Extract rows from file_1 based on matching the first two columns from a file_2
0
File_1
##chr pos rc allele_count allele_states deletion_sum snp_type most_variable_allele diff:1-2 diff:1-3 diff:1-4 diff:1-5 diff:1-6 diff:1-7 diff:1-8 diff:1-9 diff:1-10 diff:1-11 diff:1-12 diff:2-3
MT 227 C 2 C/A 0 pop C 0 0 0 0 0 0 0.024 0 0.022 0 0 0
MT 233 G 2 G/T 0 pop G 0 0.009 0 0.012 0 0 0 0 0 0 0 0.009
MT 245 G 2 G/A 0 pop A 0 0 0 0 0 0.055 0.224 0.072 0.026 0 0 0
MT 251 C 2 C/T 0 pop C 0.276 0.034 0.231 0.005 0.027 0.036 0.025 0.002 0.107 0.034 0.034 0.309
MT 264 G 2 G/C 0 pop G 0 0 0 0.008 0 0.003 0 0 0 0 0 0
MT 286 G 2 G/T 0 pop T 0.002 0.002 0.002 0.002 0.002 0.002 0.002 0.002 0.002 0 0.002 0
MT 292 A 2 A/T 0 pop T 0 0 0 0 0.003 0 0 0.002 0 0 0 0
MT 293 G 2 G/T 0 pop G 0 0 0 0 0.003 0.002 0 0 0 0 0 0
MT 295 G 2 G/T 0 pop G 0 0.002 0.002 0 0.001 0.002 0.002 0.002 0.002 0.002 0.002 0.003
File_2
MT 251
MT 292
MT 295
desired_output
##chr pos rc allele_count allele_states deletion_sum snp_type most_variable_allele diff:1-2 diff:1-3 diff:1-4 diff:1-5 diff:1-6 diff:1-7 diff:1-8 diff:1-9 diff:1-10 diff:1-11 diff:1-12 diff:2-3
MT 251 C 2 C/T 0 pop C 0.276 0.034 0.231 0.005 0.027 0.036 0.025 0.002 0.107 0.034 0.034 0.309
MT 292 A 2 A/T 0 pop T 0 0 0 0 0.003 0 0 0.002 0 0 0 0
MT 295 G 2 G/T 0 pop G 0 0.002 0.002 0 0.001 0.002 0.002 0.002 0.002 0.002 0.002 0.003
It's similar to what was wanted in this post:Compare two files by first column. Keep rows if matching
I was using awk 'NR==FNR{a[$0]=$0;next}a[$0]' for keeping overlap with first column, but I need the entire row when they match the first two columns (chr and pos).
awk grep
asked 1 hour ago
Age87
1476
add a comment |
0
File_1
##chr pos rc allele_count allele_states deletion_sum snp_type most_variable_allele diff:1-2 diff:1-3 diff:1-4 diff:1-5 diff:1-6 diff:1-7 diff:1-8 diff:1-9 diff:1-10 diff:1-11 diff:1-12 diff:2-3
MT 227 C 2 C/A 0 pop C 0 0 0 0 0 0 0.024 0 0.022 0 0 0
MT 233 G 2 G/T 0 pop G 0 0.009 0 0.012 0 0 0 0 0 0 0 0.009
MT 245 G 2 G/A 0 pop A 0 0 0 0 0 0.055 0.224 0.072 0.026 0 0 0
MT 251 C 2 C/T 0 pop C 0.276 0.034 0.231 0.005 0.027 0.036 0.025 0.002 0.107 0.034 0.034 0.309
MT 264 G 2 G/C 0 pop G 0 0 0 0.008 0 0.003 0 0 0 0 0 0
MT 286 G 2 G/T 0 pop T 0.002 0.002 0.002 0.002 0.002 0.002 0.002 0.002 0.002 0 0.002 0
MT 292 A 2 A/T 0 pop T 0 0 0 0 0.003 0 0 0.002 0 0 0 0
MT 293 G 2 G/T 0 pop G 0 0 0 0 0.003 0.002 0 0 0 0 0 0
MT 295 G 2 G/T 0 pop G 0 0.002 0.002 0 0.001 0.002 0.002 0.002 0.002 0.002 0.002 0.003
File_2
MT 251
MT 292
MT 295
desired_output
##chr pos rc allele_count allele_states deletion_sum snp_type most_variable_allele diff:1-2 diff:1-3 diff:1-4 diff:1-5 diff:1-6 diff:1-7 diff:1-8 diff:1-9 diff:1-10 diff:1-11 diff:1-12 diff:2-3
MT 251 C 2 C/T 0 pop C 0.276 0.034 0.231 0.005 0.027 0.036 0.025 0.002 0.107 0.034 0.034 0.309
MT 292 A 2 A/T 0 pop T 0 0 0 0 0.003 0 0 0.002 0 0 0 0
MT 295 G 2 G/T 0 pop G 0 0.002 0.002 0 0.001 0.002 0.002 0.002 0.002 0.002 0.002 0.003
It's similar to what was wanted in this post:Compare two files by first column. Keep rows if matching
I was using awk 'NR==FNR{a[$0]=$0;next}a[$0]' for keeping overlap with first column, but I need the entire row when they match the first two columns (chr and pos).
