NAME¶

obicount - description of obicount

obicount counts the number of sequence records and/or the sum of the count attributes.

Example:

> obicount seq.fasta

Prints the number of sequence records contained in the seq.fasta file and the sum of their count attributes.

OBICOUNT SPECIFIC OPTIONS¶

Prints only the sum of count attributes. If a sequence has no count attribute, its default count is 1.

Example:

> obicount -a seq.fasta

For all sequence records contained in the seq.fasta file, prints only the sum of count attributes.

Prints only the number of sequence records.

Example:

> obicount -s seq.fasta

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.

--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.

The OBITools Development Team - LECA

2019 - 2015, OBITool Development Team

January 28, 2019

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