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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 related format¶
- --fasta
- Input file is in fasta format (including OBITools fasta extensions).
fastq related format¶
- --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 related format¶
- --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
July 27, 2019 | 1.02 13 |