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.
- --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.
- --embl
- Input file is in embl format.
- --fasta
- Input file is in fasta format (including OBITools fasta extensions).
- --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
- Input file is in ecoPCR format.
- --nuc
- Input file contains nucleic sequences.
- --prot
- Input file contains protein sequences.
- --fasta-output
- Output sequences in OBITools fasta format
- --ecopcrdb-output=<PREFIX_FILENAME>
- Creates an ecoPCR database from sequence records results
- --uppercase
- Print sequences in upper case (default is lower case)
- --DEBUG
- Sets logging in debug mode.
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