafhkljf . . . Tue 01:04:54... (8 Replies)
Discussion started by: gpk_newbie
8 Replies

7. Shell Programming and Scripting

awk? create similarity matrix by calculating overlaps between sets comprising of individual parts

Hi everyone I am very new at awk and to me the task I need to get done is very very challenging... Nevertheless, after admiring how fast and elegant issues are being solved here I am sure this is my best chance. I have a 2D data file (input file is a plain tab-delimited text file). The first... (1 Reply)
Discussion started by: stonemonkey
1 Replies

8. 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

9. Shell Programming and Scripting

Extract date from filename and create a new file

Hi, i have a filename CRED20102009.txt in a server 20102009 is the date of the file ddmmaaaa format the complete route is /dprod/informatica/Fuentes/CRED20102009.csv i want to extract the date to create a new file named Parameters.txt I need to create Parameters.txt with this... (6 Replies)
Discussion started by: angel1001
6 Replies

10. Shell Programming and Scripting

extract columns from 2 different files and create new file

Hi All, I have 2 issues while working with file. 1. I have 2 delimited(~) files. I want to extract column numbner 3 from file1 and column number 8 from file2 and paste it into file3. I have tried using cut, but not able to get answer. 2. i have 2 filxed-width file. I wanted to do same... (1 Reply)
Discussion started by: Amit.Sagpariya
1 Replies
Login or Register to Ask a Question
create_sysfile(1M)														create_sysfile(1M)

NAME
create_sysfile - create a kernel system file SYNOPSIS
[outfile] DESCRIPTION
The command creates a kernel configuration description file (system file) which can be used as input to the commands kconfig(1M) or mk_ker- nel(1M). The system file that is generated is of type version 1 (see system(4)) and is built according to the drivers required by the cur- rent system hardware. This command is intended for use during the install process when the system does not have a system file. The command uses the ioscan(1M) command to scan the system hardware and adds all drivers it can identify to run the existing hardware. If outfile is specified, the resulting system file is sent to outfile. If outfile is not specified, the output is placed in the file RETURN VALUE
Upon completion, returns with one of the following exit values: 0 Successful. 1 One or more errors were reported. DIAGNOSTICS
Errors are sent to stderr. Most of the diagnostic messages from are self-explanatory. Errors cause to halt immediately. WARNINGS
is obsolete and will be removed in a future version of HP-UX. AUTHOR
was developed by HP. SEE ALSO
ioscan(1M), kconfig(1M), mk_kernel(1M), system(4), kconfig(5). create_sysfile(1M)