Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: User input and run awk using the input
Top Forums Shell Programming and Scripting User input and run awk using the input Post 302967336 by sea on Tuesday 23rd of February 2016 01:42:52 AM
Old 02-23-2016
This:
Code:
printf "Please enter the gene(s) of interest, use a comma between multiple: "
IFS="," read -a gene
        printf "the indicated genes will now be loaded and used to calculate coverage\n"

Will not work as you expect.

In fact, you tell to only catch the first genom only, and no other.
Because you say the IFS shall be ',' which is shall be used to seperate the genoms, mainwhile, you only read 1 genom, as 'gene' will be split into as many arguments/variables as the user passes using ','.

Saying:
Replcae the IFS= part to a later procedure, when parsing the user input.
Parsing is done after reading, or if while reading, it must be a limited (say pass 3 genoms, then you mus tread 3 variables - not just one).

I'm no scientist, but afaik a genom doesnt have 'spaces' in between, so they might just seperate the genoms passed by spaces OR coma - since the IFS is removed, that doesnt matter, in fact, its even simpler to work with the passed genoms, if the users do not use ',' to seperate the list.

Only use the red parts if you insist of using coma to seperate the list, if using space its not required at all.
Code:
read genes
oIFS="$IFS"
IFS=","
for gene in $genes;do
	echo "Working with genom: $gene"
done
IFS="$oIFS"

Other than that, please make the according corrections of for loops as Don already stated.

Thank you and hope this helps
This User Gave Thanks to sea For This Post:
cmccabe
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

awk user input

Using the following I'm trying to print the user's response to the prompt Y / N but I get nothing other than the contents of $1? awk '{ printf($1 " ? (Y/N)") getline myresponse < "-" system("read myresponse") if (myresponse == "Y") { print $1... (17 Replies)
Discussion started by: gefa
17 Replies

2. Shell Programming and Scripting

AWK set FILENAME via user input

I am trying to write a awk script that prompts user for input to set the FILENAME varable. I can get it set, but I think awk is not doing anything with it. this is what I have so far #!/usr/bin/nawk -f BEGIN { FILENAME = "" printf "Enter name of file to check in : " ... (2 Replies)
Discussion started by: timj123
2 Replies

3. Shell Programming and Scripting

Reading specific contents from 1 input files and appending it to another input file

Hi guys, I am new to AWK and unix scripting. Please see below my problem and let me know if anyone you can help. I have 2 input files (example given below) Input file 2 is a standard file (it will not change) and we have to get the name (second column after comma) from it and append it... (5 Replies)
Discussion started by: sksahu
5 Replies

4. Shell Programming and Scripting

How to take input from user or awk script?

Hi Jim, I have following script,i which i need to take dynamic value . script, nawk -v v1=grep"INT_EUR" $propertifilename | cut -d"=" -F2` -F'~' '{if (NF-1 !=v1) {print "Error in " $0 " at line number "NR" tilde count " N-1}}' $filename In the above script i want to use INT_EUR as a variable... (2 Replies)
Discussion started by: Ganesh Khandare
2 Replies

5. Shell Programming and Scripting

How to get the user input recursively until the user provides valid input

Hi, echo "Enter file name of input file list along with absolute path : " read inputFileList if then for string in `cat inputFileList` do echo $string done else echo " file does not exist" fi From the above code, if the user enters a invalid file... (1 Reply)
Discussion started by: i.srini89
1 Replies

6. Shell Programming and Scripting

Awk replacing file with user input

this section of the awk code i have here takes file to work with from the user. the user specifies the file name from the command line and the file name is assigned to the variable $FLIST awk 'BEGIN { while((getline < "'${FLIST}'")>0) S FS="\n"; RS="}\n" } now, i dont want... (5 Replies)
Discussion started by: SkySmart
5 Replies

7. Shell Programming and Scripting

Script to delete files with an input for directories and an input for path/file

Hello, I'm trying to figure out how best to approach this script, and I have very little experience, so I could use all the help I can get. :wall: I regularly need to delete files from many directories. A file with the same name may exist any number of times in different subdirectories.... (3 Replies)
Discussion started by: *ShadowCat*
3 Replies

8. Shell Programming and Scripting

Read input files and merge them in given order and write them to input one param or one file

Dear Friends, I am looking for a shell script to merge input files into one file .. here is my idea: 1st paramter would be outfile file (all input files content) read all input files and merge them to input param 1 ex: if I pass 6 file names to the script then 1st file name as output file... (4 Replies)
Discussion started by: hyd1234
4 Replies

9. Programming

Keyboard User Input in awk language ?

