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moose

A tool for taxonomically selecting, grouping and summarizing pairwise alignment classifications into something more concise and readable.

authors

about

Moose groups pairwise alignments by taxonomy and alignment scores. It works safely with large data sets utilizing the Python Data Analysis Library.

dependencies

  • Python >= 3.7
  • Pandas >= 2.0.2

installation

Moose can be installed in a few ways:

From PyPI:

% pip install moose_classifier

Or cloned from Github:

% git clone https://github.com/crosenth/moose.git
% python moose/setup.py install

examples

The following examples will use results using 16s sequences aligned to a local NCBI nt database. For instructions on creating a local blast nt database see the NCBI walkthrough here and and here.

The simplest example pipes blast "10 qaccver saccver pident staxid" into the classifier and outputs a table of species level taxonomy results:

% blastn -db nt -outfmt "10 qaccver saccver pident staxid" -query sequences.fasta | classify --columns qaccver,saccver,pident,staxid
specimen,assignment_id,assignment,best_rank,max_percent,min_percent,min_threshold,reads,clusters,pct_reads
query1,0,Homo sapiens,species,99.67,99.67,0.00,1,1,100.00
query10,0,Actinobacteria*;uncultured bacterium*,species,100.00,93.21,0.00,1,1,100.00
query11,0,Bacteroidetes*;uncultured bacterium*/organism,species,100.00,91.26,0.00,1,1,100.00
query12,0,Apteryx australis*;Bacteria*;Firmicutes*,species,100.00,98.26,0.00,1,1,100.00
query13,0,Dikarya*;uncultured bacterium/eukaryote,species,100.00,82.88,0.00,1,1,100.00
query14,0,Saccharomyces cerevisiae*;uncultured eukaryote,species,100.00,99.00,0.00,1,1,100.00
query2,0,Homo sapiens;Pan troglodytes,species,97.07,95.40,0.00,1,1,100.00
query6,0,Bacteria*;Escherichia coli;Staphylococcus,species,100.00,98.62,0.00,1,1,100.00
query7,0,Bacteroidetes*;uncultured bacterium*/organism*,species,100.00,91.61,0.00,1,1,100.00
query8,0,Bacteria*;Escherichia coli;Staphylococcus,species,100.00,98.62,0.00,1,1,100.00
query9,0,Bacteria*;uncultured organism*,species,100.00,98.62,0.00,1,1,100.00

This example shows the bare minimum information required to simplify and group alignment results: a query sequence (qseqid), subject sequence (sseqid), a percent identiy (pident) and a subject taxonomy id (staxid). If the staxid column is unavailable an accession to taxonomy id map file can be used with the --seq-info argument. Results are output in csv format.

Sending the blastn results to a standalone file we can look a bit closer at what happened. And for purposes of this walkthrough the csv output will be displated in as a nicely formatted table:

% blastn -outfmt "10 qaccver saccver pident staxid" -query sequences.fasta -out blast.csv
% wc --lines blast.csv
1084 blast.csv
% classify --columns qaccver,saccver,pident,staxid blast.csv
specimen,assignment_id,assignment,best_rank,max_percent,min_percent,min_threshold,reads,clusters,pct_reads
|----------+---------------+------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|
| specimen | assignment_id | assignment                                     | best_rank | max_percent | min_percent | min_threshold | reads | clusters | pct_reads |
|----------+---------------+------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|
| query1   | 0             | Homo sapiens                                   | species   | 99.67       | 99.67       | 0.00          | 1     | 1        | 100.00    |
| query10  | 0             | Actinobacteria*;uncultured bacterium*          | species   | 100.00      | 93.21       | 0.00          | 1     | 1        | 100.00    |
| query11  | 0             | Bacteroidetes*;uncultured bacterium*/organism  | species   | 100.00      | 91.26       | 0.00          | 1     | 1        | 100.00    |
| query12  | 0             | Apteryx australis*;Bacteria*;Firmicutes*       | species   | 100.00      | 98.26       | 0.00          | 1     | 1        | 100.00    |
| query13  | 0             | Dikarya*;uncultured bacterium/eukaryote        | species   | 100.00      | 82.88       | 0.00          | 1     | 1        | 100.00    |
| query14  | 0             | Saccharomyces cerevisiae*;uncultured eukaryote | species   | 100.00      | 99.00       | 0.00          | 1     | 1        | 100.00    |
| query2   | 0             | Homo sapiens;Pan troglodytes                   | species   | 97.07       | 95.40       | 0.00          | 1     | 1        | 100.00    |
| query6   | 0             | Bacteria*;Escherichia coli;Staphylococcus      | species   | 100.00      | 98.62       | 0.00          | 1     | 1        | 100.00    |
| query7   | 0             | Bacteroidetes*;uncultured bacterium*/organism* | species   | 100.00      | 91.61       | 0.00          | 1     | 1        | 100.00    |
| query8   | 0             | Bacteria*;Escherichia coli;Staphylococcus      | species   | 100.00      | 98.62       | 0.00          | 1     | 1        | 100.00    |
| query9   | 0             | Bacteria*;uncultured organism*                 | species   | 100.00      | 98.62       | 0.00          | 1     | 1        | 100.00    |
|----------+---------------+------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|

