| OBISTAT(1) | OBITools | OBISTAT(1) |
NAME¶
obistat - description of obistat
obistats computes basic statistics for attribute values of sequence records. The sequence records can be categorized or not using one or several -c options. By default, only the number of sequence records and the total count are computed for each category. Additional statistics can be computed for attribute values in each category, like:
- minimum value (-m option)
- maximum value (-M option)
- mean value (-a option)
- variance (-v option)
- standard deviation (-s option)
The result is a contingency table with the different categories in rows, and the computed statistics in columns.
OBISTAT SPECIFIC OPTIONS¶
TIP:
Example:
> obistat -c sample -c seq_length seq.fasta
This command prints the number of sequence records and total count for each combination of sample and sequence length.
Example:
> obistat -c sample -m seq_length seq.fastq
This command computes the minimum sequence length observed for each sample.
Example:
> obistat -c sample -M seq_length seq.fastq
This command computes the maximum sequence length observed for each sample.
Example:
> obistat -c sample -a seq_length seq.fastq
This command computes the mean sequence length observed for each sample.
- -v <KEY>, --variance=<KEY>
- Computes the variance of attribute <KEY> for each category.
Example:
> obistat -c genus_name -v reverse_error seq.fastq
This command computes the variance of the number of errors observed in the reverse primer for each genus.
- -s <KEY>, -std-dev=<KEY>
- Computes the standard deviation of attribute <KEY> for each category.
Example:
> obistat -c genus_name -s reverse_error seq.fastq
This command computes the standard deviation of the number of errors observed in the reverse primer for each genus.
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.
TAXONOMY RELATED OPTIONS¶
- -d <FILENAME>, --database=<FILENAME>
- ecoPCR taxonomy Database name
- -t <FILENAME>, --taxonomy-dump=<FILENAME>
- NCBI Taxonomy dump repository name
COMMON OPTIONS¶
- -h, --help
- Shows this help message and exits.
- --DEBUG
- Sets logging in debug mode.
OBISTAT USED SEQUENCE ATTRIBUTE¶
- •
- count
AUTHOR¶
The OBITools Development Team - LECA
COPYRIGHT¶
2019 - 2015, OBITool Development Team
| January 28, 2019 | 1.02 12 |