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.TH "OBITAB" "1" "Jul 27, 2019" " 1.02 13" "OBITools"
.SH NAME
obitab \- description of obitab
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.sp
\fI\%obitab\fP command converts sequence file to a tabular file that
can be open by a spreadsheet program or R.
.SH OBITAB SPECIFIC OPTIONS
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.B \-n <NOT AVAILABLE STRING>, \-\-na\-string=<NOT AVAILABLE STRING>
String written in the table for the not available values
(default value \fBNA\fP).
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.B \-\-output\-field\-separator=<STRING>
Field separator for the tabular file
(default value \fBTAB\fP).
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.B \-o, \-\-output\-seq
Adds an extra column at the end of the table for
the sequence itself.
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.B \-d, \-\-no\-definition
Removes column containing the sequence definition in
the output tab file.
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.B \-a <KEY>, \-\-omit\-attribute=<KEY>
Attributes whose key is in this list will not be printed in
the output tab 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.
.UNINDENT
.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).
.UNINDENT
.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.
.UNINDENT
.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 EXAMPLE
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.INDENT 3.5
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.INDENT 3.5
.sp
.nf
.ft C
> obitab \-d \-o seq1.fasta > seq1.txt
.ft P
.fi
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.sp
Reformats all sequence records present in the \fBseq1.fasta\fP file
into a tabular file without outputing the sequence definition but
with an extra column containing the sequence itself. The result is
stored in the \fBseq1.txt\fP file.
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.SH AUTHOR
The OBITools Development Team - LECA
.SH COPYRIGHT
2019 - 2015, OBITool Development Team
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