1,084 lines of blast results are conveniently grouped taxonomically and with a single row per specimen query sequence.

Taxonomy grouping is accomplished with a lineages table that can be specified using the --lineages argument. If a lineages file is not supplied it will be generated automatically using NCBI taxonomy data by default. A Moose classify built lineages table can be saved to a file using the lineages-out command which will speed up subsequent classify runs:

classify --columns qaccver,saccver,pident,staxid --lineages-out lineages.csv --specimen one blast.csv

Taxonomony grouping

By default, classifications are taxonomically grouped according to --max-group-size with 3 being the default. Classification names will start at the species level by default and recursively regroup at a higher taxonomony until --max-group-size is satisfied.

By increasing the --max-group-size 5:

classify --columns qaccver,saccver,pident,staxid --lineages lineages.csv --max-group-size 5 blast.csv
|----------+---------------+---------------------------------------------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|
| specimen | assignment_id | assignment                                                                                                          | best_rank | max_percent | min_percent | min_threshold | reads | clusters | pct_reads |
|----------+---------------+---------------------------------------------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|
| query1   | 0             | Homo sapiens                                                                                                        | species   | 99.67       | 99.67       | 0.00          | 1     | 1        | 100.00    |
| query10  | 0             | Actinomycetales bacterium 'ARUP UnID 260'*;Corynebacterium*;uncultured actinobacterium/bacterium*                   | species   | 100.00      | 93.21       | 0.00          | 1     | 1        | 100.00    |
| query11  | 0             | Prevotella*;uncultured Bacteroidales bacterium*;uncultured Bacteroidetes bacterium;uncultured bacterium*/organism   | species   | 100.00      | 91.26       | 0.00          | 1     | 1        | 100.00    |
| query12  | 0             | Apteryx australis*;Bacilli*;Staphylococcus*;bacterium*;uncultured Firmicutes bacterium*;uncultured bacterium*       | species   | 100.00      | 98.26       | 0.00          | 1     | 1        | 100.00    |
| query13  | 0             | Saccharomycetales*;Xanthophyllomyces dendrorhous;uncultured bacterium/eukaryote                                     | species   | 100.00      | 82.88       | 0.00          | 1     | 1        | 100.00    |
| query14  | 0             | Saccharomyces cerevisiae*;uncultured eukaryote                                                                      | species   | 100.00      | 99.00       | 0.00          | 1     | 1        | 100.00    |
| query2   | 0             | Homo sapiens;Pan troglodytes                                                                                        | species   | 97.07       | 95.40       | 0.00          | 1     | 1        | 100.00    |
| query6   | 0             | Escherichia coli;Staphylococcus;bacterium CulaenoE10F;human oral bacterium C20;uncultured bacterium*                | species   | 100.00      | 98.62       | 0.00          | 1     | 1        | 100.00    |
| query7   | 0             | Prevotella*;uncultured Bacteroidales bacterium*;uncultured Bacteroidetes bacterium*;uncultured bacterium*/organism* | species   | 100.00      | 91.61       | 0.00          | 1     | 1        | 100.00    |
| query8   | 0             | Escherichia coli;Staphylococcus;bacterium CulaenoE10F;human oral bacterium C20;uncultured bacterium*                | species   | 100.00      | 98.62       | 0.00          | 1     | 1        | 100.00    |
| query9   | 0             | Bacteria*;Escherichia coli;Staphylococcus;uncultured organism*                                                      | species   | 100.00      | 98.62       | 0.00          | 1     | 1        | 100.00    |
|----------+---------------+---------------------------------------------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|

