Usage:   seqTools.pl  []
 
Command: format   Format the FASTA record(s).
         revcom   Reverse and complement the FASTA record(s).
         length   Get the length of FASTA record(s).
         content  Calculate the GC content of FASTA record(s).
         search   Find subseq in the FASTA record(s).
         subseq   Extract sub|full-seq from the FASTA record(s).
 
Author:  Yixf, yixf1986@gmail.com
Version: v2.0
 
Notes:  1. A similar webtool developed by lh3: http://lh3lh3.users.sourceforge.net/fasta.shtml
        2. When you search, you can use RegExp supported by Perl.
        3. When you extract the sub|full-seq, you can use RegExp in the Name|ID (-n Name|ID) to match more than one record. But the RegExp must be in the double quotation marks, for example, "chrd+".
        4. The RegExp use case-sensitive mode.
 
Versions: v1.0, 2011-06-01
          v2.0, 2011-11-03

Usage:    seqTools.pl subseq [options]
 
Options:  -i STR   Input file in FASTA format.
          -o STR   Output file in FASTA format.
          -n STR   Name|ID of the FASTA record. [.+]
          -s INT   Start of the subsequence. [1]
          -e INT   End of the subsequence. [0]
 
Notes:    1. You can use RegExp supported by Perl in the Name|ID (-n Name|ID) to match more than one record. But the RegExp must be in the double quotation marks, for example, "chrd+".
          2. The RegExp use case-sensitive mode.
          3. ".+" for the Name|ID means all records in the input file.
          4. Start and End use the 1-based coordinate system, where the first base is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence.
          5. "0" for the End means to the end of the record, that is to say, the End will be set to the Length.
          6. If Start OR End is larger than the length of the record, they will be set to the Length.