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Top Forums UNIX for Dummies Questions & Answers print multiple lines from text file based on pattern list Post 302555416 by Oyster on Wednesday 14th of September 2011 04:41:04 PM
Old 09-14-2011
print multiple lines from text file based on pattern list

I have a text file with a list of items/patterns:

ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig12238
ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig34624
ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig56875
ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig70306
ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig71435
...

I would like to print those lines which match from a tab-delimited file containing many many more lines:

...
ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig60558 1086
ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig60559 641 95 14.038 ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig60559 731
ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig60560 620 1406 245.247 ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig60560 625
ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig60561 609 208 36.771
...

Can grep process a pattern file? It seems as if it should, however, I have not had success. sed, awk? Please help. Thanks.
 

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FNMATCH(3)						     Linux Programmer's Manual							FNMATCH(3)

NAME
fnmatch - match filename or pathname SYNOPSIS
#include <fnmatch.h> int fnmatch(const char *pattern, const char *string, int flags); DESCRIPTION
The fnmatch() function checks whether the string argument matches the pattern argument, which is a shell wildcard pattern. The flags argument modifies the behavior; it is the bitwise OR of zero or more of the following flags: FNM_NOESCAPE If this flag is set, treat backslash as an ordinary character, instead of an escape character. FNM_PATHNAME If this flag is set, match a slash in string only with a slash in pattern and not by an asterisk (*) or a question mark (?) metacharacter, nor by a bracket expression ([]) containing a slash. FNM_PERIOD If this flag is set, a leading period in string has to be matched exactly by a period in pattern. A period is considered to be leading if it is the first character in string, or if both FNM_PATHNAME is set and the period immediately follows a slash. FNM_FILE_NAME This is a GNU synonym for FNM_PATHNAME. FNM_LEADING_DIR If this flag (a GNU extension) is set, the pattern is considered to be matched if it matches an initial segment of string which is followed by a slash. This flag is mainly for the internal use of glibc and is implemented only in certain cases. FNM_CASEFOLD If this flag (a GNU extension) is set, the pattern is matched case-insensitively. FNM_EXTMATCH If this flag (a GNU extension) is set, extended patterns are supported, as introduced by 'ksh' and now supported by other shells. The extended format is as follows, with pattern-list being a '|' separated list of patterns. '?(pattern-list)' The pattern matches if zero or one occurrences of any of the patterns in the pattern-list match the input string. '*(pattern-list)' The pattern matches if zero or more occurrences of any of the patterns in the pattern-list match the input string. '+(pattern-list)' The pattern matches if one or more occurrences of any of the patterns in the pattern-list match the input string. '@(pattern-list)' The pattern matches if exactly one occurrence of any of the patterns in the pattern-list match the input string. '!(pattern-list)' The pattern matches if the input string cannot be matched with any of the patterns in the pattern-list. RETURN VALUE
Zero if string matches pattern, FNM_NOMATCH if there is no match or another nonzero value if there is an error. ATTRIBUTES
For an explanation of the terms used in this section, see attributes(7). +----------+---------------+--------------------+ |Interface | Attribute | Value | +----------+---------------+--------------------+ |fnmatch() | Thread safety | MT-Safe env locale | +----------+---------------+--------------------+ CONFORMING TO
POSIX.1-2001, POSIX.1-2008, POSIX.2. The FNM_FILE_NAME, FNM_LEADING_DIR, and FNM_CASEFOLD flags are GNU extensions. SEE ALSO
sh(1), glob(3), scandir(3), wordexp(3), glob(7) COLOPHON
This page is part of release 4.15 of the Linux man-pages project. A description of the project, information about reporting bugs, and the latest version of this page, can be found at https://www.kernel.org/doc/man-pages/. GNU
2015-12-28 FNMATCH(3)
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