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.TH "OBISPLIT" "1" "Jan 28, 2019" " 1.02 12" "OBITools"
.SH NAME
obisplit \- description of obisplit
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\fI\%obisplit\fP 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 
(\fB\-p\fP 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 \fB\-u\fP option.
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.INDENT 3.5
Example:
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> obisplit \-p experiment_ \-t mode  
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The above command splits the sequence input file according to the \fBmode\fP attribute. 
This attribute is created by the \fBsolexapairend\fP tool and its value can be set to  
either \fBjoined\fP or \fBalignment\fP\&. The prefix \fBexperiment_\fP is put before
each subfile name. Two subfiles will thus be created: \fBexperiment_joined\fP and 
\fBexperiment_alignment\fP\&.
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.SH OBISPLIT SPECIFIC OPTIONS
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.TP
.B \-p <PREFIX FILENAME>, \-\-prefix=<PREFIX FILENAME>
Prefix added to each subfile name.
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.B \-t <KEY>, \-\-tag\-name=<KEY>
Attribute key used to split the sequence file.
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.B \-u <FILENAME>, \-\-undefined=<FILENAME>
Name of the file where sequence records without attribute \fB<KEY>\fP are stored.
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.SH OPTIONS TO SPECIFY INPUT FORMAT
.SS Restrict the analysis to a sub\-part of the input file
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.B \-\-skip <N>
The N first sequence records of the file are discarded from the analysis and
not reported to the output file
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.B \-\-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 \fI–skip\fP option.
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.SS Sequence annotated format
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.B \-\-genbank
Input file is in genbank format.
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.B \-\-embl
Input file is in embl format.
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.SS fasta related format
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.B \-\-fasta
Input file is in fasta format (including
OBITools fasta extensions).
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.SS fastq related format
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.B \-\-sanger
Input file is in Sanger fastq format (standard
fastq used by HiSeq/MiSeq sequencers).
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.B \-\-solexa
Input file is in fastq format produced by
Solexa (Ga IIx) sequencers.
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.SS ecoPCR related format
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.B \-\-ecopcr
Input file is in ecoPCR format.
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.B \-\-ecopcrdb
Input is an ecoPCR database.
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.SS Specifying the sequence type
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.B \-\-nuc
Input file contains nucleic sequences.
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.B \-\-prot
Input file contains protein sequences.
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.SH COMMON OPTIONS
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.B \-h, \-\-help
Shows this help message and exits.
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.B \-\-DEBUG
Sets logging in debug mode.
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.SH AUTHOR
The OBITools Development Team - LECA
.SH COPYRIGHT
2019 - 2015, OBITool Development Team
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