NAME

       obitab - description of obitab

       obitab  command converts sequence file to a tabular file that can be open by a spreadsheet
       program or R.

OBITAB SPECIFIC OPTIONS

       -n <NOT AVAILABLE STRING>, --na-string=<NOT AVAILABLE STRING>
              String written in the table for the not available values (default value NA).

       --output-field-separator=<STRING>
              Field separator for the tabular file (default value TAB).

       -o, --output-seq
              Adds an extra column at the end of the table for the sequence itself.

       -d, --no-definition
              Removes column containing the sequence definition in the output tab file.

       -a <KEY>, --omit-attribute=<KEY>
              Attributes whose key is in this list will not be printed in the output tab 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.

EXAMPLE

              > obitab -d -o seq1.fasta > seq1.txt

          Reformats all sequence records present in the  seq1.fasta  file  into  a  tabular  file
          without  outputing  the  sequence  definition  but  with an extra column containing the
          sequence itself. The result is stored in the seq1.txt file.

AUTHOR

       The OBITools Development Team - LECA

COPYRIGHT

       2019 - 2015, OBITool Development Team

 1.02 12                                   Jan 28, 2019                                 OBITAB(1)