NAME

       obicomplement - description of obicomplement

       obicomplement reverse-complements the sequence records.

          TIP:
              The  identifiers of the sequence records are modified by appending to them the _CMP
              suffix.

          TIP:
              a attribute with key complemented and value sets to True is added on each  reversed
              complemented sequence record.

       By  using  the selection option set, it is possible to reverse complement only a subset of
       the sequence records included in the  input  file.  The  selected  sequence  are  reversed
       complemented, others are stored without modification
          Example 1:

              > obicomplement seq.fasta > seqRC.fasta

          Reverses complements all sequence records from the seq.fasta file and stores the result
          to the seqRC.fasta file.

          Example 2:

              > obicomplement -s 'A{10,}$' seq.fasta > seqRC.fasta

          Reverses complements sequence records from the seq.fasta file only if they finish by at
          least 10 A. Others sequences are stored without modification.

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                          OBICOMPLEMENT(1)