Match patterns from one file awk not working

up vote
1
down vote

favorite

I want to match strings from a pattern file to look into Source.txt file.

pattern_list.txt has 139k lines

Source.txt more than 5 millions lines

If I use grep like this it tooks 2 seconds to get the output.

grep -F -f pattern_list.txt Source.txt > Output.txt

But if I try with this AWK script it gets stuck and after 10 min I need to stop because nothing happens.

awk 'NR==FNR a[$1]; next 

for (i in a) if ($0 ~ i) print $0

 ' FS=, OFS=, pattern_list.txt Source.txt > Output.txt

pattern_list is like this

21051
99888
95746

and source.txt like this

72300,2,694
21051,1,694
63143,3,694
25223,2,694
99888,8,694
53919,2,694
51059,2,694

What it wrong with my AWK script?

I'm running on Cygwin in Windows.

edited Nov 11 at 7:06

codeforester

17.4k83864

asked Nov 10 at 20:44

Ger Cas

320111

3

Another approach: join -t "," <(sort pattern_list) <(sort source.txt)
– Cyrus
Nov 10 at 21:10

Possible duplicate of Fastest way to find lines of a file from another larger file in Bash
– codeforester
Nov 11 at 7:06

@codeforester Hi, I was asking more about why my awk script was so slow, than that ask the fastest way to do it in perl, grep, bash or other tools.
– Ger Cas
Nov 11 at 12:44

Since your awk code is trying to exactly what the accepted answer in the linked post is doing, I considered it a duplicate, or at least, related.
– codeforester
Nov 11 at 17:23

add a comment |

up vote
1
down vote

favorite

I want to match strings from a pattern file to look into Source.txt file.

pattern_list.txt has 139k lines

Source.txt more than 5 millions lines

If I use grep like this it tooks 2 seconds to get the output.

grep -F -f pattern_list.txt Source.txt > Output.txt

But if I try with this AWK script it gets stuck and after 10 min I need to stop because nothing happens.

awk 'NR==FNR a[$1]; next 

for (i in a) if ($0 ~ i) print $0

 ' FS=, OFS=, pattern_list.txt Source.txt > Output.txt

pattern_list is like this

21051
99888
95746

and source.txt like this

72300,2,694
21051,1,694
63143,3,694
25223,2,694
99888,8,694
53919,2,694
51059,2,694

What it wrong with my AWK script?

I'm running on Cygwin in Windows.

edited Nov 11 at 7:06

codeforester

17.4k83864

asked Nov 10 at 20:44

Ger Cas

320111

3

Another approach: join -t "," <(sort pattern_list) <(sort source.txt)
– Cyrus
Nov 10 at 21:10

Possible duplicate of Fastest way to find lines of a file from another larger file in Bash
– codeforester
Nov 11 at 7:06

@codeforester Hi, I was asking more about why my awk script was so slow, than that ask the fastest way to do it in perl, grep, bash or other tools.
– Ger Cas
Nov 11 at 12:44

Since your awk code is trying to exactly what the accepted answer in the linked post is doing, I considered it a duplicate, or at least, related.
– codeforester
Nov 11 at 17:23

add a comment |

up vote
1
down vote

favorite

I want to match strings from a pattern file to look into Source.txt file.

pattern_list.txt has 139k lines

Source.txt more than 5 millions lines

If I use grep like this it tooks 2 seconds to get the output.

grep -F -f pattern_list.txt Source.txt > Output.txt

But if I try with this AWK script it gets stuck and after 10 min I need to stop because nothing happens.

awk 'NR==FNR a[$1]; next 

for (i in a) if ($0 ~ i) print $0

 ' FS=, OFS=, pattern_list.txt Source.txt > Output.txt

pattern_list is like this

21051
99888
95746

and source.txt like this

72300,2,694
21051,1,694
63143,3,694
25223,2,694
99888,8,694
53919,2,694
51059,2,694

What it wrong with my AWK script?

I'm running on Cygwin in Windows.

edited Nov 11 at 7:06

codeforester

17.4k83864

asked Nov 10 at 20:44

Ger Cas

320111

I want to match strings from a pattern file to look into Source.txt file.

pattern_list.txt has 139k lines

Source.txt more than 5 millions lines

If I use grep like this it tooks 2 seconds to get the output.

grep -F -f pattern_list.txt Source.txt > Output.txt

But if I try with this AWK script it gets stuck and after 10 min I need to stop because nothing happens.

awk 'NR==FNR a[$1]; next 

for (i in a) if ($0 ~ i) print $0

 ' FS=, OFS=, pattern_list.txt Source.txt > Output.txt

pattern_list is like this

21051
99888
95746

and source.txt like this

72300,2,694
21051,1,694
63143,3,694
25223,2,694
99888,8,694
53919,2,694
51059,2,694

What it wrong with my AWK script?

I'm running on Cygwin in Windows.

awk pattern-matching

edited Nov 11 at 7:06

codeforester

17.4k83864

asked Nov 10 at 20:44

Ger Cas

320111

edited Nov 11 at 7:06

codeforester

17.4k83864

asked Nov 10 at 20:44

Ger Cas

320111

edited Nov 11 at 7:06

codeforester

17.4k83864

edited Nov 11 at 7:06

codeforester

17.4k83864

edited Nov 11 at 7:06

codeforester

17.4k83864

asked Nov 10 at 20:44

Ger Cas

320111

asked Nov 10 at 20:44

Ger Cas

320111

asked Nov 10 at 20:44

Ger Cas

320111

3

Another approach: join -t "," <(sort pattern_list) <(sort source.txt)
– Cyrus
Nov 10 at 21:10

Possible duplicate of Fastest way to find lines of a file from another larger file in Bash
– codeforester
Nov 11 at 7:06

@codeforester Hi, I was asking more about why my awk script was so slow, than that ask the fastest way to do it in perl, grep, bash or other tools.
– Ger Cas
Nov 11 at 12:44

Since your awk code is trying to exactly what the accepted answer in the linked post is doing, I considered it a duplicate, or at least, related.
– codeforester
Nov 11 at 17:23

add a comment |

3

Another approach: join -t "," <(sort pattern_list) <(sort source.txt)
– Cyrus
Nov 10 at 21:10

Possible duplicate of Fastest way to find lines of a file from another larger file in Bash
– codeforester
Nov 11 at 7:06

@codeforester Hi, I was asking more about why my awk script was so slow, than that ask the fastest way to do it in perl, grep, bash or other tools.
– Ger Cas
Nov 11 at 12:44

Since your awk code is trying to exactly what the accepted answer in the linked post is doing, I considered it a duplicate, or at least, related.
– codeforester
Nov 11 at 17:23

Another approach: join -t "," <(sort pattern_list) <(sort source.txt)
– Cyrus
Nov 10 at 21:10

Possible duplicate of Fastest way to find lines of a file from another larger file in Bash
– codeforester
Nov 11 at 7:06

@codeforester Hi, I was asking more about why my awk script was so slow, than that ask the fastest way to do it in perl, grep, bash or other tools.
– Ger Cas
Nov 11 at 12:44

Since your awk code is trying to exactly what the accepted answer in the linked post is doing, I considered it a duplicate, or at least, related.
– codeforester
Nov 11 at 17:23

add a comment |

2 Answers
2

active

oldest

votes

up vote
2
down vote

accepted

if you are doing literal match this should be faster than your approach

$ awk -F, 'NR==FNRa[$0]; next $1 in aprint $1,$3,$8,$20' pattern_list source > output

However, I think sort/join will still be faster than grep and awk.

edited Nov 10 at 23:55

answered Nov 10 at 21:22

karakfa

47.6k52738

Excellent. Now the execution time with your awk script is less than 4 seconds. But since my original source file has several fields how to say in your script that print only $3, $8 and $20 for the matched strings?
– Ger Cas
Nov 10 at 23:10

just print required fields, see the update.
– karakfa
Nov 10 at 23:56

Can't improve on karakfa's answer, but for grep vs awk performance tests see polydesmida.info/BASHing/2018-10-24.html
– user2138595
Nov 11 at 6:57

@karakfa Thanks a lot. It works exactly as I wanted.
– Ger Cas
Nov 11 at 12:36

@user2138595 Thanks for share the info. Yes, is what I understood in theory and practice, that awk is champion in speed.
– Ger Cas
Nov 11 at 12:37

add a comment |

up vote
2
down vote

If increasing performance is your goal, you'll need to multithread this (AWK is unlikely faster, perhaps slower?).

If I were you, I'd partition the source file, then search each part:

$ split -l 100000 src.txt src_part
$ ls src_part* | xargs -n1 -P4 fgrep -f pat.txt > matches.txt
$ rm src_part*

answered Nov 10 at 21:00

Rafael

4,34372038

Thanks for answer, but what I know is that awk is faster than grep. So, I don't know what happens here.
– Ger Cas
Nov 10 at 21:06

1

@GerCas I doubt that is true as AWK has to parse the script, then run. grep, on the other hand, is heavily optimized for its purpose.
– Rafael
Nov 10 at 21:09

add a comment |

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2 Answers
2

active

oldest

votes

2 Answers
2

active

oldest

votes

up vote
2
down vote

accepted

if you are doing literal match this should be faster than your approach

$ awk -F, 'NR==FNRa[$0]; next $1 in aprint $1,$3,$8,$20' pattern_list source > output

However, I think sort/join will still be faster than grep and awk.

edited Nov 10 at 23:55

answered Nov 10 at 21:22

karakfa

47.6k52738

Excellent. Now the execution time with your awk script is less than 4 seconds. But since my original source file has several fields how to say in your script that print only $3, $8 and $20 for the matched strings?
– Ger Cas
Nov 10 at 23:10

just print required fields, see the update.
– karakfa
Nov 10 at 23:56

Can't improve on karakfa's answer, but for grep vs awk performance tests see polydesmida.info/BASHing/2018-10-24.html
– user2138595
Nov 11 at 6:57

@karakfa Thanks a lot. It works exactly as I wanted.
– Ger Cas
Nov 11 at 12:36

@user2138595 Thanks for share the info. Yes, is what I understood in theory and practice, that awk is champion in speed.
– Ger Cas
Nov 11 at 12:37

add a comment |

up vote
2
down vote

accepted

if you are doing literal match this should be faster than your approach

$ awk -F, 'NR==FNRa[$0]; next $1 in aprint $1,$3,$8,$20' pattern_list source > output

However, I think sort/join will still be faster than grep and awk.

edited Nov 10 at 23:55

answered Nov 10 at 21:22

karakfa

47.6k52738

Excellent. Now the execution time with your awk script is less than 4 seconds. But since my original source file has several fields how to say in your script that print only $3, $8 and $20 for the matched strings?
– Ger Cas
Nov 10 at 23:10

just print required fields, see the update.
– karakfa
Nov 10 at 23:56

Can't improve on karakfa's answer, but for grep vs awk performance tests see polydesmida.info/BASHing/2018-10-24.html
– user2138595
Nov 11 at 6:57

@karakfa Thanks a lot. It works exactly as I wanted.
– Ger Cas
Nov 11 at 12:36

@user2138595 Thanks for share the info. Yes, is what I understood in theory and practice, that awk is champion in speed.
– Ger Cas
Nov 11 at 12:37

add a comment |

up vote
2
down vote

accepted

if you are doing literal match this should be faster than your approach

$ awk -F, 'NR==FNRa[$0]; next $1 in aprint $1,$3,$8,$20' pattern_list source > output

However, I think sort/join will still be faster than grep and awk.

edited Nov 10 at 23:55

answered Nov 10 at 21:22

karakfa

47.6k52738

if you are doing literal match this should be faster than your approach

$ awk -F, 'NR==FNRa[$0]; next $1 in aprint $1,$3,$8,$20' pattern_list source > output

However, I think sort/join will still be faster than grep and awk.

edited Nov 10 at 23:55

answered Nov 10 at 21:22

karakfa

47.6k52738

edited Nov 10 at 23:55

answered Nov 10 at 21:22

karakfa

47.6k52738

answered Nov 10 at 21:22

karakfa

47.6k52738

answered Nov 10 at 21:22

karakfa

47.6k52738

Excellent. Now the execution time with your awk script is less than 4 seconds. But since my original source file has several fields how to say in your script that print only $3, $8 and $20 for the matched strings?
– Ger Cas
Nov 10 at 23:10

just print required fields, see the update.
– karakfa
Nov 10 at 23:56

Can't improve on karakfa's answer, but for grep vs awk performance tests see polydesmida.info/BASHing/2018-10-24.html
– user2138595
Nov 11 at 6:57

@karakfa Thanks a lot. It works exactly as I wanted.
– Ger Cas
Nov 11 at 12:36

@user2138595 Thanks for share the info. Yes, is what I understood in theory and practice, that awk is champion in speed.
– Ger Cas
Nov 11 at 12:37

add a comment |

Excellent. Now the execution time with your awk script is less than 4 seconds. But since my original source file has several fields how to say in your script that print only $3, $8 and $20 for the matched strings?
– Ger Cas
Nov 10 at 23:10

just print required fields, see the update.
– karakfa
Nov 10 at 23:56

Can't improve on karakfa's answer, but for grep vs awk performance tests see polydesmida.info/BASHing/2018-10-24.html
– user2138595
Nov 11 at 6:57

@karakfa Thanks a lot. It works exactly as I wanted.
– Ger Cas
Nov 11 at 12:36

@user2138595 Thanks for share the info. Yes, is what I understood in theory and practice, that awk is champion in speed.
– Ger Cas
Nov 11 at 12:37

Excellent. Now the execution time with your awk script is less than 4 seconds. But since my original source file has several fields how to say in your script that print only $3, $8 and $20 for the matched strings?
– Ger Cas
Nov 10 at 23:10

just print required fields, see the update.
– karakfa
Nov 10 at 23:56

Can't improve on karakfa's answer, but for grep vs awk performance tests see polydesmida.info/BASHing/2018-10-24.html
– user2138595
Nov 11 at 6:57

@karakfa Thanks a lot. It works exactly as I wanted.
– Ger Cas
Nov 11 at 12:36

@user2138595 Thanks for share the info. Yes, is what I understood in theory and practice, that awk is champion in speed.
– Ger Cas
Nov 11 at 12:37

add a comment |

up vote
2
down vote

If increasing performance is your goal, you'll need to multithread this (AWK is unlikely faster, perhaps slower?).

If I were you, I'd partition the source file, then search each part:

$ split -l 100000 src.txt src_part
$ ls src_part* | xargs -n1 -P4 fgrep -f pat.txt > matches.txt
$ rm src_part*

answered Nov 10 at 21:00

Rafael

4,34372038

Thanks for answer, but what I know is that awk is faster than grep. So, I don't know what happens here.
– Ger Cas
Nov 10 at 21:06

1

@GerCas I doubt that is true as AWK has to parse the script, then run. grep, on the other hand, is heavily optimized for its purpose.
– Rafael
Nov 10 at 21:09

add a comment |

up vote
2
down vote

If increasing performance is your goal, you'll need to multithread this (AWK is unlikely faster, perhaps slower?).

If I were you, I'd partition the source file, then search each part:

$ split -l 100000 src.txt src_part
$ ls src_part* | xargs -n1 -P4 fgrep -f pat.txt > matches.txt
$ rm src_part*

answered Nov 10 at 21:00

Rafael

4,34372038

Thanks for answer, but what I know is that awk is faster than grep. So, I don't know what happens here.
– Ger Cas
Nov 10 at 21:06

1

@GerCas I doubt that is true as AWK has to parse the script, then run. grep, on the other hand, is heavily optimized for its purpose.
– Rafael
Nov 10 at 21:09

add a comment |

up vote
2
down vote

If increasing performance is your goal, you'll need to multithread this (AWK is unlikely faster, perhaps slower?).

If I were you, I'd partition the source file, then search each part:

$ split -l 100000 src.txt src_part
$ ls src_part* | xargs -n1 -P4 fgrep -f pat.txt > matches.txt
$ rm src_part*

answered Nov 10 at 21:00

Rafael

4,34372038

If increasing performance is your goal, you'll need to multithread this (AWK is unlikely faster, perhaps slower?).

If I were you, I'd partition the source file, then search each part:

$ split -l 100000 src.txt src_part
$ ls src_part* | xargs -n1 -P4 fgrep -f pat.txt > matches.txt
$ rm src_part*

answered Nov 10 at 21:00

Rafael

4,34372038

answered Nov 10 at 21:00

Rafael

4,34372038

answered Nov 10 at 21:00

Rafael

4,34372038

answered Nov 10 at 21:00

Rafael

4,34372038

Thanks for answer, but what I know is that awk is faster than grep. So, I don't know what happens here.
– Ger Cas
Nov 10 at 21:06

1

@GerCas I doubt that is true as AWK has to parse the script, then run. grep, on the other hand, is heavily optimized for its purpose.
– Rafael
Nov 10 at 21:09

add a comment |

Thanks for answer, but what I know is that awk is faster than grep. So, I don't know what happens here.
– Ger Cas
Nov 10 at 21:06

1

@GerCas I doubt that is true as AWK has to parse the script, then run. grep, on the other hand, is heavily optimized for its purpose.
– Rafael
Nov 10 at 21:09

Thanks for answer, but what I know is that awk is faster than grep. So, I don't know what happens here.
– Ger Cas
Nov 10 at 21:06

@GerCas I doubt that is true as AWK has to parse the script, then run. grep, on the other hand, is heavily optimized for its purpose.
– Rafael
Nov 10 at 21:09

add a comment |

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