Sponsored Content
Top Forums Shell Programming and Scripting Randomly selecting sequences and generating specific output files Post 302786545 by Xterra on Wednesday 27th of March 2013 05:25:41 PM
Old 03-27-2013
Scrutinizer,
I am afraid I do not understand your script. I get some error when trying to run the script.
Am I missing something?
X
Code:
awk -v s=3 -v iter=1 '
  NR==FNR { 
    next 
  }
  FNR==1 {
    if(!set) {
      srand;
      n=NR-1
      for(i=1; i<=s; i++) {
        line=0
        while(!line || line in A) line=int(rand*n)+1
        A[line]
      }
      set=1
    }
    close(f)
    f=FILENAME ".out" iter
  } 
  FNR in A {
    print > f
  }
' infile1.txt infile1.txt infile2.txt
awk: cmd. line:7: srand;
awk: cmd. line:7: ^ syntax error
awk: cmd. line:11: while(!line || line in A) line=int(rand*n)+1
awk: cmd. line:11: ^ syntax error
awk: cmd. line:11: while(!line || line in A) line=int(rand*n)+1
awk: cmd. line:11:

---------- Post updated at 05:25 PM ---------- Previous update was at 05:24 PM ----------

Hanson44,
Sheel scripting will be ok too.
Thanks!
X
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Generating files of specific size

I've been working on getting a script to take size, dir name and file name variables from an input file and creating the same dir structure along with the file of specific size. An example of the input file: size/dirname/filename 2100/JAN_06/12345ABC.TCC 2354/FEB_06/24564XYZ.NOS... (2 Replies)
Discussion started by: nxd25
2 Replies

2. UNIX for Dummies Questions & Answers

randomly renaming files

I have a directory of files that look like filename 001.ext, filename 002.ext, etc. I'd like to rename the files with unique random numbered names, so that the original filenames are stripped and the files are given a new, random number name. I'm not super new to UNIX, but I don't often use it for... (2 Replies)
Discussion started by: platz
2 Replies

3. Shell Programming and Scripting

PERL - Selecting specific files based on 'date stamp' values

Hi, I've list of files in a directory, which have date stamp value in their names. ex: abc_data_20071102.csv, abc_data_20091221.csv, abc_data_20100110.csv, abc_data_20100222.csv, abc_data_20080620.csv,... etc., I need to select and process only files, within the given date... (4 Replies)
Discussion started by: ganapati
4 Replies

4. Shell Programming and Scripting

Trimming sequences based on specific pattern

My files look like this And I need to cut the sequences at the last "A" found in the following 'pattern' -highlighted for easier identification, the pattern is the actual file is not highlighted. The expected result should look like this Thus, all the sequences would end with AGCCCTA... (2 Replies)
Discussion started by: Xterra
2 Replies

5. Shell Programming and Scripting

Removing specific sequences from file

My file looks like this But I need to remove the entry with the identifier >Reference1 along with the entire sequence. Thus, I will end up having the following file Thanks in advance! (2 Replies)
Discussion started by: Xterra
2 Replies

6. UNIX for Dummies Questions & Answers

Selecting specific line using awk

Hi, I would like to get the specific line from the file taking specific coloumn as reference. Thanks and Regards (1 Reply)
Discussion started by: kkarthik_kaja
1 Replies

7. Shell Programming and Scripting

Selecting sequences based on scores

I have two files with thousands of sequences of different lengths. infile1 contains the actual sequences and infile2 the scores for each A, T, G and C in infile1. Something like this: infile1: >HZVJKYI01ECH5R TTGATGTGCCAGCTGCCGTTGGTGTGCCAA >HZVJKYI01AQWJ8 GGATATGATGATGAACTGGTTTGGCACACC... (4 Replies)
Discussion started by: Xterra
4 Replies

8. Shell Programming and Scripting

Help with selecting files from "diff" output

I have two directories Dir_A and Dir_A_Arc. Need help with a shell script. The shell script needs to take the path to these two directories as parameters $1 and $2. The script needs to check if any files exist in these directories and if either of the directories are empty then exit... (5 Replies)
Discussion started by: gaurav99
5 Replies

9. UNIX for Beginners Questions & Answers

Split Command Generating Incomplete Output Files

Hello All, May i please know how do i ensure my split command would NOT generate incomplete output files like below, the last lines in each file is missing some columns or last line is complete. split -b 50GB File File_ File_aa |551|70210203|xxxxxxx|12/22/2010 20:44:58|11/01/2010... (1 Reply)
Discussion started by: Ariean
1 Replies

10. UNIX for Beginners Questions & Answers

How to add specific bases at the beginning and ending of all the fasta sequences?

Hi, I have to add 7 bases of specific nucleotide at the beginning and ending of all the fasta sequences of a file. For example, I have a multi fasta file namely test.fasta as given below test.fasta >TalAA18_Xoo_CIAT_NZ_CP033194.1:_2936369-2939570:+1... (1 Reply)
Discussion started by: dineshkumarsrk
1 Replies
IGAWK(1)							 Utility Commands							  IGAWK(1)

NAME
igawk - gawk with include files SYNOPSIS
igawk [ all gawk options ] -f program-file [ -- ] file ... igawk [ all gawk options ] [ -- ] program-text file ... DESCRIPTION
Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1). AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like @include getopt.awk in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path. OPTIONS
See gawk(1) for a full description of the AWK language and the options that gawk supports. EXAMPLES
cat << EOF > test.awk @include getopt.awk BEGIN { while (getopt(ARGC, ARGV, "am:q") != -1) ... } EOF igawk -f test.awk SEE ALSO
gawk(1) Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995. AUTHOR
Arnold Robbins (arnold@skeeve.com). Free Software Foundation Nov 3 1999 IGAWK(1)
All times are GMT -4. The time now is 10:37 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy