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  • filter sequence by length

    Hi,

    To filter sequencesby length from a fasta file, I'm using now a bioperl script. But is there an another method (faster) ?

    here's my little script


    Code:
    #!/usr/bin/perl
    
    use warnings;
    use strict;
    use Bio::SeqIO;
    
    
    my $file = $ARGV[0]; 
    my $min = $ARGV[1];
    my $max = $ARGV[2];
    my $out = $ARGV[3];
    
    open (FILE, ">>$out") or die ("Error : Cannot open file $out for writing..!\n");
    
    my $seq_in  = Bio::SeqIO->new( -format => 'fasta',-file => $file);
    
    while( my $seq1 = $seq_in->next_seq() ) {	
    	
    	my $id  = $seq1->primary_id;
    	chomp $id;
    	my $seq = $seq1->seq;
    	chomp $seq;
    	my $lseq = length($seq);
    	if($lseq>=$min && $lseq <=$max){
    		print FILE ">",$id,"\n",$seq,"\n";	
    	}
    }

  • #2
    You could try Galaxy:

    Galaxy is a community-driven web-based analysis platform for life science research.


    It's very fast and you can do different type of analysis.

    Comment


    • #3
      Thanks,

      is it possible to have this tool in command line ?

      Comment


      • #4
        From Galaxy i don't think is possible. But probably if you search you may find a similar script.

        Comment


        • #5
          With Biopieces (www.biopieces.org) you can do:

          Code:
          read_fasta -i test.fna | grab -e 'SEQ_LEN > 10' | grab -e 'SEQ_LEN <= 100' | write_fasta -x
          Cheers,


          Martin

          Comment


          • #6
            Originally posted by Giorgio C View Post
            From Galaxy i don't think is possible. But probably if you search you may find a similar script.
            This is a command line tool that is included in the Galaxy distribution. I've included the code below.

            To get any tool that is included with Galaxy, follow the instructions at http://getgalaxy.org/. Tools are defined in the tools directory. Many will have dependencies (although the one below does not).

            Code:
            #!/usr/bin/env python
            """
            Input: fasta, minimal length, maximal length
            Output: fasta
            Return sequences whose lengths are within the range.
            """
            
            import sys, os
            
            assert sys.version_info[:2] >= ( 2, 4 )
            
            def stop_err( msg ):
                sys.stderr.write( msg )
                sys.exit()
            
            def __main__():
                input_filename = sys.argv[1]
                try:
                    min_length = int( sys.argv[2] )
                except:
                    stop_err( "Minimal length of the return sequence requires a numerical value." )
                try:
                    max_length = int( sys.argv[3] )
                except:
                    stop_err( "Maximum length of the return sequence requires a numerical value." )
                output_filename = sys.argv[4]
                output_handle = open( output_filename, 'w' )
                tmp_size = 0 #-1
                tmp_buf = ''
                at_least_one = 0
                for line in file(input_filename):
                    if not line or line.startswith('#'):
                        continue
                    if line[0] == '>':
                        if min_length <= tmp_size <= max_length or (min_length <= tmp_size and max_length == 0):
                            output_handle.write(tmp_buf)
                            at_least_one = 1
                        tmp_buf = line
                        tmp_size = 0                                                       
                    else:
                        if max_length == 0 or tmp_size < max_length:
                            tmp_size += len(line.rstrip('\r\n'))
                            tmp_buf += line
                # final flush of buffer
                if min_length <= tmp_size <= max_length or (min_length <= tmp_size and max_length == 0):
                    output_handle.write(tmp_buf.rstrip('\r\n'))
                    at_least_one = 1
                output_handle.close()
                if at_least_one == 0:
                    print "There is no sequence that falls within your range."
            
            if __name__ == "__main__" : __main__()

            Comment


            • #7
              Very useful. Thanks

              Comment

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