NAME

     edit_fff.pl - edit fasta fragment file (.fff) file

SYNOPSIS

     edit_fff.pl [options] {input_fff_file} {output_fff_file}

DESCRIPTION

     edit_fff.pl is a program which reads an input fasta fragment
     file  (.fff),  edits  it  as  directed, and then outputs the
     edited version to an output .fff file.

OPTIONS

     -help
          Print help information.

     -min_length1 <val>
          Delete sequence pairs whose first  sequence  length  is
          less than val.

     -min_length2 <val>
          Delete sequence pairs whose second sequence  length  is
          less than val.

     -max_length1 <val>
          Delete sequence pairs whose first  sequence  length  is
          greater than val.

     -max_length2 <val>
          Delete sequence pairs whose second sequence  length  is
          greater than val.

     -del_eq_length
          Delete sequence pairs whose first and  second  sequence
          length are equal.

     -min_diff <val>
          Delete sequence pairs whose first sequence length minus
          the second sequence length is less than val.

     -del_seq1
          Delete all first sequences.

     -del_seq2
          Delete all second sequences.

     -only_seq1
          Output only first sequences. (Equivalent to -del_seq2.)

     -del_seq2
          Output   only   second   sequences.   (Equivalent    to
          -del_seq1.)

     -only_chr <chr_name>
          Output only sequences from chromosone chr_name.

     -list <list_file>
          Output only sequences listed in file list_file.

     -list_col <val>
          Column containing list of sequences in file  list_file.
          Default is 1 (first column.)

     -strip_blanks
          Delete blanks after ">" in fasta sequence  description.
          Needed for applying blat to fasta sequences.

SEE ALSO

     generate_RLGS(1), rlgs7.pl(1), fff2cnm.pl(1)

AUTHORS

     Rephael Wenger (The Ohio State University)