v0.16.0

wwood · Nov 24, 2023 · 7f11ae3 · 7f11ae3
1 parent 4a6803d
commit 7f11ae3
Show file tree

Hide file tree

Showing 11 changed files with 39 additions and 18 deletions.
diff --git a/build_docs.py b/build_docs.py
@@ -52,7 +52,7 @@ def get_version(relpath):
     logging.info("Done updating [RELEASE_TAG] in Installation.md to {}".format(version))
 
     subdir_and_commands = [
-        ['tools', ['data','pipe','appraise','summarise','renew','supplement','read_fraction']],
+        ['tools', ['data','pipe','appraise','summarise','renew','supplement','microbial_fraction']],
         ['advanced', ['makedb','query','condense','seqs','create','metapackage']]
     ]
 
@@ -66,7 +66,7 @@ def get_version(relpath):
                 # Remove everything before the options section
                 splitters = {
                     'pipe': 'COMMON OPTIONS',
-                    'read_fraction': 'OPTIONS',
+                    'microbial_fraction': 'OPTIONS',
                     'data': 'OPTIONS',
                     'summarise': 'INPUT',
                     'makedb': 'REQUIRED ARGUMENTS',

diff --git a/docs/Installation.md b/docs/Installation.md
@@ -20,45 +20,45 @@ After this, you'll also need to procure the reference data (the "metapackage").
 ## Installation via DockerHub
 A docker image generated from the conda package is [available](https://hub.docker.com/r/wwood/singlem) on DockerHub. After installing Docker, run the following:
 ```
-docker pull wwood/singlem:0.15.1
+docker pull wwood/singlem:0.16.0
 ```
 
 Test if it works by running
 ```
-docker run wwood/singlem:0.15.1 -h
+docker run wwood/singlem:0.16.0 -h
 ```
 
 If the sequence data to be analyzed is in the current working directory, SingleM `pipe` can be used like so:
 ```
-docker run -v `pwd`:`pwd` wwood/singlem:0.15.1 pipe --sequences \
+docker run -v `pwd`:`pwd` wwood/singlem:0.16.0 pipe --sequences \
     `pwd`/my.fastq.gz -p `pwd`/my.profile.csv --threads 4
 ```
 Two things to note:
 
 1. The default SingleM reference data is included in the docker image, so running [singlem data](/tools/data) is not necessary for this installation method - you can jump straight to using `pipe`.
-2. You should not specify `singlem` in the command line, as this is automatic. Simply use e.g. `docker run wwood/singlem:0.15.1 pipe -h`.
+2. You should not specify `singlem` in the command line, as this is automatic. Simply use e.g. `docker run wwood/singlem:0.16.0 pipe -h`.
 
 
 ## Installation via Singularity / Apptainer
 SingleM can be installed via [Singularity](https://sylabs.io/singularity/) or [Apptainer](https://apptainer.org). After installing Singularity or Apptainer, run the following:
 ```
-singularity pull docker://wwood/singlem:0.15.1
+singularity pull docker://wwood/singlem:0.16.0
 ```
 
 Test if it works by running
 ```
-singularity run singlem_0.15.1.sif -h
+singularity run singlem_0.16.0.sif -h
 ```
 
 If the sequence data to be analyzed is in the current working directory, SingleM `pipe` can be used like so:
 ```
-singularity run -B `pwd`:`pwd` singlem_0.15.1.sif pipe --sequences \
+singularity run -B `pwd`:`pwd` singlem_0.16.0.sif pipe --sequences \
     `pwd`/my.fastq.gz -p `pwd`/my.profile.csv --threads 4
 ```
 Two things to note:
 
 1. The default SingleM reference data is included in the docker image, so running [singlem data](/tools/data) is not necessary for this installation method - you can jump straight to using `pipe`.
-2. You should not specify `singlem` in the command line, as this is automatic. Simply use e.g. `singularity run singlem_0.15.1.sif pipe -h`.
+2. You should not specify `singlem` in the command line, as this is automatic. Simply use e.g. `singularity run singlem_0.16.0.sif pipe -h`.
 
 
 ## Installation via PyPI

diff --git a/docs/preludes/read_fraction_prelude.md → docs/preludes/microbial_fraction_prelude.md b/docs/preludes/read_fraction_prelude.md → docs/preludes/microbial_fraction_prelude.md
diff --git a/docs/tools/appraise.md b/docs/tools/appraise.md
@@ -87,7 +87,7 @@ INEXACT APPRAISAL OPTIONS
 **\--sequence-identity** *SEQUENCE_IDENTITY*
 
   sequence identity cutoff to use if \--imperfect is specified
-    [default: \~species level divergence i.e. 0.95]
+    [default: \~species level divergence i.e. 0.9666666666666667]
 
 PLOTTING-RELATED OPTIONS
 ========================

diff --git a/docs/tools/read_fraction.md → docs/tools/microbial_fraction.md b/docs/tools/read_fraction.md → docs/tools/microbial_fraction.md
@@ -1,8 +1,8 @@
 ---
-title: SingleM read_fraction
+title: SingleM microbial_fraction
 ---
-# singlem read_fraction
-The 'read_fraction' subcommand can be used to estimate the fraction of reads
+# singlem microbial_fraction
+The 'microbial_fraction' subcommand can be used to estimate the fraction of reads
 from a metagenome that are assigned to Bacteria and Archaea compared to e.g.
 phages or eukaryotes.
 

diff --git a/docs/tools/pipe.md b/docs/tools/pipe.md
@@ -152,6 +152,12 @@ LESS COMMON OPTIONS
   Ignore reads aligning in less than this many positions to each
     protein HMM when using \--no-diamond-prefilter [default: 24]
 
+**\--max-species-divergence** INT
+
+  Maximum number of different bases acids to allow between a sequence
+    and the best hit in the database so that it is assigned to the
+    species level. [default: 2]
+
 **\--exclude-off-target-hits**
 
   Exclude hits that are not in the target domain of each SingleM

diff --git a/docs/tools/renew.md b/docs/tools/renew.md
@@ -128,6 +128,12 @@ LESS COMMON ARGUMENTS SHARED WITH \'PIPE\'
   Ignore reads aligning in less than this many positions to each
     protein HMM when using \--no-diamond-prefilter [default: 24]
 
+**\--max-species-divergence** INT
+
+  Maximum number of different bases acids to allow between a sequence
+    and the best hit in the database so that it is assigned to the
+    species level. [default: 2]
+
 **\--exclude-off-target-hits**
 
   Exclude hits that are not in the target domain of each SingleM

diff --git a/docs/tools/summarise.md b/docs/tools/summarise.md
@@ -94,7 +94,7 @@ TRANSFORMATION
 **\--cluster-id** *CLUSTER_ID*
 
   Sequence clustering identity cutoff if \--cluster is used [default:
-    0.95 i.e. 95.0%]
+    0.9666666666666667 i.e. 96.66666666666667%]
 
 **\--taxonomy** *TAXONOMY*
 

diff --git a/docs/tools/supplement.md b/docs/tools/supplement.md
@@ -15,6 +15,10 @@ OPTIONS
 
   FASTA files of new genomes
 
+**\--new-genome-fasta-files-list** *NEW_GENOME_FASTA_FILES_LIST* [*NEW_GENOME_FASTA_FILES_LIST* \...]
+
+  File containing FASTA file paths of new genomes
+
 **\--new-taxonomies** *NEW_TAXONOMIES*
 
   newline separated file containing taxonomies of new genomes
@@ -45,7 +49,12 @@ OPTIONS
 **\--gtdbtk-output-directory** *GTDBTK_OUTPUT_DIRECTORY*
 
   use this GTDBtk result. Not used if \--new-taxonomies is used
-    [default: run GTDBtk]
+    [default: not set, run GTDBtk]
+
+**\--taxonomy-file** *TAXONOMY_FILE*
+
+  A 2 column tab-separated file containing each genome\'s taxonomy as
+    output by GTDBtk [default: not set, run GTDBtk]
 
 **\--output-taxonomies** *OUTPUT_TAXONOMIES*
 

diff --git a/doctave.yml b/doctave.yml
@@ -15,7 +15,7 @@ navigation:
     - path: docs/tools/summarise.md
     - path: docs/tools/renew.md
     - path: docs/tools/supplement.md
-    - path: docs/tools/read_fraction.md
+    - path: docs/tools/microbial_fraction.md
     - path: docs/tools/appraise.md
   - path: docs/advanced
     children: 

diff --git a/singlem/version.py b/singlem/version.py
@@ -1 +1 @@
-__version__ = "0.15.1"
+__version__ = "0.16.0"