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awk to match and apply condtions to matchijng files in directories
10-15-2016
awk 'FNR==NR{A[$2]=$0;next} ($2 in A){if($10>30 && $11>49){print A[$2]}}' F113.txt F113_tvc.bedF113.txt H123.txt S111.txt
F113_tvc.bed H123_tvc.bed S111_tvc.bed
(code that works perfect)
IAm=${0##*/}
InDir1='/home/cmccabe/Desktop/comparison/reference/10bp'
InDir2='/home/cmccabe/Desktop/comparison/validation/files'
OutDir='/home/cmccabe/Desktop/comparison/ref_val'
cd "$InDir1"
for file1 in *.txt
do # Grab file prefix.
p=${file1%%_*}
# Find matching file2.
file2=$(printf '%s' "$InDir2/$p"_*.vcf)
if [ ! -f "$file2" ]
then printf '%s: No single file matching %s found.\n' "$IAm" \
"$file1" >&2
continue
fi
# Create matching output filename.
out=${file2##*/}
out=${out%.vcf}_comparison.txt
printf '%s\t%s\t%s\n' "$InDir1/$file1" "$file2" "$OutDir/$out"
done | awk '
BEGIN { FS = OFS = "\t"
}
{ in1 = $1
in2 = $2
out = $3
print "Reading from " in1
while((getline < in1) == 1)
f1[$2 OFS $4 OFS $5]
close(in1)
print "Reading from " in2
while((getline < in2) == 1)
f2[$2 OFS $4 OFS $5]
close(in2)
print "Writing to " out
print "Match:" > out
for(k in f1)
if(k in f2) {
print k > out
delete f1[k]
delete f2[k]
}
print "Missing in Reference but found in IDP:" > out
for(k in f2) {
print k > out
delete f2[k]
}
print "Missing in IDP but found in Reference:" > out
for(k in f1) {
print k > out
delete f1[k]
}
close(out)
print "***"
}'IAm=${0##*/}
InDir1='/home/cmccabe/Desktop/comparison/missing' -- updated path to .txt files
InDir2='/home/cmccabe/Desktop/comparison/test_tvc' -- updated path to .bed files
OutDir='/home/cmccabe/Desktop/comparison/final' -- updated path to output
cd "$InDir1"
for file1 in *.txt
do # Grab file prefix.
p=${file1%%_*}
# Find matching file2.
file2=$(printf '%s' "$InDir2/$p"_*.bed) -- updated extension
if [ ! -f "$file2" ]
then printf '%s: No single file matching %s found.\n' "$IAm" \
"$file1" >&2
continue
fi
# Create matching output filename.
out=${file2##*/}
out=${out%.vcf}_final.txt -- updated output
printf '%s\t%s\t%s\n' "$InDir1/$file1" "$file2" "$OutDir/$out"
done | awk '
BEGIN { FS = OFS = "\t"
}
{ in1 = $1
in2 = $2
out = $3
print "Reading from " in1
while((getline < in1) == 1)
f1[$2] -- updated to look for each $2 in the .txt file
close(in1)
print "Reading from " in2
while((getline < in2) == 1)
f2[$2] -- updated to look for each $2 from the .txt file in the matching .bed file
close(in2)
print "Writing to " out
print "Match in both files and meet criteria:" > out
for(k in f1)
if(k in f2) {
print k > out
delete f1[k]
delete f2[k]
}
print "Missing in comparison:" > out
for(k in f2) {
print k > out
delete f2[k]
}
close(out)
print "***"
}'Missing in IDP but found in Reference: 2 166848646 G A exonic SCN1A 68 13 16;20 0;0 17;15 0;0 0;0 0;0 c.[5139C>T]+[=] 52.94 2 166245888 G A exonic SCN1A 68 13 16;20 0;0 17;15 0;0 0;0 0;0 c.[5500G>T]+[=] 32
Chrom Position Gene Sym Target ID Type Zygosity Genotype Ref Variant Var Freq Qual Coverage Ref Cov Var Cov chr2 166245425 SCN2A AMPL5155065355 SNP Het C/T C T 54 100 50 23 27 chr2 166848646 SCN1A AMPL1543060606 SNP Het G/A G A 52.9411764706 100 68 32 36
Match in both files and meet criteria: 2 166848646 G A exonic SCN1A 68 13 16;20 0;0 17;15 0;0 0;0 0;0 c.[5139C>T]+[=] 52.94 Missing in comparison: 2 166245888 G A exonic SCN1A 68 13 16;20 0;0 17;15 0;0 0;0 0;0 c.[5500G>T]+[=] 32
.
10-15-2016
10-15-2016
for file in "/home/cmccabe/Desktop/comparison/missing/*.txt"
do
file1="/home/cmccabe/Desktop/comparison/test_tvc/${file%%.txt}"
if [[ -f file1 ]]
then
awk 'FNR==NR{A[$2]=$0;next} ($2 in A){if($10>30 && $11>49){print A[$2] >> "Match_in_both_files_and_meet_criteria";delete A[$2]}} END{for(i in A){print A[i] >> "out_no_match_found_values"}}' $file $file1 > /home/cmccabe/Desktop/comparison/final/${file}_final.txt
fi
done.awk: cmd. line:1: fatal: cannot open file `/home/cmccabe/Desktop/comparison/test_tvc//home/cmccabe/Desktop/comparison/missing/*' for reading (No such file or directory)
10-15-2016
10-15-2016
cd /home/cmccabe/Desktop/comparison/missing
for file in *.txt
do
file1="/home/cmccabe/Desktop/comparison/test_tvc/${file%%.txt}"
if [[ -f file1 ]]
then
awk 'FNR==NR{A[$2]=$0;Q=FILENAME;next} ($2 in A){if($10>30 && $11>49){print A[$2] >> "Match_in_both_files_and_meet_criteria";print "Match found in both the files named " Q " and " FILENAME " is: " A[$2];delete A[$2]}} END{print "NON-matched lines between file named "Q " and " FILENAME " are: ";for(i in A){print A[i] >> "out_no_match_found_values";print A[i]}}' $file $file1 > /home/cmccabe/Desktop/comparison/final/Output_final_file.txt
fi
done.
10-15-2016
10-15-2016
cd /home/cmccabe/Desktop/comparison/missing
for file in *.txt
do
file1="/home/cmccabe/Desktop/comparison/test_tvc/${file%%.txt}.bed"
if [[ -f file1 ]]
then
awk 'FNR==NR{A[$2]=$0;Q=FILENAME;next} ($2 in A){if($10>30 && $11>49){print A[$2] >> "/home/cmccabe/Desktop/comparison/missing/Match_in_both_files_and_meet_criteria";print "Match found in both the files named " Q " and " FILENAME " is: " A[$2];delete A[$2]}} END{print "NON-matched lines between file named "Q " and " FILENAME " are: ";for(i in A){print A[i] >> "/home/cmccabe/Desktop/comparison/missing/out_no_match_found_values";print A[i]}}' $file $file1 > /home/cmccabe/Desktop/comparison/final/Output_final_file.txt
fi
done.|
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