Sponsored Content
Top Forums UNIX for Dummies Questions & Answers read regex from ID file, print regex and line below from source file Post 302712149 by pathunkathunk on Monday 8th of October 2012 07:45:53 PM
Old 10-08-2012
jim, thanks for taking a look.

Using the code you provide, I get the following in terminal:
Quote:
awk: illegal primary in regular expression >m.54555 g.54555 ORF g.54555 m.54555 type:internal len:137 (+) comp1001102_c0_seq1:3-416(+) at ) comp1001102_c0_seq1:3-416(+)
input record number 3, file source.txt
source line number 3
cat newfile returns:
Quote:
> comp100001_c0_seq1
comp1002314_c0_seq1
>m.49518 g.49518 ORF g.49518 m.49518 type:internal len:169 (-) comp100001_c0_seq1:3-509(-)
FHPPVSDSCKRCDMYKNQIKIAPENEKIQLNADHELHLRKAESARNGMNNDVELCKTDPNKVTVIAFDLMKTLSTPSLSVGVAYYKRQLSTYNLGIHNLT TNDAYMYVWNESMASRGPQEIGSCLLHFIKNYVHTEQLIMYSDQCGGQNRNIKMALICNFVVGSNDYLP
>m.54555 g.54555 ORF g.54555 m.54555 type:internal len:137 (+) comp1001102_c0_seq1:3-416(+)
Just to verify, here are the input files:
Quote:
$ cat source.txt
>m.49518 g.49518 ORF g.49518 m.49518 type:internal len:169 (-) comp100001_c0_seq1:3-509(-)
FHPPVSDSCKRCDMYKNQIKIAPENEKIQLNADHELHLRKAESARNGMNNDVELCKTDPNKVTVIAFDLMKTLSTPSLSVGVAYYKRQLSTYNLGIHNLT TNDAYMYVWNESMASRGPQEIGSCLLHFIKNYVHTEQLIMYSDQCGGQNRNIKMALICNFVVGSNDYLP
>m.54555 g.54555 ORF g.54555 m.54555 type:internal len:137 (+) comp1001102_c0_seq1:3-416(+)
YGDLDDSALDAEGPAGPVYRFSRRKSDTKSDDNSQSNGEGVMMMINGELVKVEQLKREEIINCTCGYTEEDGLMIQCDLCLCWQHGHCNGIEREKDVPEK YICYICSHPYRQRPSRKYIHDQDWIKEGKLVSLTKRK
>m.54557 g.54557 ORF g.54557 m.54557 type:internal len:113 (+) comp1002314_c0_seq1:2-343(+)
SIKARQIYDSRGNPTVEVDLVTENGLFRAAVPSGASTGVHEALELRDNDKSMYHGKSVFKAVDNINSIIAPELLKANIEVTEQAEIDNFLLKLDGTPNKS KLGANAILGVSLA
$ cat ID.txt
comp100001_c0_seq1
comp1002314_c0_seq1
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

awk - print file contents except regex

Hello, I have a file which has user information. Each user has 2 variables with the same name like Email: testuser1 Email: testuser1@test.com Email: testuser2 Email: testuser2@test.com My intention is to delete the ones without the '@' symbol. When I run this statement awk '/^Email:/&&!/@/'... (6 Replies)
Discussion started by: rmsagar
6 Replies

2. Shell Programming and Scripting

print first few lines, then apply regex on a specific column to print results.

abc.dat tty cpu tin tout us sy wt id 0 0 7 3 19 71 extended device statistics r/s w/s kr/s kw/s wait actv wsvc_t asvc_t %w %b device 0.0 133.2 0.0 682.9 0.0 1.0 0.0 7.2 0 79 c1t0d0 0.2 180.4 0.1 5471.2 3.0 2.8 16.4 15.6 15 52 aaaaaa1-xx I want to skip first 5 line... (4 Replies)
Discussion started by: kchinnam
4 Replies

3. Shell Programming and Scripting

read file line by line print column wise

I have a .csv file which is seperated with (;) inputfile --------- ZZZZ;AAAA;BBB;CCCC;DDD;EEE; YYYY;BBBB;CCC;DDDD;EEE;FFF; ... ... reading file line by line till end of file. while reading each line output format should be . i need to print only specific columns let say 5th... (2 Replies)
Discussion started by: rocking77
2 Replies

