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.TH "OBISAMPLE" "1" "Jul 27, 2019" " 1.02 13" "OBITools"
.SH NAME
obisample \- description of obisample
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\fI\%obisample\fP randomly resamples sequence records with or without replacement.
.SH OBISAMPLE SPECIFIC OPTIONS
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.B \-s ###, \-\-sample\-size ###
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Specifies the size of the generated sample.
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.IP \(bu 2
without the \fB\-a\fP option, sample size is expressed as the exact number of sequence
records to be sampled (default: number of sequence records in the input file).
.IP \(bu 2
with the \fB\-a\fP option, sample size is expressed as a fraction of the
sequence record numbers in the input file
(expressed as a number between 0 and 1).
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\fIExample:\fP
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.ft C
> obisample \-s 1000 seq1.fasta > seq2.fasta
.ft P
.fi
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Samples randomly 1000 sequence records from the \fBseq1.fasta\fP file, with replacement,
and saves them in the \fBseq2.fasta\fP file.
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.B \-a, \-\-approx\-sampling
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Switches the resampling algorithm to an approximative one,
useful for large files.
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The default algorithm selects exactly the number of sequence records
specified with the \fB\-s\fP option. When the \fB\-a\fP option is set,
each sequence record has a probability to be selected related to the
\fBcount\fP attribute of the sequence record and the \fB\-s\fP fraction.
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\fIExample:\fP
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.ft C
> obisample \-s 0.5 \-a seq1.fastq > seq2.fastq
.ft P
.fi
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Samples randomly half of the sequence records of the \fBseq1.fastq\fP file,
without replacement,
and saves them in the \fBseq2.fastq\fP file.
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.B \-w, \-\-without\-replacement
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Asks for sampling without replacement.
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\fIExample:\fP
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.nf
.ft C
> obisample \-s 1000 \-w seq1.fasta > seq2.fasta
.ft P
.fi
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Samples randomly 1000 sequence records from the \fBseq1.fasta\fP file, without replacement
(the input file must contain at least 1000 sequences), and saves them in the \fBseq2.fasta\fP file.
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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 OBISAMPLE USED SEQUENCE ATTRIBUTE
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.IP \(bu 2
count
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.SH AUTHOR
The OBITools Development Team - LECA
.SH COPYRIGHT
2019 - 2015, OBITool Development Team
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