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OBITAB(1) OBITools OBITAB(1)

NAME

obitab - description of obitab

obitab command converts sequence file to a tabular file that can be open by a spreadsheet program or R.

OBITAB SPECIFIC OPTIONS

-n <NOT AVAILABLE STRING>, --na-string=<NOT AVAILABLE STRING>
String written in the table for the not available values (default value NA).

--output-field-separator=<STRING>
Field separator for the tabular file (default value TAB).

-o, --output-seq
Adds an extra column at the end of the table for the sequence itself.

-d, --no-definition
Removes column containing the sequence definition in the output tab file.

-a <KEY>, --omit-attribute=<KEY>
Attributes whose key is in this list will not be printed in the output tab file.

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.

EXAMPLE

> obitab -d -o seq1.fasta > seq1.txt


Reformats all sequence records present in the seq1.fasta 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 seq1.txt file.



AUTHOR

The OBITools Development Team - LECA

COPYRIGHT

2019 - 2015, OBITool Development Team
January 28, 2019 1.02 12