And

classify --columns qaccver,saccver,pident,staxid --lineages lineages.csv --max-group-size 9 blast.csv
|----------+---------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|
| specimen | assignment_id | assignment                                                                                                                                                                    | best_rank | max_percent | min_percent | min_threshold | reads | clusters | pct_reads |
|----------+---------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|
| query1   | 0             | Homo sapiens                                                                                                                                                                  | species   | 99.67       | 99.67       | 0.00          | 1     | 1        | 100.00    |
| query10  | 0             | Actinomycetales bacterium 'ARUP UnID 260'*;Corynebacterium*;uncultured actinobacterium/bacterium*                                                                             | species   | 100.00      | 93.21       | 0.00          | 1     | 1        | 100.00    |
| query11  | 0             | Prevotella amnii/bivia;Prevotella sp. 3-5;uncultured Bacteroidales bacterium*;uncultured Bacteroidetes bacterium;uncultured Prevotella sp.*;uncultured bacterium*/organism    | species   | 100.00      | 91.26       | 0.00          | 1     | 1        | 100.00    |
| query12  | 0             | Apteryx australis*;Bacilli*;Staphylococcus*;bacterium*;uncultured Firmicutes bacterium*;uncultured bacterium*                                                                 | species   | 100.00      | 98.26       | 0.00          | 1     | 1        | 100.00    |
| query13  | 0             | Saccharomycetales*;Xanthophyllomyces dendrorhous;uncultured bacterium/eukaryote                                                                                               | species   | 100.00      | 82.88       | 0.00          | 1     | 1        | 100.00    |
| query14  | 0             | Saccharomyces cerevisiae*;uncultured eukaryote                                                                                                                                | species   | 100.00      | 99.00       | 0.00          | 1     | 1        | 100.00    |
| query2   | 0             | Homo sapiens;Pan troglodytes                                                                                                                                                  | species   | 97.07       | 95.40       | 0.00          | 1     | 1        | 100.00    |
| query6   | 0             | Escherichia coli;Staphylococcus;bacterium CulaenoE10F;human oral bacterium C20;uncultured bacterium*                                                                          | species   | 100.00      | 98.62       | 0.00          | 1     | 1        | 100.00    |
| query7   | 0             | Prevotella amnii/bivia*;Prevotella sp. 3-5;uncultured Bacteroidales bacterium*;uncultured Bacteroidetes bacterium*;uncultured Prevotella sp.*;uncultured bacterium*/organism* | species   | 100.00      | 91.61       | 0.00          | 1     | 1        | 100.00    |
| query8   | 0             | Escherichia coli;Staphylococcus;bacterium CulaenoE10F;human oral bacterium C20;uncultured bacterium*                                                                          | species   | 100.00      | 98.62       | 0.00          | 1     | 1        | 100.00    |
| query9   | 0             | Escherichia coli;Staphylococcus;bacterium CulaenoE10F;human oral bacterium C20;uncultured bacterium*/organism*                                                                | species   | 100.00      | 98.62       | 0.00          | 1     | 1        | 100.00    |
|----------+---------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|

And using --max-group-size 1:

