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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.

Example: 

> 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
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.

--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