NAME

       obiconvert - description of obiconvert

       obiconvert converts sequence files to different output formats.  See the documentation for
       more details on the different formats.

       Input files can be in :

          · fasta format

          · extended OBITools fasta format

          · Sanger fastq format

          · Solexa fastq format

          · ecoPCR format

          · ecoPCR database format

          · GenBank format

          · EMBL format

       obiconvert converts those files to the :

          · extended OBITools fasta format

          · Sanger fastq format

          · ecoPCR database format

       If no file name is specified, data is read from standard input.

       Examples:

              > obiconvert --ecopcrdb --fasta-output \
                'my_ecopcr_database' > sequences.fasta

          Converts an ecoPCR database in a sequence file in extended OBITools fasta format.

TAXONOMY RELATED OPTIONS

       -d <FILENAME>, --database=<FILENAME>
              ecoPCR taxonomy Database name

       -t <FILENAME>, --taxonomy-dump=<FILENAME>
              NCBI Taxonomy dump repository name

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.

OPTIONS TO SPECIFY OUTPUT FORMAT

   Standard output format
       --fasta-output
              Output sequences in OBITools fasta format

       --fastq-output
              Output sequences in Sanger fastq format

   Generating an ecoPCR database
       --ecopcrdb-output=<PREFIX_FILENAME>
              Creates an ecoPCR database from sequence records results

   Miscellaneous option
       --uppercase
              Print sequences in upper case (default is lower case)

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                             OBICONVERT(1)