I have a question on pattern matching. I have a file with multiple patterns in it, say pattern.txt
我有关于模式匹配的问题。我有一个包含多个模式的文件,比如pattern.txt
Locus3039v1rpkm6.85
Locus3041v1rpkm6.84
Locus3042v1rpkm6.84
地址3039v1rpkm6.85 Locus3041v1rpkm6.84 Locus3042v1rpkm6.84
And the test file to search is file.txt -
要搜索的测试文件是file.txt -
Locus3039v1rpkm6.85 gi|350401309|ref|XM_003486067.1| 0 10 85 328 253 8e-12 78.8
Locus3039v1rpkm6.85 gi|350401301|ref|XM_003486066.1| 0 10 85 566 491 8e-12 78.8
Locus3039v1rpkm6.85 gi|350401298|ref|XM_003486065.1| 0 10 85 500 425 8e-12 78.8
Locus3039v1rpkm6.85 gi|340723355|ref|XM_003400008.1| 0 10 106 566 470 3e-11 77.0
Locus3039v1rpkm6.85 gi|340723353|ref|XM_003400007.1| 0 10 106 496 400 3e-11 77.0
Locus3039v1rpkm6.85 gi|359323056|ref|XM_003639939.1| 0 27 104 322 245 9e-05 55.4
Locus3039v1rpkm6.85 gi|359323055|ref|XM_543849.4| 0 27 104 241 164 9e-05 55.4
Locus3039v1rpkm6.85 gi|354503991|ref|XM_003514015.1| 0 27 103 335 259 0.004 50.0
Locus3039v1rpkm6.85 gi|341599927|emb|AM412059.2| 1 63 100 1645525 1645489 6.8 39.2
Locus3039v1rpkm6.85 gi|340003223|emb|HE572590.1| 1 63 100 1671652 1671616 6.8 39.2
Locus3041v1rpkm6.84 gi|337757426|emb|FQ859181.1| 1 61 114 2772617 2772667 0.60 42.8
Locus3041v1rpkm6.84 gi|159889572|gb|CP000875.1| 0 5 40 1185295 1185330 0.60 42.8
Locus3041v1rpkm6.84 gi|158107272|gb|CP000820.1| 0 2 34 5594193 5594161 0.60 42.8
Locus3041v1rpkm6.84 gi|156844486|ref|XM_001645256.1| 83 140 793 850 0.60 42.8
Locus3041v1rpkm6.84 gi|339305108|gb|CP001503.2| 0 58 94 3006529 3006565 2.1 41.0
Locus3041v1rpkm6.84 gi|247533203|gb|CP001607.1| 0 1 40 1268073 1268034 2.1 41.0
Locus3041v1rpkm6.84 gi|367050653|ref|XM_003655658.1| 0 75 103 843 871 7.3 39.2
Locus3041v1rpkm6.84 gi|347002178|gb|CP003012.1| 0 75 103 2986236 2986208 7.3 39.2
Locus3043v1rpkm6.84 gi|332015867|gb|HQ658110.1| 0 9 31 4151 4129 0.49 42.8
Locus3043v1rpkm6.84 gi|254946573|gb|CP001619.1| 1 9 43 4243052 4243019 0.49 42.8
Locus3043v1rpkm6.84 gi|329755665|gb|JF715057.1| 0 11 42 110968 110937 1.7 41.0
Locus3043v1rpkm6.84 gi|9937515|gb|AF294752.1| 0 48 79 2081 2050 1.7 41.0
I want to match each pattern for the first 5 hits and move to the next pattern for the 1st five and so on.
我希望匹配前5个命中的每个模式,然后移动到前5个的下一个模式,依此类推。
I tried
grep -i -m 5 -f pattern.txt file.txt > out.txt
grep -i -f pattern.txt -m 5 file.txt > out.txt
But I am getting only the top 5 for the first pattern and ending. Where am I going wrong? Is there a parameter to perform this required function?
但是我只获得了第一个模式的前五名并且结束了。我哪里错了?是否有参数来执行此必需功能?
3 个解决方案
#1
4
Try this:
for pat in $(cat pattern.txt); do grep -i -m 5 $pat file.txt; done > out.txt
Which means
- For each pattern in
pattern.txt, grep the first 5 matched record. - Append the result to out.txt
对于pattern.txt中的每个模式,grep前5个匹配的记录。
将结果附加到out.txt
EDIT
As @dogbane mentioned in his comment, this is a UUOC. Here is my improved answer:
正如@dogbane在评论中提到的,这是一个UUOC。这是我改进的答案:
for pat in $(< pattern.txt); do grep -i -m 5 $pat file.txt; done > out.txt
Also look at this answer.
