diff --git a/.flake8 b/.flake8 new file mode 100644 index 0000000..919ce57 --- /dev/null +++ b/.flake8 @@ -0,0 +1,14 @@ +[flake8] +ignore = E226,E302,E41 +max-line-length = 88 +exclude = + .git, + __pycache__, + build, + dist, + scripts/*, + docs/*, + .venv/*, + .pytest_cache/*, + .devcontainer/*, + .vscode/*, diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md new file mode 100644 index 0000000..dd84ea7 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -0,0 +1,38 @@ +--- +name: Bug report +about: Create a report to help us improve +title: '' +labels: '' +assignees: '' + +--- + +**Describe the bug** +A clear and concise description of what the bug is. + +**To Reproduce** +Steps to reproduce the behavior: +1. Go to '...' +2. Click on '....' +3. Scroll down to '....' +4. See error + +**Expected behavior** +A clear and concise description of what you expected to happen. + +**Screenshots** +If applicable, add screenshots to help explain your problem. + +**Desktop (please complete the following information):** + - OS: [e.g. iOS] + - Browser [e.g. chrome, safari] + - Version [e.g. 22] + +**Smartphone (please complete the following information):** + - Device: [e.g. iPhone6] + - OS: [e.g. iOS8.1] + - Browser [e.g. stock browser, safari] + - Version [e.g. 22] + +**Additional context** +Add any other context about the problem here. diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md new file mode 100644 index 0000000..bbcbbe7 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -0,0 +1,20 @@ +--- +name: Feature request +about: Suggest an idea for this project +title: '' +labels: '' +assignees: '' + +--- + +**Is your feature request related to a problem? Please describe.** +A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] + +**Describe the solution you'd like** +A clear and concise description of what you want to happen. + +**Describe alternatives you've considered** +A clear and concise description of any alternative solutions or features you've considered. + +**Additional context** +Add any other context or screenshots about the feature request here. diff --git a/.github/workflows/isocomp.yaml b/.github/workflows/python-package.yml similarity index 63% rename from .github/workflows/isocomp.yaml rename to .github/workflows/python-package.yml index 63a375d..955097b 100644 --- a/.github/workflows/isocomp.yaml +++ b/.github/workflows/python-package.yml @@ -1,24 +1,19 @@ -name: Python package with Poetry and MkDocs Deploy +name: Python package with Poetry on: push: - branches: - - main - - develop + branches: [ "main", "develop" ] pull_request: - branches: - - main - - develop + branches: [ "main", "develop" ] jobs: build: + + runs-on: ubuntu-latest strategy: fail-fast: false matrix: - os: [ubuntu-latest, macos-latest, windows-latest] - python-version: ["3.9", "3.10", "3.11"] - - runs-on: ${{ matrix.os }} + python-version: ["3.9"] steps: - uses: actions/checkout@v2 @@ -40,6 +35,7 @@ jobs: run: | poetry install - name: Lint with flake8 using Poetry + continue-on-error: true run: | # stop the build if there are Python syntax errors or undefined names poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics @@ -48,27 +44,3 @@ jobs: - name: Test with pytest using Poetry run: | poetry run python -m pytest - - deploy: - needs: build - runs-on: ubuntu-latest - - steps: - - name: Checkout code - uses: actions/checkout@v2 - - - name: Install MkDocs - run: pip install mkdocs - - - name: Build MkDocs documentation - run: mkdocs build - - - name: Deploy to GitHub Pages - run: | - git config user.name "GitHub Actions" - git config user.email "actions@github.com" - mkdocs gh-deploy --force - - - name: Clean up - run: | - rm -rf site diff --git a/README.md b/README.md index 932c6f1..7ea11e3 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,5 @@ +[![Python package with Poetry](https://github.com/cmatKhan/isocomp/actions/workflows/python-package.yml/badge.svg)](https://github.com/cmatKhan/isocomp/actions/workflows/python-package.yml) + # Isocomp: comparing high-quality IsoSeq3 isoforms between samples ![](images/logo.png) diff --git a/docs/api/api_tutorial.ipynb b/docs/api/api_tutorial.ipynb index ea78a39..8fd7320 100644 --- a/docs/api/api_tutorial.ipynb +++ b/docs/api/api_tutorial.ipynb @@ -115,260 +115,6 @@ "c1.unique_id" ] }, - { - "cell_type": "code", - "execution_count": 12, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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\n", - "
