以下のような大きな入力ファイルがあります。 「PRIMER_LEFT_NUM_RETURNED」がゼロでない場合は、対応するSEQUENCE_ID、SEQUENCE_TEMPLATE、PRIMER_LEFT_NUM_RETURNED、PRIMER_RIGHT_NUM_RETURNED、PRIMER_INTERNAL_NUM_RETURNED、PRIMER_PAIR_NUM_RETURNE、 。
入力ファイル：
SEQUENCE_ID=Contig1
SEQUENCE_TEMPLATE=AAGTCGCCCCTCCAT
PRIMER_LEFT_NUM_RETURNED=2
PRIMER_RIGHT_NUM_RETURNED=2
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=5
PRIMER_PAIR_0_PENALTY=7.398828
PRIMER_LEFT_0_SEQ=AAGTCGCCCC
PRIMER_RIGHT_0_SEQ=aaaagaca
PRIMER_LEFT_0=0,20
PRIMER_RIGHT_0=69,20
PRIMER_LEFT_0_END_STABILITY=2
PRIMER_RIGHT_0_END_STABILITY=3
PRIMER_PAIR_0_PRODUCT_SIZE=70
PRIMER_PAIR_1_PENALTY=7.78
PRIMER_LEFT_1_PENALTY=1
PRIMER_RIGHT_1_PENALTY=6.7
PRIMER_LEFT_1_SEQ=AAGTCGCCCCTCCA
PRIMER_RIGHT_1_SEQ=aaaagacagagaG
PRIMER_LEFT_1=0,19
PRIMER_RIGHT_1=69,25
PRIMER_LEFT_1_END_STABILITY=3
PRIMER_RIGHT_1_END_STABILITY=3
PRIMER_PAIR_1_PRODUCT_SIZE=70
=
SEQUENCE_ID=Contig31
SEQUENCE_TEMPLATE=ACCCCTTTTT
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=0
=
SEQUENCE_ID=Contig22
SEQUENCE_TEMPLATE=CCGTCGCCCC
PRIMER_LEFT_NUM_RETURNED=3
PRIMER_RIGHT_NUM_RETURNED=3
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=5
PRIMER_PAIR_0_PENALTY=7
PRIMER_LEFT_0_SEQ=AAGTCGCC
PRIMER_RIGHT_0_SEQ=agaGAGTA
PRIMER_LEFT_0=0,20
PRIMER_RIGHT_0=69,20
PRIMER_LEFT_0_END_STABILITY=2
PRIMER_RIGHT_0_END_STABILITY=3
PRIMER_PAIR_0_PRODUCT_SIZE=70
PRIMER_PAIR_1_PENALTY=7
PRIMER_LEFT_1_PENALTY=1
PRIMER_RIGHT_1_PENALTY=6
PRIMER_LEFT_1_SEQ=AAGTCGC
PRIMER_RIGHT_1_SEQ=aaaag
PRIMER_LEFT_1=0,19
PRIMER_RIGHT_1=69,25
PRIMER_LEFT_1_END_STABILITY=3
PRIMER_RIGHT_1_END_STABILITY=3
PRIMER_PAIR_1_PRODUCT_SIZE=73
PRIMER_PAIR_2_PENALTY=7
PRIMER_LEFT_2_PENALTY=1
PRIMER_RIGHT_2_PENALTY=6
PRIMER_LEFT_2_SEQ=AAGTCGC
PRIMER_RIGHT_2_SEQ=aaaag
PRIMER_LEFT_2=0,19
PRIMER_RIGHT_2=69,25
PRIMER_LEFT_2_END_STABILITY=3
PRIMER_RIGHT_2_END_STABILITY=3
PRIMER_PAIR_2_PRODUCT_SIZE=75
=
予想出力：
SEQUENCE_ID=Contig1
SEQUENCE_TEMPLATE=AAGTCGCCCCTCCAT
PRIMER_LEFT_NUM_RETURNED=2
PRIMER_RIGHT_NUM_RETURNED=2
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=5
PRIMER_PAIR_0_PENALTY=7.398828
PRIMER_LEFT_0_SEQ=AAGTCGCCCC
PRIMER_RIGHT_0_SEQ=aaaagaca
PRIMER_LEFT_0=0,20
PRIMER_RIGHT_0=69,20
PRIMER_LEFT_0_END_STABILITY=2
PRIMER_RIGHT_0_END_STABILITY=3
PRIMER_PAIR_0_PRODUCT_SIZE=70
=
SEQUENCE_ID=Contig22
SEQUENCE_TEMPLATE=CCGTCGCCCC
PRIMER_LEFT_NUM_RETURNED=3
PRIMER_RIGHT_NUM_RETURNED=3
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=5
PRIMER_PAIR_0_PENALTY=7
PRIMER_LEFT_0_SEQ=AAGTCGCC
PRIMER_RIGHT_0_SEQ=agaGAGTA
PRIMER_LEFT_0=0,20
PRIMER_RIGHT_0=69,20
PRIMER_LEFT_0_END_STABILITY=2
PRIMER_RIGHT_0_END_STABILITY=3
PRIMER_PAIR_0_PRODUCT_SIZE=70
=
私はawkを使って解決しようとしましたが、行と列の形ではないので解決できませんでした。この問題の解決にご協力いただきありがとうございます。ありがとうございます。
ベストアンサー1
入力データは段落中心なので、一行ずつ読みずに段落別に読みましょう。
awk -v RS="\n=\n" '
/PRIMER_LEFT_NUM_RETURNED=[^0]/ {
n = split($0, lines, /\n/)
for (i=1; i<=n; i++) {
if (lines[i] ~ /^(SEQUENCE_ID|SEQUENCE_TEMPLATE|PRIMER_LEFT_NUM_RETURNED|PRIMER_RIGHT_NUM_RETURNED|PRIMER_INTERNAL_NUM_RETURNED|PRIMER_PAIR_NUM_RETURNED|[^=]+_0[^=]*)=/)
print lines[i]
}
print "="
}
' input.file
またはPerlと同等のもの（より読みやすい「拡張」正規表現を許可する）
perl -0777 -ne '
BEGIN {
$wanted = qr{
^ # at the beginning of the string
(?: SEQUENCE_ID # match one of these words
| SEQUENCE_TEMPLATE
| PRIMER_LEFT_NUM_RETURNED
| PRIMER_RIGHT_NUM_RETURNED
| PRIMER_INTERNAL_NUM_RETURNED
| PRIMER_PAIR_NUM_RETURNED
| [^=]+_0[^=]*
)
= # followed by an equal sign
}x
}
for (split /^=$/m) {
if (/PRIMER_LEFT_NUM_RETURNED=[^0]/) {
print join("\n", grep {$_ =~ $wanted} split /\n/), "\n=\n";
}
}
# or, as a single command:
#
# print
# map {join("\n", grep {$_ =~ $wanted} split /\n/) . "\n=\n"}
# grep {/PRIMER_LEFT_NUM_RETURNED=[^0]/}
# split /^=$/m
' input.file