classify --columns qaccver,saccver,pident,staxid --lineages lineages.csv --max-group-size 1 blast.csv
|----------+---------------+--------------+--------------+-------------+-------------+---------------+-------+----------+-----------|
| specimen | assignment_id | assignment   | best_rank    | max_percent | min_percent | min_threshold | reads | clusters | pct_reads |
|----------+---------------+--------------+--------------+-------------+-------------+---------------+-------+----------+-----------|
| query1   | 0             | Homo sapiens | species      | 99.67       | 99.67       | 0.00          | 1     | 1        | 100.00    |
| query10  | 0             | Bacteria*    | superkingdom | 100.00      | 93.21       | 0.00          | 1     | 1        | 100.00    |
| query11  | 0             | root*        | root         | 100.00      | 91.26       | 0.00          | 1     | 1        | 100.00    |
| query12  | 0             | root*        | root         | 100.00      | 98.26       | 0.00          | 1     | 1        | 100.00    |
| query13  | 0             | root*        | root         | 100.00      | 82.88       | 0.00          | 1     | 1        | 100.00    |
| query14  | 0             | Eukaryota*   | superkingdom | 100.00      | 99.00       | 0.00          | 1     | 1        | 100.00    |
| query2   | 0             | Homininae    | subfamily    | 97.07       | 95.40       | 0.00          | 1     | 1        | 100.00    |
| query6   | 0             | Bacteria*    | superkingdom | 100.00      | 98.62       | 0.00          | 1     | 1        | 100.00    |
| query7   | 0             | root*        | root         | 100.00      | 91.61       | 0.00          | 1     | 1        | 100.00    |
| query8   | 0             | Bacteria*    | superkingdom | 100.00      | 98.62       | 0.00          | 1     | 1        | 100.00    |
| query9   | 0             | root*        | root         | 100.00      | 98.62       | 0.00          | 1     | 1        | 100.00    |
|----------+---------------+--------------+--------------+-------------+-------------+---------------+-------+----------+-----------|

Using the --specimen argument the results can be grouped together to further simplify the results:

classify --columns qaccver,saccver,pident,staxid --lineages lineages.csv --max-group-size 1 --specimen one blast.csv
|----------+---------------+--------------+--------------+-------------+-------------+---------------+-------+----------+-----------|
| specimen | assignment_id | assignment   | best_rank    | max_percent | min_percent | min_threshold | reads | clusters | pct_reads |
|----------+---------------+--------------+--------------+-------------+-------------+---------------+-------+----------+-----------|
| one      | 0             | root*        | root         | 100.00      | 82.88       | 0.00          | 5     | 5        | 45.45     |
| one      | 1             | Bacteria*    | superkingdom | 100.00      | 93.21       | 0.00          | 3     | 3        | 27.27     |
| one      | 2             | Homo sapiens | species      | 99.67       | 99.67       | 0.00          | 1     | 1        | 9.09      |
| one      | 3             | Homininae    | subfamily    | 97.07       | 95.40       | 0.00          | 1     | 1        | 9.09      |
| one      | 4             | Eukaryota*   | superkingdom | 100.00      | 99.00       | 0.00          | 1     | 1        | 9.09      |
|----------+---------------+--------------+--------------+-------------+-------------+---------------+-------+----------+-----------|

If --columns is not specified the classifier will check for a header with minimum qseqid,sseqid,pident columns. If no header than blast outfmt 6 columns are assumed.

Alignment selection

TODO

Rank thresholds

The Moose classifier is built to accept dynamic thresholds for any taxonomic to provide the best possible classification using the --rank-thresholds argument. An example input looks like this:

% cl rank_thresholds.csv
|--------+------+---------+--------+-------+-------+--------+-------+---------|
| tax_id | root | kingdom | phylum | class | order | family | genus | species | subspecies |
|--------+------+---------+--------+-------+-------+--------+-------+---------|
| 1      | 75.0 | 75.0    | 80.0   | 90.0  | 93.0  | 95.0   | 97.0  |  99.0   |
|--------+------+---------+--------+-------+-------+--------+-------+---------|

Any tax_id can be specified in a rank thresholds file. If a tax_id is not present the rank thresholds file the classifier will work its way up the reference sequence's taxonomy lineage in order to assign rank thresholds.

The classifier will use the rank threshold table to select the lowest possible best hits available for classification. Example usage:

classify --columns qaccver,saccver,pident,staxid --lineages lineages.csv --rank-thresholds rank_thresholds.csv --specimen one blast.csv
|----------+---------------+-----------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|
| specimen | assignment_id | assignment                                                                        | best_rank | max_percent | min_percent | min_threshold | reads | clusters | pct_reads |
|----------+---------------+-----------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|
| one      | 0             | Bacteroidetes*;uncultured bacterium*/organism*                                    | species   | 100.00      | 99.27       | 99.00         | 2     | 2        | 18.18     |
| one      | 1             | Bacteria*;Escherichia coli;Staphylococcus                                         | species   | 100.00      | 99.31       | 99.00         | 2     | 2        | 18.18     |
| one      | 2             | Saccharomyces cerevisiae*;uncultured eukaryote                                    | species   | 100.00      | 99.33       | 99.00         | 1     | 1        | 9.09      |
| one      | 3             | Homo sapiens                                                                      | species   | 99.67       | 99.67       | 99.00         | 1     | 1        | 9.09      |
| one      | 4             | Homo                                                                              | genus     | 97.07       | 97.07       | 97.00         | 1     | 1        | 9.09      |
| one      | 5             | Clavispora lusitaniae*                                                            | species   | 100.00      | 100.00      | 99.00         | 1     | 1        | 9.09      |
| one      | 6             | Bacteria*;uncultured organism*                                                    | species   | 100.00      | 99.31       | 99.00         | 1     | 1        | 9.09      |
| one      | 7             | Apteryx australis*;Bacteria*;Firmicutes*                                          | species   | 100.00      | 99.31       | 99.00         | 1     | 1        | 9.09      |
| one      | 8             | Actinomycetales bacterium 'ARUP UnID 260'*;Corynebacterium*;uncultured bacterium* | species   | 100.00      | 99.64       | 99.00         | 1     | 1        | 9.09      |
|----------+---------------+-----------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|

There are a few things to notice when using a rank thresholds table. The first is the min_percent column will correspond to the lowest rank threshold used for hit selection. The second is the difference in classifications after dropping hits below the min_threshold.

Lastly, the genus level Homo classification was not rolled into the Homo sapiens classification because the rank thresholds table determined that the best hits available for that query sequence could only be classified at the genus level. This is despite the fact that the genus level Homo classification was derived from Homo sapien reference sequences. What the rank thresholds table defines is classification uncertainty. So, despite the Homo sapien reference sequences hits the classifier could not determine the query sequence was in fact Homo sapien but only of genus level Homo origin.

Specimen map

A three column specimen,qseqid,weight file included using the --specimen-map argument. An example might look like this:

cat specimen_map.csv
one,query1,100
one,query2,95
one,query6,75
one,query7,70
one,query8,65
one,query9,60
one,query10,55
one,query11,50
one,query12,45
one,query13,40
one,query14,35
classify --columns qaccver,saccver,pident,staxid --lineages lineages.csv --rank-thresholds rank_thresholds.csv --specimen-map specimen_map.csv blast.csv | cl
|----------+---------------+-----------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|
| specimen | assignment_id | assignment                                                                        | best_rank | max_percent | min_percent | min_threshold | reads | clusters | pct_reads |
|----------+---------------+-----------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|
| one      | 0             | Bacteria*;Escherichia coli;Staphylococcus                                         | species   | 100.00      | 99.31       | 99.00         | 140   | 2        | 20.29     |
| one      | 1             | Bacteroidetes*;uncultured bacterium*/organism*                                    | species   | 100.00      | 99.27       | 99.00         | 120   | 2        | 17.39     |
| one      | 2             | Homo sapiens                                                                      | species   | 99.67       | 99.67       | 99.00         | 100   | 1        | 14.49     |
| one      | 3             | Homo                                                                              | genus     | 97.07       | 97.07       | 97.00         | 95    | 1        | 13.77     |
| one      | 4             | Bacteria*;uncultured organism*                                                    | species   | 100.00      | 99.31       | 99.00         | 60    | 1        | 8.70      |
| one      | 5             | Actinomycetales bacterium 'ARUP UnID 260'*;Corynebacterium*;uncultured bacterium* | species   | 100.00      | 99.64       | 99.00         | 55    | 1        | 7.97      |
| one      | 6             | Apteryx australis*;Bacteria*;Firmicutes*                                          | species   | 100.00      | 99.31       | 99.00         | 45    | 1        | 6.52      |
| one      | 7             | Clavispora lusitaniae*                                                            | species   | 100.00      | 100.00      | 99.00         | 40    | 1        | 5.80      |
| one      | 8             | Saccharomyces cerevisiae*;uncultured eukaryote                                    | species   | 100.00      | 99.33       | 99.00         | 35    | 1        | 5.07      |
|----------+---------------+-----------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|

