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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

imager::largesamples

Imager::LargeSamples(3pm)				User Contributed Perl Documentation				 Imager::LargeSamples(3pm)

NAME

       Imager::LargeSamples - track/document large sample support

SYNOPSIS

	 # make a large sample image
	 my $im = Imager->new(..., bits => 16);

	 # call some method
	 my $result = $im->$method(...);

	 # was the image modified at its full sample size

DESCRIPTION

       Imager has had in-memory support for large samples for years now, but many methods still don't work at the higher sample size when supplied
       with a large sample image.

       This document will track which methods support large samples and which don't, for future improvements.

Support by method
	 Method       Support	 Notes
	 ------       -------	 -----
	 arc	      Partial	 [1]
	 box	      Partial	 [2]
	 circle       Partial	 [1]
	 convert      Full
	 copy	      Full
	 crop	      Full
	 difference   Full
	 filter       Partial	 Depends on the filter.
	 flip	      Full
	 flood_fill   Partial	 [1]
	 getpixel     Full
	 getsamples   Full
	 getscanline  Full
	 map	      None
	 masked       Full
	 matrix_transform
		      Full
	 paste	      Full
	 polygon      Partial	 [1]
	 polyline     None
	 read	      Partial	 See L<File format large sample support>
	 read_multi   Partial	 See L<File format large sample support>
	 rotate       Full
	 rubthrough   Full
	 scale	      Partial	 Some qtypes support large samples
	 scaleX       None
	 scaleY       None
	 setpixel     Full
	 setscanline  Full
	 string       Full	 Preserves large samples, but most font drivers
				 generate 8 or fewer bits of levels of coverage.
	 transform    None
	 transform2   None
	 write	      Partial	 See L<File format large sample support>
	 write_multi  Partial	 See L<File format large sample support>

       [1] filling an area using the fill parameter works at the full depth of the image, using filled => 1 and color works at 8-bits/sample

       [2] box() will fill the area at the supplied color, but outline at 8-bits/sample.

File format large sample support
	 Format    Format samples    Imager support
	 ------    --------------    --------------
	 BMP	   8		     8
	 GIF	   8		     8
	 ICO	   8		     8
	 JPEG	   8, 12	     8
	 PBM	   1		     1
	 PGM/PPM   1-16 	     read any, writes 8, 16
	 PNG	   1, 2, 4, 8, 16    8
	 RAW			     8
	 SGI	   8, 16	     8, 16
	 TGA	   8		     8
	 TIFF	   (many)	     read/write 8, 16, 32 contig rgb/grey images
				     read/write bi-level
				     read/write 4/8 paletted images

Filter larger sample support
	 Filter      Large sample support
	 ------      --------------------
	 autolevels	 No
	 bumpmap	 No
	 bumpmap_complex No
	 contrast	 No
	 conv		 Yes
	 fountain	 Yes
	 gaussian	 Yes
	 gradgen	 No
	 hardinvert	 Yes
	 mosaic 	 No
	 postlevels	 No
	 radnoise	 No
	 turbnoise	 No
	 unsharpmask	 Yes
	 watermark	 No

AUTHOR

       Tony Cook <tonyc@cpan.org>

perl v5.14.2							    2011-06-06						 Imager::LargeSamples(3pm)
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