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awk match to update contents of file
09-07-2016
Match: 68521889 C T 167099158 A G 18122506 G A
.... .... .... 68521889 C T 1 2 .... 167099158 A G 1 2 .... 18122506 G A 1 2
awk '
BEGIN { FS = OFS = "\t"
}
NR == 1 {
outfile = FILENAME
}
FNR == NR {
i[++ic] = $1","$2","$3
}
{ if($2 in o)
o[$2] = $2 OFS $3 OFS $4
}
END { for(j = 1; j <= ic; j++)
print o[i[j]] > outfile
}' file1 file268521889 C T 1 167099158 A G 1 18122506 G A 1
09-07-2016
09-07-2016
awk '
BEGIN {FS = OFS = "\t"
}
NR == 1 {
outfile = FILENAME
}
FNR == NR {
o[i[++ic] = $1 FS $2 FS $3]
}
{if($2 FS $4 FS $5 in o)
o[$2 FS $4 FS $5] = $2 OFS $4 OFS $5 OFS $50 OFS $51 OFS $52 OFS $53
}
END {for(j = 1; j <= ic; j++)
print o[i[j]] > outfile
}' file1 file2Match: 68521889 C T 167099158 A G 18122506 G A
68521889 C T GOOD 50 het 4 167099158 A G GOOD 210 hom 55 18122506 G A GOOD 189 het 8
Match: 68521889 C T GOOD 50 het 4 167099158 A G GOOD 210 hom 55 18122506 G A GOOD 189 het 8
09-07-2016
awk '
BEGIN {FS = OFS = "\t"
}
NR == 1 {
outfile = FILENAME
}
FNR == NR {
o[i[++ic] = $1 FS $2 FS $3]
}
{if($2 FS $4 FS $5 in o)
o[$2 FS $4 FS $5] = $2 OFS $4 OFS $5 OFS $50 OFS $51 OFS $52 OFS $53
}
END {for(j = 1; j <= ic; j++)
print o[i[j]] > outfile
}' file1 file2Match: 68521889 C T 167099158 A G 18122506 G A
68521889 C T GOOD 50 het 4 167099158 A G GOOD 210 hom 55 18122506 G A GOOD 189 het 8
Match: 68521889 C T GOOD 50 het 4 167099158 A G GOOD 210 hom 55 18122506 G A GOOD 189 het 8
awk '
BEGIN { FS = OFS = "\t"
}
NR == 1 {
outfile = FILENAME
}
FNR == NR {
o[i[++ic] = $1 OFS $2 OFS $3] = $0
next
}
{ if($2 OFS $4 OFS $5 in o)
o[$2 OFS $4 OFS $5] = $2 OFS $4 OFS $5 OFS $50 OFS $51 OFS $52 OFS $53
}
END { for(j = 1; j <= ic; j++)
print o[i[j]] > outfile
}' file1 file2awk '
BEGIN { FS = OFS = "\t"
}
NR == 1 {
# Save the output file pathname from the pathname naming the 1st input
# file.
outfile = FILENAME
}
FNR == NR {
# For each line in the 1st input file set i[line#] to the three fields
# in the 1st input file (and keep a count of the number of lines in
# that file (ic) that make up that key, and set o[key] to the entire
# input line.
o[i[++ic] = $1 OFS $2 OFS $3] = $0
next # This line was missing in my original script, but since there
# was only one field in file1 and there were no empty lines in
# file1, it didn't affect the final output. With the new input
# file formats, this line must be included to guarantee correct
# results.
}
{ # Set key to the key fields from file2. If this key is present in the
# o[] array, set o[key] to the desired otuput for this key.
if((key = $2 OFS $4 OFS $5) in o)
o[key] = key OFS $50 OFS $51 OFS $52 OFS $53
}
END { # Now that we have processed all of the data in both input files,
# overwrite the 1st input file with the desired output replacing each
# line in that file with its original contents (if there was no match)
# or the collected fields from the 2nd input file (if there was a
# match).
for(j = 1; j <= ic; j++)
print o[i[j]] > outfile
}' file1 file2|
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