From 3f1278de88c4868d630824bf303b5a1e582dd43a Mon Sep 17 00:00:00 2001 From: Andrew Tritt Date: Fri, 23 Jun 2023 22:54:12 -0600 Subject: [PATCH] Add documentation for bins and sequences (#41) --- docs/source/usage.rst | 35 +++++++++++++++++++++++++++-------- 1 file changed, 27 insertions(+), 8 deletions(-) diff --git a/docs/source/usage.rst b/docs/source/usage.rst index 9305b49..5fcfb84 100644 --- a/docs/source/usage.rst +++ b/docs/source/usage.rst @@ -5,7 +5,28 @@ GTNet comes with multiple commands. The simplest way of running GTNet is to use .. code:: bash - gtnet classify data/small.fna > data/small.tax.csv + gtnet classify genome.fna > genome.tax.csv + +This command generates one classification for the entire file, and should be used to get classification for metagenome bin. +Use the ``-s/--seqs`` flag to get classifications for the individual sequences in ``genome.fna`` + +.. Attention:: + The first time you run ``classify`` and ``predict`` (see below), the model file will be downloaded and stored in the same + directory that the *gtnet* package is installed in. Therefore, for the this to be successful, you must have write privileges + on the directory that *gtnet* is installed in. + + +.. code:: bash + + gtnet classify --seqs genome.fna > genome.seqs.tax.csv + + +The ``classify`` command can take multiple fasta files, and will produce line per file in the output. For example, the following +command will contain two lines: + +.. code:: bash + + gtnet classify bin1.fna bin2.fna > bins.tax.csv GTNet steps @@ -18,15 +39,12 @@ want to experiment with different false-positive rates. Getting predictions ^^^^^^^^^^^^^^^^^^^ -To get predictinos for all sequences in a Fasta file, use the ``predict`` subcommand. +To get predictinos for all sequences in a Fasta file, use the ``predict`` subcommand. This command also accepts multiple fasta files +and the ``-s/--seqs`` argument for getting predictions for individual sequences. .. code:: bash - gtnet predict data/small.fna > data/small.tax.raw.csv - -The first time you run ``predict``, the model file will be downloaded and stored in the -same directory that the *gtnet* package is installed in. Therefore, for the this to be successful, -you must have write privileges on the directory that *gtnet* is installed in. + gtnet predict genome.fna > genome.tax.raw.csv Filtering predictions ^^^^^^^^^^^^^^^^^^^^^ @@ -36,8 +54,9 @@ to a desired false-positive rate. .. code:: bash - gtnet filter --fpr 0.05 data/small.tax.raw.csv > data/small.tax.csv + gtnet filter --fpr 0.05 genome.tax.raw.csv > genome.tax.csv +The ``filter`` command supports predictions for whole files and individual sequences. GPU acceleration ----------------