Hi, does someone know how to make a keyboard data input in the AWK programming language ? Regards Zabo (6 Replies)
Discussion started by: Zabo
6 Replies

10. Shell Programming and Scripting

awk command to search based on 5 user input fields

Field1=”” Field2=”” Field3=”” Field4=”” Field5=”” USER INPUT UP TO 5 FIELDS awk -F , '{ if ( $3 == Field1 && $6 == Field2 && $8 == Field3 && $9 == Field4 && $10 == Field5) print $0 }' /tmp/rodney.outD INPUT FILE (Rodney.outD): ... (3 Replies)
Discussion started by: rmerrird
3 Replies

LEARN ABOUT DEBIAN

tigr-glimmer3

TIGR-GLIMMER(1) 					      General Commands Manual						   TIGR-GLIMMER(1)

NAME

       tigr-glimmer -- Find/Score potential genes in genome-file using the probability model in icm-file

SYNOPSIS

       tigr-glimmer3 [genome-file]  [icm-file]	[[options]]

DESCRIPTION

       tigr-glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. tigr-glimmer (Gene Locator and
       Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.
       The IMM approach, described in our Nucleic Acids Research paper on tigr-glimmer 1.0 and in our subsequent paper on tigr-glimmer 2.0, uses a
       combination of Markov models from 1st through 8th-order, weighting each model according to its predictive power. tigr-glimmer 1.0  and  2.0
       use 3-periodic nonhomogenous Markov models in their IMMs.

       tigr-glimmer  is the primary microbial gene finder at TIGR, and has been used to annotate the complete genomes of B. burgdorferi (Fraser et
       al., Nature, Dec. 1997), T. pallidum (Fraser et al., Science, July 1998), T.  maritima,	D.  radiodurans,  M.  tuberculosis,  and  non-TIGR
       projects  including  C.	trachomatis,  C. pneumoniae, and others. Its analyses of some of these genomes and others is available at the TIGR
       microbial database site.

       A special version of tigr-glimmer designed for small eukaryotes, GlimmerM, was used to find the genes in chromosome 2 of the malaria  para-
       site,  P. falciparum.. GlimmerM is described in S.L. Salzberg, M. Pertea, A.L. Delcher, M.J. Gardner, and H. Tettelin, "Interpolated Markov
       models for eukaryotic gene finding," Genomics 59 (1999), 24-31.	Click here (http://www.tigr.org/software/glimmerm/) to visit the  GlimmerM
       site, which includes information on how to download the GlimmerM system.

       The  tigr-glimmer  system consists of two main programs. The first of these is the training program, build-imm. This program takes an input
       set of sequences and builds and outputs the IMM for them. These sequences can be complete genes or just partial orfs.  For  a  new  genome,
       this  training  data  can  consist of those genes with strong database hits as well as very long open reading frames that are statistically
       almost certain to be genes. The second program is glimmer, which uses this IMM to identify putative genes in an entire genome. tigr-glimmer
       automatically  resolves	conflicts  between  most overlapping genes by choosing one of them. It also identifies genes that are suspected to
       truly overlap, and flags these for closer inspection by the user. These ``suspect'' gene candidates have been a very  small  percentage	of
       the total for all the genomes analyzed thus far.  tigr-glimmer is a program that...

OPTIONS

       -C n	 Use n as GC percentage of independent model

		 Note:	n should be a percentage, e.g., -C 45.2

       -f	 Use ribosome-binding energy to choose start codon

       +f	 Use first codon in orf as start codon

       -g n	 Set minimum gene length to n

       -i filename
		 Use filename	to select regions of bases that are off limits, so that no bases within that area will be examined

       -l	 Assume linear rather than circular genome, i.e., no wraparound

       -L filename
		 Use filename to specify a list of orfs that should be scored separately, with no overlap rules

       -M	 Input is a multifasta file of separate genes to be scored separately, with no overlap rules

       -o n	 Set minimum overlap length to n.  Overlaps shorter than this are ignored.

       -p n	 Set minimum overlap percentage to n%.	Overlaps shorter than this percentage of *both* strings are ignored.

       -q n	 Set the maximum length orf that can be rejected because of the independent probability score column to (n - 1)

       -r	 Don't use independent probability score column

       +r	 Use independent probability score column

       -r	 Don't use independent probability score column

       -s s	 Use string s as the ribosome binding pattern to find start codons.

       +S	 Do  use stricter independent intergenic model that doesn't give probabilities to in-frame stop codons.  (Option is obsolete since
		 this is now the only behaviour

       -t n	 Set threshold score for calling as gene to n.	If the in-frame score >= n, then the region is given a	number	and  considered  a
		 potential gene.

       -w n	 Use "weak" scores on tentative genes n or longer.  Weak scores ignore the independent probability score.

SEE ALSO

       tigr-adjust  (1),  tigr-anomaly	 (1),  tigr-build-icm (1), tigr-check (1), tigr-codon-usage (1), tigr-compare-lists (1), tigr-extract (1),
       tigr-generate (1), tigr-get-len (1), tigr-get-putative (1), tigr-glimmer3 (1), tigr-long-orfs (1)

       http://www.tigr.org/software/glimmer/

       Please see the readme in /usr/share/doc/glimmer for a description on how to use Glimmer.

AUTHOR

       This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@debian.org for the Debian system.

																   TIGR-GLIMMER(1)
All times are GMT -4. The time now is 12:46 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy