obicount - description of obicount
obicount counts the number of sequence records and/or the
sum of the count attributes.
Example:
Prints the number of sequence records contained in the
seq.fasta file and the sum of their count attributes.
- -a, --all
Prints only the sum of count attributes. If a
sequence has no count attribute, its default count is 1.
Example:
For all sequence records contained in the seq.fasta file,
prints only the sum of count attributes.
- -s, --sequence
Prints only the number of sequence records.
Example:
Prints only the number of sequence records contained in the
seq.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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