NAME

       obicount - description of obicount

       obicount counts the number of sequence records and/or the sum of the count attributes.

       Example:

              > obicount seq.fasta

          Prints  the  number  of sequence records contained in the seq.fasta file and the sum of
          their count attributes.

OBICOUNT SPECIFIC OPTIONS

       -a, --all
                 Prints only the sum of count attributes.  If a sequence has no count  attribute,
                 its default count is 1.

              Example:

                        > obicount -a seq.fasta

                 For all sequence records contained in the seq.fasta file, prints only the sum of
                 count attributes.

       -s, --sequence
                 Prints only the number of sequence records.

              Example:

                     > obicount -s seq.fasta

                 Prints only the number of sequence records contained in the seq.fasta file.

OPTIONS TO SPECIFY INPUT FORMAT

   Restrict the analysis to a sub-part of the input file
       --skip <N>
              The N first sequence records of the file are discarded from the  analysis  and  not
              reported to the output file

       --only <N>
              Only  the N next sequence records of the file are analyzed. The following sequences
              in the file are neither analyzed, neither reported to the output file.  This option
              can be used conjointly with the –skip option.

   Sequence annotated format
       --genbank
              Input file is in genbank format.

       --embl Input file is in embl format.

   fasta related format
       --fasta
              Input file is in fasta format (including OBITools fasta extensions).

   fastq related format
       --sanger
              Input  file  is  in  Sanger  fastq  format  (standard  fastq  used  by  HiSeq/MiSeq
              sequencers).

       --solexa
              Input file is in fastq format produced by Solexa (Ga IIx) sequencers.

   ecoPCR related format
       --ecopcr
              Input file is in ecoPCR format.

       --ecopcrdb
              Input is an ecoPCR database.

   Specifying the sequence type
       --nuc  Input file contains nucleic sequences.

       --prot Input file contains protein sequences.

COMMON OPTIONS

       -h, --help
              Shows this help message and exits.

       --DEBUG
              Sets logging in debug mode.

OBICOUNT ADDED SEQUENCE ATTRIBUTE

          · count

AUTHOR

       The OBITools Development Team - LECA

COPYRIGHT

       2019 - 2015, OBITool Development Team

 1.02 12                                   Jan 28, 2019                               OBICOUNT(1)