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Full Discussion: Reading from file bash command
Top Forums Shell Programming and Scripting Reading from file bash command Post 303003159 by nans on Friday 8th of September 2017 07:26:40 AM
Old 09-08-2017
Reading from file bash command
Hello, I have a file in the following format

Code:
id sample platform R1 R2 gene1 gene2 gene3
1       abc     llumina       R1_001.fastq.gz      R2_001.fastq.gz   apoe    prnpp    asp
2       def     llumina       R1_001.fastq.gz      R2_001.fastq.gz   apoe    prnpp    
3       ghi     llumina       R1_001.fastq.gz      R2_001.fastq.gz   apoe

The first 6 columns are always filled, the last two columns are only for some entries. So I have a main script that reads this file to process these ids further. I generally use

Code:
while id sample platform R1 R2 gene1
do
<mainscript.sh>
done < samples.txt

But how can I include the last two columns as well to run the command as many entries under the variable gene2 and gene3 are empty.

This is what i have tried so far to read all the lines in the file and if variable under gene2 and/or gene3 are empty, to move to the next line

Code:
while read  id sample platform R1 R2 gene1 gene2 gene3
do
echo "$id $sample $gene1 $gene2" | {
        read  id sample platform R1 R2 gene1 gene2
        [ -z "$gene2" ] && continue
        for i in $gene2; do eval echo "\"$i\""; done
 }
 
 done < samples.txt

I could do it for gene2 but wasnt able to implement it for gene3

any suggestions would be helpful

thank you
 

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LEARN ABOUT DEBIAN

gr_plot_char

GR_PLOT_CHAR(1) 						   User Commands						   GR_PLOT_CHAR(1)

NAME

       gr_plot_char - plot samples versus time for byte/char data

SYNOPSIS

       gr_plot_char: [options] input_filenames

DESCRIPTION

       Takes  a  GNU  Radio  byte/char binary file and displays the samples versus time.  You can set the block size to specify how many points to
       read in at a time and the start position in the file. By default, the system assumes a sample rate of 1, so in time, each sample is plotted
       versus  the  sample  number.  To set a true time axis, set the sample rate (-R or --sample-rate) to the sample rate used when capturing the
       samples.

OPTIONS

       -h, --help
	      show this help message and exit

       -B BLOCK, --block=BLOCK
	      Specify the block size [default=1000]

       -s START, --start=START
	      Specify where to start in the file [default=0]

       -R SAMPLE_RATE, --sample-rate=SAMPLE_RATE
	      Set the sampler rate of the data [default=1.0]

SEE ALSO

       gr_plot_char(1)	gr_plot_const(1)  gr_plot_fft_c(1)  gr_plot_fft_f(1)  gr_plot_float(1)	 gr_plot_int(1)   gr_plot_iq(1)   gr_plot_psd_c(1)
       gr_plot_psd_f(1)  gr_plot_qt(1)	gr_plot_short(1)

gr_plot_char 3.5						   December 2011						   GR_PLOT_CHAR(1)
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