moose-classifier 0.12__tar.gz → 0.13__tar.gz

moose_classifier-0.13/.github/workflows/unnittests.yml

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+name: unittests
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+  schedule:
+    - cron: '0 6 * * 1'  # 6am Monday
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.12', '3.11', '3.10', '3.9']
+    steps:
+    -
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    -
+      uses: actions/checkout@v3
+    -
+      name: Install and test
+      run: |
+        python -m pip install .
+        python -m unittest

moose_classifier-0.13/.gitignore

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+*.pyc
+build/
+dist
+*.egg-info
+test_output

moose_classifier-0.13/PKG-INFO

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+Metadata-Version: 2.4
+Name: moose_classifier
+Version: 0.13
+Summary: Alignment based taxonomic classifier
+Author: Chris Rosenthal
+Author-email: crosenth@gmail.com
+Maintainer-email: Dan Hoogestraat <dhoogest@uw.edu>
+License-Expression: GPL-3.0-only
+Project-URL: repository, https://github.com/crosenth/moose
+Keywords: bioinformatics,blast,classifier,dna,genetics,genomics,ncbi,rna
+Classifier: Environment :: Console
+Classifier: Intended Audience :: End Users/Desktop
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+Requires-Dist: pandas>=2.0.2
+
+# moose
+
+A tool for taxonomically selecting, grouping and summarizing pairwise
+alignment classifications into something more concise and readable.
+
+## authors
+
+* [Noah Hoffman](https://github.com/nhoffman)
+* [Tim Holland](https://github.com/tholland)
+* [Daniel Hoogestraat](https://github.com/dhoogest)
+* [Tyler Land](https://github.com/tyleraland)
+* [Steve Salipante](mailto:stevesal@uw.edu)
+* [Chris Rosenthal](mailto:crosenth@gmail.com)
+
+## 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](https://pandas.pydata.org/) >= 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](https://www.ncbi.nlm.nih.gov/sites/books/NBK537770/) and
+and [here](https://www.ncbi.nlm.nih.gov/sites/books/NBK279688/).
+
+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.
+
+

{moose_classifier-0.12 → moose_classifier-0.13}/pyproject.toml

@@ -1,3 +1,7 @@
+[build-system]
+requires = ["setuptools>=64", "setuptools-scm>=8"]
+build-backend = "setuptools.build_meta"
+
 [project]
 authors = [
   {email = "crosenth@gmail.com"},
@@ -6,24 +10,29 @@ authors = [
 classifiers = [
   "Environment :: Console",
   "Intended Audience :: End Users/Desktop",
-  "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
   "Operating System :: OS Independent",
   "Programming Language :: Python :: 3"
 ]
 dependencies = ["pandas>=2.0.2"]
 description = "Alignment based taxonomic classifier"
+dynamic = ["version"]
 keywords = [
   "bioinformatics", "blast", "classifier", "dna",
   "genetics", "genomics", "ncbi", "rna"
 ]
-license = {file = "LICENSE"}
+license = "GPL-3.0-only"
+maintainers = [
+  {email = "dhoogest@uw.edu", name="Dan Hoogestraat"}
+]
 name = "moose_classifier"
 readme = "README.md"
 requires-python = ">=3.7"
-version = "0.12"
 
 [project.urls]
 repository = "https://github.com/crosenth/moose"
 
 [project.scripts]
 classify = "classify:main"
+
+[tool.setuptools_scm]
+# can be empty if no extra settings are needed, presence enables setuptools-scm

moose_classifier-0.13/requirements.txt

@@ -0,0 +1,6 @@
+sphinx
+ghp-import
+twine
+tox
+flake8
+taxtastic