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Full Discussion: Search for string and display those NOT found
Top Forums Shell Programming and Scripting Search for string and display those NOT found Post 302118166 by aigles on Saturday 19th of May 2007 11:57:54 AM
Old 05-19-2007
The following awk program display all the strings that have not been found in any of the input files. The strings are to be searched are read from the first input file.
Code:
#!/usr/bin/awk -f
# Filename: not_found

#
# Strings file.
#

NR==FNR {
   string_found[$1] = 0; # 0 = No, >0 = Yes
   next;
}

#
# New data file.
# Build array with strings not yet found
#

FNR==1 {
   for (str in string_found) {
      if (string_found[str] == 0) {
         strings[str]++;
         strings_count++;
      }
   }
   if (strings_count == 0) exit;
}

#
# Input data;
# Search data for strings not yet found
#

{
   for (str in strings) {
      if ($0 ~ str) {
         string_found[str]++;
         delete strings[str];
         if (--strings_count == 0) exit;
      }
   }
}

#
# No more files or allstrings have been found
# Print strings not found
#

END {
   for (str in string_found)
      if (string_found[str] == 0) print str;
}

The file string_list contains the strings to be search.
The file strings_not_found will contain the strings that have not be found in any of the files.
Don't put files string_list and strings_not_found in one of the directories that you want to scan.

Code:
chmod +rx not_found
not_found string_list $(find . -type f) > strings_not_found

Jean-Pierre.
 

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LEARN ABOUT DEBIAN

fastacmd

FASTACMD(1)						     NCBI Tools User's Manual						       FASTACMD(1)

NAME

       fastacmd - retrieve FASTA sequences from a BLAST database

SYNOPSIS

       fastacmd [-] [-D N] [-I] [-L start,stop] [-P N] [-S N] [-T] [-a] [-c] [-d str] [-i str] [-l N] [-o filename] [-p type] [-s str] [-t]

DESCRIPTION

       fastacmd retrieves FASTA formatted sequences from a blast(1) database formatted using the `-o' option.  An example fastacmd call would be

								fastacmd -d nr -s p38398

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -D N   Dump the entire database in some format:
	      1      fasta
	      2      GI list
	      3      Accession.version list

       -I     Print database information only (overrides all other options)

       -L start,stop
	      Range of sequence to extract (0 in start is beginning of sequence, 0 in stop is end of sequence, default is whole sequence)

       -P N   Retrieve sequences with Protein Identification Group (PIG) N.

       -S N   Strand on subsequence (nucleotide only):
	      1      top (default)
	      2      bottom

       -T     Print taxonomic information for requested sequence(s)

       -a     Retrieve duplicate accessions

       -c     Use ^A (01) as non-redundant defline separator

       -d str Database (default is nr)

       -i str Input file with GIs/accessions/loci for batch retrieval

       -l N   Line length for sequence (default = 80)

       -o filename
	      Output file (default = stdout)

       -p type
	      Type of file:
	      G      guess (default): look for protein, then nucleotide
	      T      protein
	      F      nucleotide

       -s str Comma-delimited search string(s).  GIs, accessions, loci, or fullSeq-id strings may be used, e.g., 555, AC147927, 'gnl|dbname|tag'

       -t     Definition line should contain target GI only

EXIT STATUS

	      0      Completed successfully.
	      1      An error (other than those below) occurred.
	      2      The BLAST database was not found.
	      3      A search (accession, GI, or taxonomy info) failed.
	      4      No taxonomy database was found.

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       blast(1), /usr/share/doc/blast2/fastacmd.html.

NCBI
								    2005-11-04							       FASTACMD(1)
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