read regex from ID file, print regex and line below from source file
I have a file of protein sequences with headers (my source file). Based on a list of IDs (which are included in some of the headers), I'd like to print out only the specified sequences, with only the ID as header.
In other words, I'd like to search source.txt for the terms in IDs.txt, and print the ID as well as the sequence. Ideally the process would continue even if an ID is not found in the source file. All headers in source.txt are of similar format.
I am able to pull out the sequences based on the ID one-by-one, but this is slow and doesn't give me the header.
I also tried extracting the entire header and the sequence by modifying a script I had for a sequence file with different header type, but again it's one-by-one it only prints the header.
As is probably clear, I'm still pretty low on the learning curve. Any help would be really appreciated!
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)
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)
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)
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)
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)
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)
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)
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)
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
LEARN ABOUT LINUX
re_comp
RE_COMP(3) Linux Programmer's Manual RE_COMP(3)NAME
re_comp, re_exec - BSD regex functions
SYNOPSIS
#define _REGEX_RE_COMP
#include <sys/types.h>
#include <regex.h>
char *re_comp(char *regex);
int re_exec(char *string);
DESCRIPTION
re_comp() is used to compile the null-terminated regular expression pointed to by regex. The compiled pattern occupies a static area, the
pattern buffer, which is overwritten by subsequent use of re_comp(). If regex is NULL, no operation is performed and the pattern buffer's
contents are not altered.
re_exec() is used to assess whether the null-terminated string pointed to by string matches the previously compiled regex.
RETURN VALUE
re_comp() returns NULL on successful compilation of regex otherwise it returns a pointer to an appropriate error message.
re_exec() returns 1 for a successful match, zero for failure.
CONFORMING TO
4.3BSD.
NOTES
These functions are obsolete; the functions documented in regcomp(3) should be used instead.
SEE ALSO regcomp(3), regex(7), GNU regex manual
COLOPHON
This page is part of release 3.27 of the Linux man-pages project. A description of the project, and information about reporting bugs, can
be found at http://www.kernel.org/doc/man-pages/.
GNU 1995-07-14 RE_COMP(3)