4. Shell Programming and Scripting

Bash script to send lines of file to new file based on Regex

I have a file that looks like this: cat includes CORP-CRASHTEST-BU e:\crashplan\ CORP-TEST /usr/openv/java /usr/openv/logs /usr/openv/man CORP-LABS_TEST /usr/openv/java /usr/openv/logs /usr/openv/man What I want to do is make three new files with just those selections. So the three... (4 Replies)
Discussion started by: newbie2010
4 Replies

5. Shell Programming and Scripting

Using regex's from file1, print line and line after matches in file2

Good day, I have a list of regular expressions in file1. For each match in file2, print the containing line and the line after. file1: file2: Output: I can match a regex and print the line and line after awk '{lines = $0} /Macrosiphum_rosae/ {print lines ; print lines } ' ... (1 Reply)
Discussion started by: pathunkathunk
1 Replies

6. Shell Programming and Scripting

Regex: print matched line and exact pattern match

Hi experts, I have a file with regexes which is used for automatic searches on several files (40+ GB). To do some postprocessing with the grep result I need the matching line as well as the match itself. I know that the latter could be achieved with grep's -o option. But I'm not aware of a... (2 Replies)
Discussion started by: stresing
2 Replies

7. Shell Programming and Scripting

Failure using regex with awk in 'while read file' loop

I have a file1.txt with several 100k lines, each of which has a column 9 containing one of 60 "label" identifiers. Using an labels.txt file containing a list of labels, I'd like to extract 200 random lines from file1.txt for each of the labels in index.txt. Using a contrived mini-example: $ cat... (8 Replies)
Discussion started by: pathunkathunk
8 Replies

8. UNIX for Advanced & Expert Users

sed REGEX to print multiple occurrences of a pattern from a line

I have a line that I need to parse through and extract a pattern that occurs multiple times in it. Example line: getInfoCall: info received please proceed, getInfoCall: info received please proceed, getInfoCall: info received please proceed, getInfoCall: info received please proceed,... (4 Replies)
Discussion started by: Vidhyaprakash
4 Replies

9. Shell Programming and Scripting

(n)awk: print regex search output lines in one line

Hello. I have been looking high and low for the solution for this. I seems there should be a simple answer, but alas. I have a big xml file, and I need to extract certain information from specific items. The information I need can be found between a specific set of tags. let's call them... (2 Replies)
Discussion started by: Tobias-Reiper
2 Replies

10. Shell Programming and Scripting

Sendmail K command regex: adding exclusion/negative lookahead to regex -a@MATCH

I'm trying to get some exclusions into our sendmail regular expression for the K command. The following configuration & regex works: LOCAL_CONFIG # Kcheckaddress regex -a@MATCH +<@+?\.++?\.(us|info|to|br|bid|cn|ru) LOCAL_RULESETS SLocal_check_mail # check address against various regex... (0 Replies)
Discussion started by: RobbieTheK
0 Replies
Digest(3)							   OCaml library							 Digest(3)

NAME
Digest - MD5 message digest. Module Module Digest Documentation Module Digest : sig end MD5 message digest. This module provides functions to compute 128-bit ``digests'' of arbitrary-length strings or files. The digests are of cryptographic qual- ity: it is very hard, given a digest, to forge a string having that digest. The algorithm used is MD5. This module should not be used for secure and sensitive cryptographic applications. For these kind of applications more recent and stronger cryptographic primitives should be used instead. type t = string The type of digests: 16-character strings. val compare : t -> t -> int The comparison function for 16-character digest, with the same specification as Pervasives.compare and the implementation shared with String.compare . Along with the type t , this function compare allows the module Digest to be passed as argument to the functors Set.Make and Map.Make . Since 4.00.0 val string : string -> t Return the digest of the given string. val substring : string -> int -> int -> t Digest.substring s ofs len returns the digest of the substring of s starting at character number ofs and containing len characters. val channel : Pervasives.in_channel -> int -> t If len is nonnegative, Digest.channel ic len reads len characters from channel ic and returns their digest, or raises End_of_file if end-of-file is reached before len characters are read. If len is negative, Digest.channel ic len reads all characters from ic until end-of-file is reached and return their digest. val file : string -> t Return the digest of the file whose name is given. val output : Pervasives.out_channel -> t -> unit Write a digest on the given output channel. val input : Pervasives.in_channel -> t Read a digest from the given input channel. val to_hex : t -> string Return the printable hexadecimal representation of the given digest. val from_hex : string -> t Convert a hexadecimal representation back into the corresponding digest. Raise Invalid_argument if the argument is not exactly 32 hexadec- imal characters. Since 4.00.0 OCamldoc 2014-06-09 Digest(3)
All times are GMT -4. The time now is 01:40 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy