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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

String written in the table for the not available values (default value NA).

Field separator for the tabular file (default value TAB).

Adds an extra column at the end of the table for the sequence itself.

Removes column containing the sequence definition in the output tab file.

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

The N first sequence records of the file are discarded from the analysis and not reported to the output file

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

Input file is in genbank format.

Input file is in embl format.

Input file is in fasta format (including OBITools fasta extensions).

Input file is in Sanger fastq format (standard fastq used by HiSeq/MiSeq sequencers).

Input file is in fastq format produced by Solexa (Ga IIx) sequencers.

Input file is in ecoPCR format.

Input is an ecoPCR database.

Specifying the sequence type

Input file contains nucleic sequences.

Input file contains protein sequences.

COMMON OPTIONS

Shows this help message and exits.

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

July 27, 2019 1.02 13