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| OBIDISTRIBUTE(1) | OBITools | OBIDISTRIBUTE(1) |
NAME¶
obidistribute - description of obidistribute
obidistribute distributes equitably a set of sequence records over several files (No sequence records are printed on standard output).
The number of files is set using the -n option (required). File names are build with a prefix if provided (-p``option) and the file number (1 to ``n).
Example:
> obidistribute -n 10 -p 'part' seq.fastq
Distribute the sequence records contained in the seq.fastq file and distributes them over files part_1.fastq to part_10.fastq.
OBIDISTRIBUTE SPECIFIC OPTIONS¶
- -n <INT>, --number=<INT>
- Number of files to distribute over.
- -p <STRING>, --prefix=<STRING>
- Prefix added at each file name.
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.
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.
AUTHOR¶
The OBITools Development Team - LECA
COPYRIGHT¶
2019 - 2015, OBITool Development Team
| July 27, 2019 | 1.02 13 |