The classifer will interpret each qseqid in the specimen map file as part of the specimen. If a qseqid is not included in the blast.csv results then a classification of [no blast result] will be assigned:

cat specimen_map.csv
one,query1,100
one,query2,95
one,query3,90
one,query4,85
one,query5,80
one,query6,75
one,query7,70
one,query8,65
one,query9,60
one,query10,55
one,query11,50
one,query12,45
one,query13,40
one,query14,35
classify --columns qaccver,saccver,pident,staxid --lineages lineages.csv --rank-thresholds rank_thresholds.csv --specimen-map specimen_map.csv blast.csv
|----------+---------------+-----------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|
| specimen | assignment_id | assignment                                                                        | best_rank | max_percent | min_percent | min_threshold | reads | clusters | pct_reads |
|----------+---------------+-----------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|
| one      | 0             | [no blast result]                                                                 |           |             |             |               | 255   | 3        | 26.98     |
| one      | 1             | Bacteria*;Escherichia coli;Staphylococcus                                         | species   | 100.00      | 99.31       | 99.00         | 140   | 2        | 14.81     |
| one      | 2             | Bacteroidetes*;uncultured bacterium*/organism*                                    | species   | 100.00      | 99.27       | 99.00         | 120   | 2        | 12.70     |
| one      | 3             | Homo sapiens                                                                      | species   | 99.67       | 99.67       | 99.00         | 100   | 1        | 10.58     |
| one      | 4             | Homo                                                                              | genus     | 97.07       | 97.07       | 97.00         | 95    | 1        | 10.05     |
| one      | 5             | Bacteria*;uncultured organism*                                                    | species   | 100.00      | 99.31       | 99.00         | 60    | 1        | 6.35      |
| one      | 6             | Actinomycetales bacterium 'ARUP UnID 260'*;Corynebacterium*;uncultured bacterium* | species   | 100.00      | 99.64       | 99.00         | 55    | 1        | 5.82      |
| one      | 7             | Apteryx australis*;Bacteria*;Firmicutes*                                          | species   | 100.00      | 99.31       | 99.00         | 45    | 1        | 4.76      |
| one      | 8             | Clavispora lusitaniae*                                                            | species   | 100.00      | 100.00      | 99.00         | 40    | 1        | 4.23      |
| one      | 9             | Saccharomyces cerevisiae*;uncultured eukaryote                                    | species   | 100.00      | 99.33       | 99.00         | 35    | 1        | 3.70      |
|----------+---------------+-----------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|

Multiple specimens can be specified with qseqids of the same name:

cat specimen_map.csv
one,query1,100
one,query2,95
one,query3,90
one,query4,85
one,query5,80
one,query6,75
one,query7,70
one,query8,65
one,query9,60
one,query10,55
one,query11,50
one,query12,45
one,query13,40
one,query14,35
two,query3,1000
two,query6,500
two,query1,25
two,query8,900
classify --columns qaccver,saccver,pident,staxid --lineages lineages.csv --rank-thresholds rank_thresholds.csv --specimen-map specimen_map.csv blast.csv
|----------+---------------+-----------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|
| specimen | assignment_id | assignment                                                                        | best_rank | max_percent | min_percent | min_threshold | reads | clusters | pct_reads |
|----------+---------------+-----------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|
| one      | 0             | [no blast result]                                                                 |           |             |             |               | 255   | 3        | 26.98     |
| one      | 1             | Bacteria*;Escherichia coli;Staphylococcus                                         | species   | 100.00      | 99.31       | 99.00         | 140   | 2        | 14.81     |
| one      | 2             | Bacteroidetes*;uncultured bacterium*/organism*                                    | species   | 100.00      | 99.27       | 99.00         | 120   | 2        | 12.70     |
| one      | 3             | Homo sapiens                                                                      | species   | 99.67       | 99.67       | 99.00         | 100   | 1        | 10.58     |
| one      | 4             | Homo                                                                              | genus     | 97.07       | 97.07       | 97.00         | 95    | 1        | 10.05     |
| one      | 5             | Bacteria*;uncultured organism*                                                    | species   | 100.00      | 99.31       | 99.00         | 60    | 1        | 6.35      |
| one      | 6             | Actinomycetales bacterium 'ARUP UnID 260'*;Corynebacterium*;uncultured bacterium* | species   | 100.00      | 99.64       | 99.00         | 55    | 1        | 5.82      |
| one      | 7             | Apteryx australis*;Bacteria*;Firmicutes*                                          | species   | 100.00      | 99.31       | 99.00         | 45    | 1        | 4.76      |
| one      | 8             | Clavispora lusitaniae*                                                            | species   | 100.00      | 100.00      | 99.00         | 40    | 1        | 4.23      |
| one      | 9             | Saccharomyces cerevisiae*;uncultured eukaryote                                    | species   | 100.00      | 99.33       | 99.00         | 35    | 1        | 3.70      |
| two      | 0             | Bacteria*;Escherichia coli;Staphylococcus                                         | species   | 100.00      | 99.31       | 99.00         | 1400  | 2        | 57.73     |
| two      | 1             | [no blast result]                                                                 |           |             |             |               | 1000  | 1        | 41.24     |
| two      | 2             | Homo sapiens                                                                      | species   | 99.67       | 99.67       | 99.00         | 25    | 1        | 1.03      |
|----------+---------------+-----------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|

