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 :
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fasta format
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extended OBITools fasta format
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Sanger fastq format
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Solexa fastq format
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ecoPCR format
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ecoPCR database format
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GenBank format
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EMBL format
obiconvert converts those files to the :
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extended OBITools fasta format
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Sanger fastq format
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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>
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ecoPCR taxonomy Database name
- -t <FILENAME>, --taxonomy-dump=<FILENAME>
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NCBI Taxonomy dump repository name
OPTIONS TO SPECIFY INPUT FORMAT
Restrict the analysis to a sub-part of the input file
- --skip <N>
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The N first sequence records of the file are discarded from the analysis and not reported to the output file
- --only <N>
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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
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Input file is in genbank format.
- --embl
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Input file is in embl format.
fasta related format
- --fasta
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Input file is in fasta format (including OBITools fasta extensions).
fastq related format
- --sanger
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Input file is in Sanger fastq format (standard fastq used by HiSeq/MiSeq sequencers).
- --solexa
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Input file is in fastq format produced by Solexa (Ga IIx) sequencers.
ecoPCR related format
- --ecopcr
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Input file is in ecoPCR format.
- --ecopcrdb
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Input is an ecoPCR database.
Specifying the sequence type
- --nuc
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Input file contains nucleic sequences.
- --prot
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Input file contains protein sequences.
OPTIONS TO SPECIFY OUTPUT FORMAT
Standard output format
- --fasta-output
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Output sequences in OBITools fasta format
- --fastq-output
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Output sequences in Sanger fastq format
Generating an ecoPCR database
- --ecopcrdb-output=<PREFIX_FILENAME>
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Creates an ecoPCR database from sequence records results
Miscellaneous option
- --uppercase
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Print sequences in upper case (default is lower case)
COMMON OPTIONS
- -h, --help
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Shows this help message and exits.
- --DEBUG
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Sets logging in debug mode.
AUTHOR
The OBITools Development Team - LECA
COPYRIGHT
2019 - 2015, OBITool Development Team