obiconvert: converts sequence files to different output formats

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.

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.

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.