obisort - description of obisort
obisort sorts sequence records according to the value of a
given attribute, which can be either numeric or alphanumeric.
- -k <KEY>,
--key=<KEY>
Attribute used to sort the sequence records.
Example:
> obisort -k count seq1.fasta > seq2.fasta
Sorts the sequence records of file seq1.fasta according to
their count (numeric order) and prints the results in the
seq2.fasta file.
- -r, --reverse
Example:
> obisort -r -k count seq1.fastq > seq2.fastq
Sorts the sequence records of file seq1.fasta according to
their count (reverse numeric order) and prints the results in the
seq2.fasta 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.
- --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.
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