diff --git a/docs/source/building_splici_index.rst b/docs/source/building_splici_index.rst index ad29586..e3a698c 100644 --- a/docs/source/building_splici_index.rst +++ b/docs/source/building_splici_index.rst @@ -1,5 +1,5 @@ ################################################################################# -(Deprecated since v0.10.0)Preparing an expanded transcriptome reference for quantification with alevin-fry +(Deprecated since v0.10.0) Preparing an expanded transcriptome reference for quantification with alevin-fry ################################################################################# The USA mode in alevin-fry requires an expanded index reference, in which sequences represent spliced and unspliced transcripts. Pyroe provides CLI programs and python functions to build the pre-defined expanded references, the spliced + intronic (*splici*) reference, which includes the spliced transcripts plus the (merged and collapsed) intronic sequences of each gene and the spliced + unspliced (*spliceu*) reference, which consists of the spliced transcripts plus the unspliced transcript (genes' entire genomic interval) of each gene. The ``make_splici_txome()`` and ``make_spliceu_txome()`` python functions are designed to make the *splici* and *spliceu* reference by taking a genome FASTA file and a gene annotation GTF file as the input. Furthermore, the diff --git a/docs/source/geneid_to_name.rst b/docs/source/geneid_to_name.rst index f8cdbde..d3fba3e 100644 --- a/docs/source/geneid_to_name.rst +++ b/docs/source/geneid_to_name.rst @@ -1,4 +1,4 @@ -(Deprecated since v0.10.0)Generating a gene id to gene name mapping +(Deprecated since v0.10.0) Generating a gene id to gene name mapping ========================================= It is often useful to perform analyses with gene *names* rather than gene *identifiers*. The `convert `_ command of ``pyroe`` allows you to specify an id to name mapping so that the converted output matrix will be labeled with gene names rather than identifiers. However, you must provide it with a 2-column tab-separated file mapping IDs to names. This command can help you with that task. diff --git a/docs/source/index.rst b/docs/source/index.rst index 51fd20a..0441e0a 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -4,9 +4,12 @@ Welcome to the documentation for pyroe What is pyroe? =================== -The pyroe package provides useful functions for analyzing single-cell or single-nucleus RNA-sequencing data using `alevin-fry`. Since `simpleaf` version 0.14.0, `roers `_, instead of pyroe, became the default augmented reference constructor for `alevin-fry` and `simpleaf`. Now, the main purpose of `pyroe` is to provide the function `load_fry` to load `alevin-fry` and `simpleaf` quantification results into Python as an `anndata `_ object, so as to perform downstream analysis provided by `scanpy `_. +The pyroe package provides useful functions for analyzing single-cell or single-nucleus RNA-sequencing data using `alevin-fry`. +The main purpose of `pyroe` is to provide the function `load_fry` to load `alevin-fry` and `simpleaf` quantification results into Python as an `anndata `_ object, so as to perform downstream analysis provided by `scanpy `_. Moreover, `pyroe` also provides functions to fetch the pre-computed quantification results from the `quantaf `_ database. -Although pyroe is available on bioconda and can be easily installed, if you encounter any problem during installation, you can also define the `load_fry` function locally in your python script by copying the function definition defined `here `_. The only dependency of `load_fry` is `scanpy `_. +In previous versions (before v 0.10.0), pyroe also provided the functions to construct the augmented transcriptome references. Since `simpleaf` version 0.14.0, `roers `_, instead of pyroe, became the default augmented reference constructor for `alevin-fry` and `simpleaf`. If you would like to use the deprecated functions to construct the augmented references, please install an older version of pyroe. Notice that old versions of pyroe are compatitble with pandas version less than 2.0.0. So, we suggest you to install the old versions of pyroe in a conda environment with a isolated environment, so as to not affect the other packages in your system. + +**To note that** although pyroe is available on bioconda and can be easily installed, if you encounter any problem during installation, you can define the `load_fry` function locally in your python script by copying the function definition defined `here `_. The only dependency of `load_fry` is `scanpy `_. Additionally, diff --git a/setup.cfg b/setup.cfg index 97056ce..6898d64 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = pyroe -version = 0.9.3 +version = 0.10.0 author = Dongze He, Rob Patro author_email = dhe17@umd.edu, rob@cs.umd.edu description = utilities of alevin-fry diff --git a/src/pyroe/__init__.py b/src/pyroe/__init__.py index fdcd1c2..ce93022 100644 --- a/src/pyroe/__init__.py +++ b/src/pyroe/__init__.py @@ -1,4 +1,4 @@ -__version__ = "0.9.3" +__version__ = "0.10.0" from pyroe.load_fry import load_fry from pyroe.fetch_processed_quant import fetch_processed_quant @@ -12,8 +12,8 @@ # from pyroe.make_txome import make_splici_txome, make_spliceu_txome # from pyroe.id_to_name import id_to_name # except ImportError: -# make_splici_txome = None -# make_spliceu_txome = None -# id_to_name = None +# make_splici_txome = None +# make_spliceu_txome = None +# id_to_name = None # flake8: noqa