obicount1
Description of obicount obicount counts the number of sequence records and/or the sum of the count attributes. example:
Options
-
-a, --all -
Prints only the sum of
countattributes. If a sequence has no count attribute, its default count is 1.Example:
> obicount -a seq.fastaFor all sequence records contained in the
seq.fastafile, prints only the sum ofcountattributes.
-
-s, --sequence -
Prints only the number of sequence records.
Example:
> obicount -s seq.fastaPrints only the number of sequence records contained in the
seq.fastafile.
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.
Options
-
-h, --help -
Shows this help message and exits.
-
--DEBUG -
Sets logging in debug mode.
Obicount added sequence attribute
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count