While read line, awk $line and write to variable - unix

Question

I am trying to split a file into different smaller files depending on the value of the fifth field. A very nice way to do this was already suggested and also here.
However, I am trying to incorporate this into a .sh script for qsub, without much success.
The problem is that in the section where the file to which output the line is specified,
i.e., f = "Alignments_" $5 ".sam" print > f
, I need to pass a variable declared earlier in the script, which specifies the directory where the file should be written. I need to do this with a variable which is built for each task when I send out the array job for multiple files.
So say $output_path = ./Sample1
I need to write something like
f = $output_path "/Alignments_" $5 ".sam" print > f
But it does not seem to like having a $variable that is not a $field belonging to awk. I don't even think it likes having two "strings" before and after the $5.
The error I get back is that it takes the first line of the file to be split (little.sam) and tries to name f like that, followed by /Alignments_" $5 ".sam" (those last three put together correctly). It says, naturally, that it is too big a name.
How can I write this so it works?
Thanks!
awk -F '[:\t]' ' # read the list of numbers in Tile_Number_List
FNR == NR {
num[$1]
next
}
# process each line of the .BAM file
# any lines with an "unknown" $5 will be ignored
$5 in num {
f = "Alignments_" $5 ".sam" print > f
} ' Tile_Number_List.txt little.sam
UPDATE, AFTER ADDING -V TO AWK AND DECLARING THE VARIABLE OPATH
input=$1
outputBase=${input%.bam}
mkdir -v $outputBase\_TEST
newdir=$outputBase\_TEST
samtools view -h $input | awk 'NR >= 18' | awk -F '[\t:]' -v opath="$newdir" '
FNR == NR {
num[$1]
next
}
$5 in num {
f = newdir"/Alignments_"$5".sam";
print > f
} ' Tile_Number_List.txt -
mkdir: created directory little_TEST'
awk: cmd. line:10: (FILENAME=- FNR=1) fatal: can't redirect to `/Alignments_1101.sam' (Permission denied)

Answer 1

awk variables are like C variables - just reference them by name to get their value, no need to stick a "$" in front of them like you do with shell variables:
awk -F '[:\t]' ' # read the list of numbers in Tile_Number_List
FNR == NR {
num[$1]
next
}
# process each line of the .BAM file
# any lines with an "unknown" $5 will be ignored
$5 in num {
output_path = "./Sample1/"
f = output_path "Alignments_" $5 ".sam"
print > f
} ' Tile_Number_List.txt little.sam

Answer 2

To pass the value of the shell variable such as $output_path to awk you need to use the -v option.
$ output_path=./Sample1/
$ awk -F '[:\t]' -v opath="$ouput_path" '
# read the list of numbers in Tile_Number_List
FNR == NR {
num[$1]
next
}
# process each line of the .BAM file
# any lines with an "unknown" $5 will be ignored
$5 in num {
f = opath"Alignments_"$5".sam"
print > f
} ' Tile_Number_List.txt little.sam
Also you still have the error from your previous question left in your script
EDIT:
The awk variable created with -v is obase but you use newdir what you want is:
input=$1
outputBase=${input%.bam}
mkdir -v $outputBase\_TEST
newdir=$outputBase\_TEST
samtools view -h "$input" | awk -F '[\t:]' -v opath="$newdir" '
FNR == NR && NR >= 18 {
num[$1]
next
}
$5 in num {
f = opath"/Alignments_"$5".sam" # <-- opath is the awk variable not newdir
print > f
}' Tile_Number_List.txt -
You should also move NR >= 18 into the second awk script.