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OBICONVERT(1) OBITools OBICONVERT(1)

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

ecoPCR taxonomy Database name

NCBI Taxonomy dump repository name

OPTIONS TO SPECIFY INPUT FORMAT

Restrict the analysis to a sub-part of the input file

The N first sequence records of the file are discarded from the analysis and not reported to the output file

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

Input file is in genbank format.

Input file is in embl format.

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

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

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

Input file is in ecoPCR format.

Input is an ecoPCR database.

Specifying the sequence type

Input file contains nucleic sequences.

Input file contains protein sequences.

OPTIONS TO SPECIFY OUTPUT FORMAT

Standard output format

--fasta-output
Output sequences in OBITools fasta format

Output sequences in Sanger fastq format

Generating an ecoPCR database

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

Miscellaneous option

Print sequences in upper case (default is lower case)

COMMON OPTIONS

Shows this help message and exits.

Sets logging in debug mode.

AUTHOR

The OBITools Development Team - LECA

COPYRIGHT

2019 - 2015, OBITool Development Team

July 27, 2019 1.02 13