obitab: converts a sequence file to a tabular file

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.

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.