还看看这个答案。
#2
2
Each time you use > you are overwriting the file with the new output, using >> instead you'll be able to append to the file:
每次使用>你都用新输出覆盖文件,使用>>而不是你能够追加到文件:
$ yourcommand >> file
#3
1
Here's one way using awk. It should be quite quick too, because file.txt is read only once:
这是使用awk的一种方式。它应该也很快,因为file.txt只读一次:
awk 'BEGIN { IGNORECASE=1 } FNR==NR { a[$0]++; next } { for (i in a) if ($0 ~ i && a[i] <= 5) { print; a[i]++ } }' patterns.txt file.txt
Results:
Locus3039v1rpkm6.85 gi|350401309|ref|XM_003486067.1| 0 10 85 328 253 8e-12 78.8
Locus3039v1rpkm6.85 gi|350401301|ref|XM_003486066.1| 0 10 85 566 491 8e-12 78.8
Locus3039v1rpkm6.85 gi|350401298|ref|XM_003486065.1| 0 10 85 500 425 8e-12 78.8
Locus3039v1rpkm6.85 gi|340723355|ref|XM_003400008.1| 0 10 106 566 470 3e-11 77.0
Locus3039v1rpkm6.85 gi|340723353|ref|XM_003400007.1| 0 10 106 496 400 3e-11 77.0
Locus3041v1rpkm6.84 gi|337757426|emb|FQ859181.1| 1 61 114 2772617 2772667 0.60 42.8
Locus3041v1rpkm6.84 gi|159889572|gb|CP000875.1| 0 5 40 1185295 1185330 0.60 42.8
Locus3041v1rpkm6.84 gi|158107272|gb|CP000820.1| 0 2 34 5594193 5594161 0.60 42.8
Locus3041v1rpkm6.84 gi|156844486|ref|XM_001645256.1| 83 140 793 850 0.60 42.8
Locus3041v1rpkm6.84 gi|339305108|gb|CP001503.2| 0 58 94 3006529 3006565 2.1 41.0
#1
4
Try this:
for pat in $(cat pattern.txt); do grep -i -m 5 $pat file.txt; done > out.txt
Which means
- For each pattern in
pattern.txt, grep the first 5 matched record. - Append the result to out.txt
对于pattern.txt中的每个模式,grep前5个匹配的记录。
将结果附加到out.txt
EDIT
As @dogbane mentioned in his comment, this is a UUOC. Here is my improved answer:
正如@dogbane在评论中提到的,这是一个UUOC。这是我改进的答案:
for pat in $(< pattern.txt); do grep -i -m 5 $pat file.txt; done > out.txt
Also look at this answer.
还看看这个答案。
#2
2
Each time you use > you are overwriting the file with the new output, using >> instead you'll be able to append to the file:
每次使用>你都用新输出覆盖文件,使用>>而不是你能够追加到文件:
$ yourcommand >> file
#3
1
Here's one way using awk. It should be quite quick too, because file.txt is read only once:
这是使用awk的一种方式。它应该也很快,因为file.txt只读一次:
awk 'BEGIN { IGNORECASE=1 } FNR==NR { a[$0]++; next } { for (i in a) if ($0 ~ i && a[i] <= 5) { print; a[i]++ } }' patterns.txt file.txt
Results:
Locus3039v1rpkm6.85 gi|350401309|ref|XM_003486067.1| 0 10 85 328 253 8e-12 78.8
Locus3039v1rpkm6.85 gi|350401301|ref|XM_003486066.1| 0 10 85 566 491 8e-12 78.8
Locus3039v1rpkm6.85 gi|350401298|ref|XM_003486065.1| 0 10 85 500 425 8e-12 78.8
Locus3039v1rpkm6.85 gi|340723355|ref|XM_003400008.1| 0 10 106 566 470 3e-11 77.0
Locus3039v1rpkm6.85 gi|340723353|ref|XM_003400007.1| 0 10 106 496 400 3e-11 77.0
Locus3041v1rpkm6.84 gi|337757426|emb|FQ859181.1| 1 61 114 2772617 2772667 0.60 42.8
Locus3041v1rpkm6.84 gi|159889572|gb|CP000875.1| 0 5 40 1185295 1185330 0.60 42.8
Locus3041v1rpkm6.84 gi|158107272|gb|CP000820.1| 0 2 34 5594193 5594161 0.60 42.8
Locus3041v1rpkm6.84 gi|156844486|ref|XM_001645256.1| 83 140 793 850 0.60 42.8
Locus3041v1rpkm6.84 gi|339305108|gb|CP001503.2| 0 58 94 3006529 3006565 2.1 41.0