" - ], - "text/plain": [ - " V1 V2\n", - "2 tx_0 tx_1\n", - "1 tx_0 tx_2\n", - "3 tx_0 tx_3\n", - "0 tx_0 tx_4\n", - "7 tx_2 tx_1\n", - "8 tx_2 tx_3\n", - "9 tx_3 tx_1\n", - "5 tx_4 tx_1\n", - "4 tx_4 tx_2\n", - "6 tx_4 tx_3" - ] - }, - "execution_count": 12, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "pd.DataFrame.from_dict(compare_utils.vector_crosser(c1.unique_id,c1.unique_id))\\\n", - "\t.sort_values(by=['V1','V2'])" - ] - }, - { - "cell_type": "code", - "execution_count": 13, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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ChromosomeSourceFeatureStartEndScoreStrandFrametranscript_idgene_idClusterunique_id
0chr1hg004_sqanti_fltrtranscript10134961014531.+.PB.13.1PB.131tx_0
1chr1hg005_sqanti_fltrtranscript10134961014531.+.PB.17.1PB.171tx_1
2chr1hg005_sqanti_fltrtranscript10134961014531.+.PB.17.2PB.171tx_2
3chr1hg002_sqanti_fltrtranscript10135031014531.+.PB.17.2PB.171tx_3
4chr1hg004_sqanti_fltrtranscript10135311014531.+.PB.13.2PB.131tx_4
\n", - "
" - ], - "text/plain": [ - "+--------------+-------------------+--------------+-----------+-------+\n", - "| Chromosome | Source | Feature | Start | +8 |\n", - "| (category) | (object) | (category) | (int32) | ... |\n", - "|--------------+-------------------+--------------+-----------+-------|\n", - "| chr1 | hg004_sqanti_fltr | transcript | 1013496 | ... |\n", - "| chr1 | hg005_sqanti_fltr | transcript | 1013496 | ... |\n", - "| chr1 | hg005_sqanti_fltr | transcript | 1013496 | ... |\n", - "| chr1 | hg002_sqanti_fltr | transcript | 1013503 | ... |\n", - "| chr1 | hg004_sqanti_fltr | transcript | 1013531 | ... |\n", - "+--------------+-------------------+--------------+-----------+-------+\n", - "Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes.\n", - "For printing, the PyRanges was sorted on Chromosome and Strand.\n", - "8 hidden columns: End, Score, Strand, Frame, transcript_id, gene_id, Cluster, ... (+ 1 more.)" - ] - }, - "execution_count": 13, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "c1" - ] - }, { "cell_type": "code", "execution_count": 24, @@ -450,45 +196,6 @@ "ia.clustered_gtf[(ia.clustered_gtf.Source == 'hg002_sqanti_fltr') & (ia.clustered_gtf.transcript_id == 'PB.17.2')]" ] }, - { - "cell_type": "code", - "execution_count": 27, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'V1': ['tx_0',\n", - " 'tx_0',\n", - " 'tx_0',\n", - " 'tx_0',\n", - " 'tx_4',\n", - " 'tx_4',\n", - " 'tx_4',\n", - " 'tx_2',\n", - " 'tx_2',\n", - " 'tx_3'],\n", - " 'V2': ['tx_4',\n", - " 'tx_2',\n", - " 'tx_1',\n", - " 'tx_3',\n", - " 'tx_2',\n", - " 'tx_1',\n", - " 'tx_3',\n", - " 'tx_1',\n", - " 'tx_3',\n", - " 'tx_1']}" - ] - }, - "execution_count": 27, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "compare_utils.vector_crosser(c1.unique_id,c1.unique_id)" - ] - }, { "cell_type": "code", "execution_count": 36, @@ -704,26 +411,6 @@ "list(c1.Chromosome)[0]" ] }, - { - "cell_type": "code", - "execution_count": 48, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'V1': ['tx_2', 'tx_2', 'tx_1'], 'V2': ['tx_1', 'tx_3', 'tx_3']}" - ] - }, - "execution_count": 48, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "compare_utils.vector_crosser(['tx_1','tx_2','tx_3'],['tx_1','tx_2','tx_3'])" - ] - }, { "cell_type": "code", "execution_count": null, diff --git a/docs/api/compare/functions/vector_crosser.md b/docs/api/compare/functions/vector_crosser.md deleted file mode 100644 index d14ba6d..0000000 --- a/docs/api/compare/functions/vector_crosser.md +++ /dev/null @@ -1,3 +0,0 @@ -# vector_crosser - -::: isocomp.Compare.vector_crosser \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 6afaa93..019e793 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -42,7 +42,6 @@ nav: - IsoformLibrary: api/compare/classes/IsoformLibrary.md - Functions: - align_isoforms: api/compare/functions/align_isoforms.md - - vector_crosser: api/compare/functions/vector_crosser.md - compare_isoforms_in_cluster: api/compare/functions/compare_isoforms_in_cluster.md - filter_comparisons: api/compare/functions/filter_comparisons.md - find_unique_isoforms: api/compare/functions/find_unique_isoforms.md diff --git a/poetry.lock b/poetry.lock index 615b51c..a2df40d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -563,6 +563,22 @@ files = [ [package.extras] devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"] +[[package]] +name = "flake8" +version = "6.1.0" +description = "the modular source code checker: pep8 pyflakes and co" +optional = false +python-versions = ">=3.8.1" +files = [ + {file = "flake8-6.1.0-py2.py3-none-any.whl", hash = "sha256:ffdfce58ea94c6580c77888a86506937f9a1a227dfcd15f245d694ae20a6b6e5"}, + {file = "flake8-6.1.0.tar.gz", hash = "sha256:d5b3857f07c030bdb5bf41c7f53799571d75c4491748a3adcd47de929e34cd23"}, +] + +[package.dependencies] +mccabe = ">=0.7.0,<0.8.0" +pycodestyle = ">=2.11.0,<2.12.0" +pyflakes = ">=3.1.0,<3.2.0" + [[package]] name = "fonttools" version = "4.39.3" @@ -1207,6 +1223,17 @@ files = [ [package.dependencies] traitlets = "*" +[[package]] +name = "mccabe" +version = "0.7.0" +description = "McCabe checker, plugin for flake8" +optional = false +python-versions = ">=3.6" +files = [ + {file = "mccabe-0.7.0-py2.py3-none-any.whl", hash = "sha256:6c2d30ab6be0e4a46919781807b4f0d834ebdd6c6e3dca0bda5a15f863427b6e"}, + {file = "mccabe-0.7.0.tar.gz", hash = "sha256:348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325"}, +] + [[package]] name = "mdit-py-plugins" version = "0.3.3" @@ -1924,6 +1951,17 @@ files = [ {file = "pycparser-2.21.tar.gz", hash = "sha256:e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206"}, ] +[[package]] +name = "pyflakes" +version = "3.1.0" +description = "passive checker of Python programs" +optional = false +python-versions = ">=3.8" +files = [ + {file = "pyflakes-3.1.0-py2.py3-none-any.whl", hash = "sha256:4132f6d49cb4dae6819e5379898f2b8cce3c5f23994194c24b77d5da2e36f774"}, + {file = "pyflakes-3.1.0.tar.gz", hash = "sha256:a0aae034c444db0071aa077972ba4768d40c830d9539fd45bf4cd3f8f6992efc"}, +] + [[package]] name = "pygments" version = "2.13.0" @@ -2547,4 +2585,4 @@ testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools" [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "6aeb2c1e8704acbd93ec1d3d989c6c8ce73c79654bc1564af07e961d8d1cb079" +content-hash = "2e36180b4564b63e58f14b7cb76e387b8cf48ce401d06b98ec4bf0d6ff55000f" diff --git a/pyproject.toml b/pyproject.toml index 6e204f9..5b4a65b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "isocomp" -version = "0.2.2" +version = "0.3.0" description = "" authors = ["Yutong Qiu ", "Chia Sin Liew ", "Rupesh Kesharwani ", "Bida Gu ", "chase mateusiak ", @@ -31,6 +31,7 @@ isocomp = "isocomp:__main__.main" [tool.poetry.group.dev.dependencies] matplotlib = "^3.7.1" autopep8 = "^2.0.4" +flake8 = "^6.1.0" [build-system] requires = ["poetry-core>=1.0.0"] diff --git a/src/isocomp/Compare/__init__.py b/src/isocomp/Compare/__init__.py index 39b2c7a..6999f9c 100644 --- a/src/isocomp/Compare/__init__.py +++ b/src/isocomp/Compare/__init__.py @@ -3,4 +3,3 @@ from .filter_comparisons import * from .find_unique_isoforms import * from .IsoformLibrary import * -from .vector_crosser import * diff --git a/src/isocomp/Compare/compare_isoforms_in_cluster.py b/src/isocomp/Compare/compare_isoforms_in_cluster.py index 3fdca7d..35eb272 100644 --- a/src/isocomp/Compare/compare_isoforms_in_cluster.py +++ b/src/isocomp/Compare/compare_isoforms_in_cluster.py @@ -1,7 +1,6 @@ import logging - +from itertools import combinations from isocomp.Coordinates import Window -from .vector_crosser import vector_crosser from .align_isoforms import align_isoforms from .IsoformLibrary import IsoformLibrary @@ -115,14 +114,15 @@ def compare_isoforms_in_cluster( # if there is only one individual in the cluster, then report all # isoforms in that cluster as unique if cluster_window.score < 2: - for tx_id in cluster_gtf.transcript_id: - isoform1_window = isoform_library.get_isoform_coord(tx_id) + for tx_id in cluster_gtf.unique_id: + isoform1_window = isoform_library\ + .get_isoform_coord(unique_id=tx_id) out.append(__output_dict(cluster, cluster_window.chr, isoform1_window)) # else there are mutiple subjects -- do an all by all comparison of the # isoforms in the cluster - # TODO parameterize the cases in which isoforms