awk grep
asked 1 hour ago
Age87
1476
add a comment |
0
0
0
File_1
##chr pos rc allele_count allele_states deletion_sum snp_type most_variable_allele diff:1-2 diff:1-3 diff:1-4 diff:1-5 diff:1-6 diff:1-7 diff:1-8 diff:1-9 diff:1-10 diff:1-11 diff:1-12 diff:2-3
MT 227 C 2 C/A 0 pop C 0 0 0 0 0 0 0.024 0 0.022 0 0 0
MT 233 G 2 G/T 0 pop G 0 0.009 0 0.012 0 0 0 0 0 0 0 0.009
MT 245 G 2 G/A 0 pop A 0 0 0 0 0 0.055 0.224 0.072 0.026 0 0 0
MT 251 C 2 C/T 0 pop C 0.276 0.034 0.231 0.005 0.027 0.036 0.025 0.002 0.107 0.034 0.034 0.309
MT 264 G 2 G/C 0 pop G 0 0 0 0.008 0 0.003 0 0 0 0 0 0
MT 286 G 2 G/T 0 pop T 0.002 0.002 0.002 0.002 0.002 0.002 0.002 0.002 0.002 0 0.002 0
MT 292 A 2 A/T 0 pop T 0 0 0 0 0.003 0 0 0.002 0 0 0 0
MT 293 G 2 G/T 0 pop G 0 0 0 0 0.003 0.002 0 0 0 0 0 0
MT 295 G 2 G/T 0 pop G 0 0.002 0.002 0 0.001 0.002 0.002 0.002 0.002 0.002 0.002 0.003
File_2
MT 251
MT 292
MT 295
desired_output
##chr pos rc allele_count allele_states deletion_sum snp_type most_variable_allele diff:1-2 diff:1-3 diff:1-4 diff:1-5 diff:1-6 diff:1-7 diff:1-8 diff:1-9 diff:1-10 diff:1-11 diff:1-12 diff:2-3
MT 251 C 2 C/T 0 pop C 0.276 0.034 0.231 0.005 0.027 0.036 0.025 0.002 0.107 0.034 0.034 0.309
MT 292 A 2 A/T 0 pop T 0 0 0 0 0.003 0 0 0.002 0 0 0 0
MT 295 G 2 G/T 0 pop G 0 0.002 0.002 0 0.001 0.002 0.002 0.002 0.002 0.002 0.002 0.003
It's similar to what was wanted in this post:Compare two files by first column. Keep rows if matching
I was using awk 'NR==FNR{a[$0]=$0;next}a[$0]' for keeping overlap with first column, but I need the entire row when they match the first two columns (chr and pos).
