Provided by: obitools_1.2.12+dfsg-2_amd64
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
-a, --all 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. -s, --sequence 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.
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.
-h, --help Shows this help message and exits. --DEBUG Sets logging in debug mode.
OBICOUNT ADDED SEQUENCE ATTRIBUTE
The OBITools Development Team - LECA
2019 - 2015, OBITool Development Team 1.02 12 Jan 28, 2019 OBICOUNT(1)