If a query sequence is not included in the specimen map but returned as part of the blast.csv results then it will be added as its own specimen:

cat specimen_map.csv
one,query1,100
one,query4,85
one,query5,80
one,query6,75
one,query7,70
classify --columns qaccver,saccver,pident,staxid --lineages lineages.csv --rank-thresholds rank_thresholds.csv --specimen-map specimen_map.csv blast.csv
|----------+---------------+-----------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|
| specimen | assignment_id | assignment                                                                        | best_rank | max_percent | min_percent | min_threshold | reads | clusters | pct_reads |
|----------+---------------+-----------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|
| one      | 0             | [no blast result]                                                                 |           |             |             |               | 165   | 2        | 40.24     |
| one      | 1             | Homo sapiens                                                                      | species   | 99.67       | 99.67       | 99.00         | 100   | 1        | 24.39     |
| one      | 2             | Bacteria*;Escherichia coli;Staphylococcus                                         | species   | 100.00      | 99.31       | 99.00         | 75    | 1        | 18.29     |
| one      | 3             | Bacteroidetes*;uncultured bacterium*/organism*                                    | species   | 100.00      | 99.27       | 99.00         | 70    | 1        | 17.07     |
| query10  | 0             | Actinomycetales bacterium 'ARUP UnID 260'*;Corynebacterium*;uncultured bacterium* | species   | 100.00      | 99.64       | 99.00         | 1     | 1        | 100.00    |
| query11  | 0             | Bacteroidetes*;uncultured bacterium*/organism                                     | species   | 100.00      | 99.27       | 99.00         | 1     | 1        | 100.00    |
| query12  | 0             | Apteryx australis*;Bacteria*;Firmicutes*                                          | species   | 100.00      | 99.31       | 99.00         | 1     | 1        | 100.00    |
| query13  | 0             | Clavispora lusitaniae*                                                            | species   | 100.00      | 100.00      | 99.00         | 1     | 1        | 100.00    |
| query14  | 0             | Saccharomyces cerevisiae*;uncultured eukaryote                                    | species   | 100.00      | 99.33       | 99.00         | 1     | 1        | 100.00    |
| query2   | 0             | Homo                                                                              | genus     | 97.07       | 97.07       | 97.00         | 1     | 1        | 100.00    |
| query8   | 0             | Bacteria*;Escherichia coli;Staphylococcus                                         | species   | 100.00      | 99.31       | 99.00         | 1     | 1        | 100.00    |
| query9   | 0             | Bacteria*;uncultured organism*                                                    | species   | 100.00      | 99.31       | 99.00         | 1     | 1        | 100.00    |
|----------+---------------+-----------------------------------------------------------------------------------+-----------+-------------+-------------+---------------+-------+----------+-----------|

copy numbers

Multiple copies of the gene may be present in a species genome which may distort the relative weight abundance of a classification. The Moose Classifier excepts a two column csv file with columns --copy-numbers:

|--------+-------|
| tax_id | count |
|--------+-------|

and will divide the final classification tax_id by the count number in this file and expressed under the corrected column in the output file. This is useful for adjusting relative abundance of species when, for example, doing 16s classifications.