obitab - description of obitab
obitab command converts sequence file to a tabular file
that can be open by a spreadsheet program or R.
- -o, --output-seq
- Adds an extra column at the end of the table for the sequence itself.
- --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.
- --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.
- --nuc
- Input file contains nucleic sequences.
- --prot
- Input file contains protein sequences.
- --DEBUG
- Sets logging in debug mode.
> 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.
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