| ECOTAXSPECIFICITY(1) | OBITools | ECOTAXSPECIFICITY(1) |
NAME¶
ecotaxspecificity - description of ecotaxspecificity
The ecotaxspecificity command evaluates barcode resolution at different taxonomic ranks.
As inputs, it takes a sequence record file annotated with taxids in the sequence header, and a database formated as an ecopcr database (see obitaxonomy) or a NCBI taxdump (see NCBI ftp site).
An example of output is reported below:
Number of sequences added in graph: 284 Number of nodes in all components: 269 Number of sequences lost: 15! rank taxon_ok taxon_total percent order 8 8 100.00 superfamily 1 1 100.00 parvorder 1 1 100.00 subkingdom 1 1 100.00 superkingdom 1 1 100.00 kingdom 3 3 100.00 phylum 5 5 100.00 infraorder 1 1 100.00 subfamily 3 3 100.00 class 6 6 100.00 species 35 176 19.89 superorder 1 1 100.00 suborder 1 1 100.00 subtribe 1 1 100.00 subclass 3 3 100.00 genus 9 15 60.00 superclass 1 1 100.00 family 10 10 100.00 tribe 2 2 100.00 subphylum 1 1 100.00
In this example, the input sequence file contains 284 sequence records, but only 269 have been examined, because taxonomic information was not recovered for the the 15 remaining ones.
“Taxon_total” refers to the number of different taxa observed at this rank in the sequence record file (when taxonomic information is available at this rank), and “taxon_ok” corresponds to the number of taxa that the barcode sequence identifies unambiguously in the taxonomic database. In this example, the sequence records correspond to 176 different species, but only 35 of these have specific barcodes. “percent” is the percentage of unambiguously identified taxa among the total number of taxa (taxon_ok/taxon_total*100).
ECOTAXSPECIFICITY SPECIFIC OPTIONS¶
Example:
> ecotaxspecificity -d my_ecopcr_database -e 5 seq.fasta
This command considers that two sequences with less than 5 differences correspond to the same barcode.
TAXONOMY RELATED OPTIONS¶
- -d <FILENAME>, --database=<FILENAME>
- ecoPCR taxonomy Database name
- -t <FILENAME>, --taxonomy-dump=<FILENAME>
- NCBI Taxonomy dump repository name
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.
COMMON OPTIONS¶
- -h, --help
- Shows this help message and exits.
- --DEBUG
- Sets logging in debug mode.
ECOTAXSPECIFICITY USED SEQUENCE ATTRIBUTE¶
- •
- taxid
AUTHOR¶
The OBITools Development Team - LECA
COPYRIGHT¶
2019 - 2015, OBITool Development Team
| July 27, 2019 | 1.02 13 |