table of contents
| OBISPLIT(1) | OBITools | OBISPLIT(1) |
NAME¶
obisplit - description of obisplit
obisplit splits the input sequence file in a set of subfiles according to the values of a given attribute. The generated subfiles are named after the values of the attribute, possibly preceded by a prefix (-p option). The sequence records for which the attribute is missing are discarded by default, or put in a file whose name is set using the -u option.
> obisplit -p experiment_ -t mode
The above command splits the sequence input file according to the mode attribute. This attribute is created by the solexapairend tool and its value can be set to either joined or alignment. The prefix experiment_ is put before each subfile name. Two subfiles will thus be created: experiment_joined and experiment_alignment.
OBISPLIT SPECIFIC OPTIONS¶
- -p <PREFIX FILENAME>, --prefix=<PREFIX FILENAME>
- Prefix added to each subfile name.
- -t <KEY>, --tag-name=<KEY>
- Attribute key used to split the sequence file.
- -u <FILENAME>, --undefined=<FILENAME>
- Name of the file where sequence records without attribute <KEY> are stored.
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.
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
| January 28, 2019 | 1.02 12 |