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Full Discussion: awk to change value in field according to another
Top Forums Shell Programming and Scripting awk to change value in field according to another Post 303027088 by cmccabe on Saturday 8th of December 2018 07:27:31 PM
Old 12-08-2018
There are two .txt files in the directory:

Code:
00-0000_regions.txt and 11-1111_regions.txt

these two .txtfiles are $bname and $pref is the digits after the _regions.txt is removed.

Code:
for file in /home/cmccabe/folder/less/*.txt ; do
     echo "$file"
     bname=$(basename "$file")
     pref="${bname%%_*.txt}"
     echo "bname: \"$bname\"   pref:\"$pref\""
     # /home/cmccabe/folder/less/exon.sh /home/cmccabe/folder/less/all_cdsV2 $file > /home/cmccabe/folder/less/${pref}_output.txt
done
/home/cmccabe/folder/less/00-0000_regions.txt
bname: "00-0000_regions.txt"   pref:"00-0000"
/home/cmccabe/folder/less/11-1111_regions.txt
bname: "11-1111_regions.txt"   pref:"11-1111"

Code:
for file in /home/cmccabe/folder/less/*.txt ; do   
       bname=$(basename "$file")
       pref=${bname%%_*.txt}
       echo "file:\"$file\"    bname:\"$bname\"    pref:\"$pref\""
       echo "output will be directed to:\"/home/cmccabe/folder/less/${pref}_output.txt\""
       #/home/cmccabe/folder/less/exon.sh /home/cmccabe/folder/less/all_cdsV2 "$file" > "/home/cmccabe/folder/less/${pref}_output.txt"
done
    file:"/home/cmccabe/folder/less/00-0000_regions.txt"    bname:"00-0000_regions.txt"    pref:"00-0000"
    output will be directed to:"/home/cmccabe/folder/less/00-0000_output.txt"
    file:"/home/cmccabe/folder/less/11-1111_regions.txt"    bname:"11-1111_regions.txt"    pref:"11-1111"

Code:
for file in /home/cmccabe/folder/less/*.txt ; do
       bname=$(basename "$file")
       pref=${bname%%_*.txt}
       #echo "file:\"$file\"    bname:\"$bname\"    pref:\"$pref\""
       #echo "output will be directed to:\"/home/cmccabe/folder/less/${pref}_output.txt\""
       set -xv
       /home/cmccabe/folder/less/exon.sh /home/cmccabe/folder/less/all_cdsV2 "$file" > "/home/cmccabe/folder/less/${pref}_output.txt"
       set +xv
done
+ /home/cmccabe/folder/less/exon.sh /home/cmccabe/folder/less/all_cdsV2 /home/cmccabe/folder/less/00-0000_output.txt

The process seems to stall and get stuck on the first file 00-0000_regions.txt.

I did also run bash -x /home/cmccabe/folder/less/exon.sh and can see that the .txt files are not getting passed to the script as input. I'm not sure why but I believe this may help:

Quote:
I also note that the exon.sh can't be the script that I supplied in post #11. That script didn't look at any of its operands; it only used the presence of one or more operands as a flag to enable debugging printouts. I will assume that you removed the debugging printf statements and the d variable and are using the two operands you are passing to exon.sh as the two filenames processed by that script.
I'm not sure I follow but I will re-read and maybe that will help. Thank you Smilie.

Code:
for file in /home/cmccabe/folder/less/*.txt ; do      bname=$(basename "$file");      pref="${bname%%_*.txt}";      bash -x /home/cmccabe/folder/less/exon.sh /home/cmccabe/folder/less/all_cdsV2 "$file" > /home/cmccabe/folder/less/${pref}_output.txt; donefor file in /home/cmccabe/folder/less/*.txt ; do      bname=$(basename "$file");      pref="${bname%%_*.txt}";      bash -x /home/cmccabe/folder/less/exon.sh /home/cmccabe/folder/less/all_cdsV2 "$file" > /home/cmccabe/folder/less/${pref}_output.txt; done
+ for file in '/home/cmccabe/folder/less/*.txt'
basename "$file"
++ basename /home/cmccabe/folder/less/00-0000_output.txt
+ bname=00-0000_output.txt
+ pref=00-0000
+ bash -x /home/cmccabe/folder/less/exon.sh /home/cmccabe/folder/less/all_cdsV2 /home/cmccabe/folder/less/00-0000_output.txt
+ awk -v d=2 '
BEGIN {	FS = "[\t_]"
	OFS = "\t"
}
FNR == NR {
	m[$1, $4, ++c[$1, $4]] = $2 + 0
	M[$1, $4, c[$1, $4]] = $3 + 0
	if(d) printf("m[%s,%s,%d]=%s,M[%s,%s,%d]=%s\n",
		$1, $4, c[$1, $4], m[$1, $4, c[$1, $4]],
		$1, $4, c[$1, $4], M[$1, $4, c[$1, $4]])
	next
}
{	if(d) printf("FNR=%d:\"%s\"\n",FNR,$0)
	for(i = 1; i <= c[$1, $4]; i++) {
		if(d) printf("m[%d]=%d,M[%d]=%d,$2=%d\n",
			i, m[$1, $4, i],
			i, M[$1, $4, i],
			$2)
		if(m[$1, $4, i] <= $2 && $2 <= M[$1, $4, i]) {
			$5 = "exon"
			break
		} else {if(m[$1, $4, i] > $2 + 0) {
				if(m[$1, $4, i] - 10 <= $2 + 0) {
					$5 = "splicing"
					break
				} else {$5 = "intron"
					break
				}
		}
	}
}
	if(i > c[$1, $4])
		$5 = "intron"
}
1'

 

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