NAME
obisort - description of obisort
obisort sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric.
OBISORT SPECIFIC OPTIONS
- -k <KEY>, --key=<KEY>
-
Attribute used to sort the sequence records.
Example:
> obisort -k count seq1.fasta > seq2.fastaSorts the sequence records of file seq1.fasta according to their count (numeric order) and prints the results in the seq2.fasta file.
- -r, --reverse
-
Sorts in reverse order.
Example:
> obisort -r -k count seq1.fastq > seq2.fastqSorts the sequence records of file seq1.fasta according to their count (reverse numeric order) and prints the results in the seq2.fasta 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.
AUTHOR
The OBITools Development Team - LECA
COPYRIGHT
2019 - 2015, OBITool Development Team