awk grep
asked 1 hour ago
Age87
1476
File_1
##chr pos rc allele_count allele_states deletion_sum snp_type most_variable_allele diff:1-2 diff:1-3 diff:1-4 diff:1-5 diff:1-6 diff:1-7 diff:1-8 diff:1-9 diff:1-10 diff:1-11 diff:1-12 diff:2-3
MT 227 C 2 C/A 0 pop C 0 0 0 0 0 0 0.024 0 0.022 0 0 0
MT 233 G 2 G/T 0 pop G 0 0.009 0 0.012 0 0 0 0 0 0 0 0.009
MT 245 G 2 G/A 0 pop A 0 0 0 0 0 0.055 0.224 0.072 0.026 0 0 0
MT 251 C 2 C/T 0 pop C 0.276 0.034 0.231 0.005 0.027 0.036 0.025 0.002 0.107 0.034 0.034 0.309
MT 264 G 2 G/C 0 pop G 0 0 0 0.008 0 0.003 0 0 0 0 0 0
MT 286 G 2 G/T 0 pop T 0.002 0.002 0.002 0.002 0.002 0.002 0.002 0.002 0.002 0 0.002 0
MT 292 A 2 A/T 0 pop T 0 0 0 0 0.003 0 0 0.002 0 0 0 0
MT 293 G 2 G/T 0 pop G 0 0 0 0 0.003 0.002 0 0 0 0 0 0
MT 295 G 2 G/T 0 pop G 0 0.002 0.002 0 0.001 0.002 0.002 0.002 0.002 0.002 0.002 0.003
File_2
MT 251
MT 292
MT 295
desired_output
##chr pos rc allele_count allele_states deletion_sum snp_type most_variable_allele diff:1-2 diff:1-3 diff:1-4 diff:1-5 diff:1-6 diff:1-7 diff:1-8 diff:1-9 diff:1-10 diff:1-11 diff:1-12 diff:2-3
MT 251 C 2 C/T 0 pop C 0.276 0.034 0.231 0.005 0.027 0.036 0.025 0.002 0.107 0.034 0.034 0.309
MT 292 A 2 A/T 0 pop T 0 0 0 0 0.003 0 0 0.002 0 0 0 0
MT 295 G 2 G/T 0 pop G 0 0.002 0.002 0 0.001 0.002 0.002 0.002 0.002 0.002 0.002 0.003
It's similar to what was wanted in this post:Compare two files by first column. Keep rows if matching
I was using awk 'NR==FNR{a[$0]=$0;next}a[$0]' for keeping overlap with first column, but I need the entire row when they match the first two columns (chr and pos).
awk grep
awk grep
asked 1 hour ago
Age87
1476
asked 1 hour ago
Age87
1476
asked 1 hour ago
Age87
1476
asked 1 hour ago
Age87
1476
asked 1 hour ago
Age87
1476
1476
add a comment |
add a comment |
1 Answer
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2
You should just test whether the first two columns are keys of the array, instead of testing the entire line with $0.
awk 'NR==FNR {a[$1" "$2] = 1; next}
FNR == 1 && FNR != NR {print} # print header
$1" "$2 in a' File_2 File_1
answered 54 mins ago
Barmar
6,9431223
Thanks! the column headers weren't added to the output, but that's trivial to do.
– Age87
40 mins ago
add a comment |
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1 Answer
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votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
2
You should just test whether the first two columns are keys of the array, instead of testing the entire line with $0.
awk 'NR==FNR {a[$1" "$2] = 1; next}
FNR == 1 && FNR != NR {print} # print header
$1" "$2 in a' File_2 File_1
answered 54 mins ago
Barmar
6,9431223
Thanks! the column headers weren't added to the output, but that's trivial to do.
– Age87
40 mins ago
add a comment |
2
You should just test whether the first two columns are keys of the array, instead of testing the entire line with $0.
awk 'NR==FNR {a[$1" "$2] = 1; next}
FNR == 1 && FNR != NR {print} # print header
$1" "$2 in a' File_2 File_1
answered 54 mins ago
Barmar
6,9431223
Thanks! the column headers weren't added to the output, but that's trivial to do.
– Age87
40 mins ago
add a comment |
2
2
2
You should just test whether the first two columns are keys of the array, instead of testing the entire line with $0.
awk 'NR==FNR {a[$1" "$2] = 1; next}
FNR == 1 && FNR != NR {print} # print header
$1" "$2 in a' File_2 File_1
answered 54 mins ago
Barmar
6,9431223
You should just test whether the first two columns are keys of the array, instead of testing the entire line with $0.
awk 'NR==FNR {a[$1" "$2] = 1; next}
FNR == 1 && FNR != NR {print} # print header
$1" "$2 in a' File_2 File_1
answered 54 mins ago
Barmar
6,9431223
edited 37 mins ago
answered 54 mins ago
Barmar
6,9431223
answered 54 mins ago
Barmar
6,9431223
answered 54 mins ago
Barmar
6,9431223
6,9431223
Thanks! the column headers weren't added to the output, but that's trivial to do.
– Age87
40 mins ago
add a comment |
Thanks! the column headers weren't added to the output, but that's trivial to do.
– Age87
40 mins ago
Thanks! the column headers weren't added to the output, but that's trivial to do.
– Age87
40 mins ago
Thanks! the column headers weren't added to the output, but that's trivial to do.
– Age87
40 mins ago
add a comment |
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