NAME

       obisort - description of obisort

       obisort  sorts  sequence records according to the value of a given attribute, which can be
       either numeric or alphanumeric.

OBISORT SPECIFIC OPTIONS

       -k <KEY>, --key=<KEY>
                 Attribute used to sort the sequence records.

              Example:

                     > obisort -k count seq1.fasta > seq2.fasta

                 Sorts the sequence records of file seq1.fasta according to their count  (numeric
                 order) and prints the results in the seq2.fasta file.

       -r, --reverse
                 Sorts in reverse order.

              Example:

                     > obisort -r -k count seq1.fastq > seq2.fastq

                 Sorts  the sequence records of file seq1.fasta according to their count (reverse
                 numeric order) and prints the results in the seq2.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.

AUTHOR

       The OBITools Development Team - LECA

COPYRIGHT

       2019 - 2015, OBITool Development Team

 1.02 12                                   Jan 28, 2019                                OBISORT(1)