are compared --eg, + # TODO parameterize the cases in which isoforms are compared --eg, # same strand, overlap threshold, different subjects else: # group transcripts by coordinates; return unique @@ -130,49 +130,39 @@ def compare_isoforms_in_cluster( .groupby(by=['Start', 'End', 'Strand'], as_index=True) for group, cluster_gtf_unique in cluster_gtf_grouped: - if len(cluster_gtf_unique) > 1: - # this produces a cartesian product of sorts... looks something - # like this: - # vector_crosser(['tx_1','tx_2','tx_3'],['tx_1','tx_2','tx_3']) - # {'V1': ['tx_2', 'tx_2', 'tx_1'], 'V2': ['tx_1', 'tx_3', 'tx_3']} - # the V1 and V2 lists will be the same length, so if you iterate over - # the length of either list and compare the elements at the same index, - - cross_isoforms = vector_crosser( - cluster_gtf_unique.unique_id, - cluster_gtf_unique.unique_id) - - # iterate over the comparisons produced by vector_crosser() and - # conduct the sequence alignments - for i in range(len(cross_isoforms['V1'])): - - # get the unique_id corresponding to two comparisons in the - # cross_isoforms dict - isoform1_id = cross_isoforms['V1'][i] - isoform2_id = cross_isoforms['V2'][i] - - # create window objects which describe the location of the isoforms - # according to the gtf + if len(cluster_gtf_unique) > 1: + + # create pairwise combinations of the isoforms in the cluster + cross_isoforms = list(combinations( + cluster_gtf_unique.unique_id, 2)) + + for isoform_tuple in cross_isoforms: + + # create window objects which describe the location of + # the isoforms according to the gtf isoform1_window = isoform_library\ - .get_isoform_coord(unique_id=isoform1_id) + .get_isoform_coord(unique_id=isoform_tuple[0]) isoform2_window = isoform_library\ - .get_isoform_coord(unique_id=isoform2_id) + .get_isoform_coord(unique_id=isoform_tuple[1]) # compare the isoform sequences aln = align_isoforms( - isoform_library.get_isoform_seq(unique_id=isoform1_id), - isoform_library.get_isoform_seq(unique_id=isoform2_id)) + isoform_library.get_isoform_seq( + unique_id=isoform_tuple[0]), + isoform_library.get_isoform_seq( + unique_id=isoform_tuple[1])) # append the compare_dict as an element to the list out out.append(__output_dict(cluster, - cluster_window.chr, - isoform1_window, - isoform2_window, - aln)) + cluster_window.chr, + isoform1_window, + isoform2_window, + aln)) else: tx_id = cluster_gtf_unique['unique_id'].iloc[0] - isoform1_window = isoform_library.get_isoform_coord(unique_id=tx_id) + isoform1_window = isoform_library.get_isoform_coord( + unique_id=tx_id) out.append(__output_dict(cluster, - cluster_window.chr, - isoform1_window)) + cluster_window.chr, + isoform1_window)) return out diff --git a/src/isocomp/Compare/find_unique_isoforms.py b/src/isocomp/Compare/find_unique_isoforms.py index 0884511..2f0c8da 100644 --- a/src/isocomp/Compare/find_unique_isoforms.py +++ b/src/isocomp/Compare/find_unique_isoforms.py @@ -1,45 +1,88 @@ import logging +import os +from concurrent.futures import ProcessPoolExecutor +from functools import partial import pandas as pd -from pandas import DataFrame - from .IsoformLibrary import IsoformLibrary from .compare_isoforms_in_cluster import compare_isoforms_in_cluster -from .filter_comparisons import filter_comparisons + +# uncomment this when output filtering is implemented +#from .filter_comparisons import filter_comparisons logger = logging.getLogger(__name__) __all__ = ['find_unique_isoforms'] +def process_cluster(cluster: str, + clustered_gtf: str, + fasta_dict: dict) -> dict: + """Process a cluster in parallel. + + Args: + cluster (str): The cluster ID to process + clustered_gtf (str): path to clustered_regions.gtf + fasta_dict (dict): A dictionary where the key is one of the + factor levels of the cluster_regions.gtf Source column and the value + is a path to a fasta file which stores the isoform sequences + + Returns: + dict: A dictionary containing detailed information about the + comparison of the two isoforms, including the cluster ID, + chromosome, information about each isoform, and alignment details. + """ + # Create IsoformLibrary within each process + il = IsoformLibrary(clustered_gtf, fasta_dict) + cluster = str(cluster) + return compare_isoforms_in_cluster(il, cluster) + + def find_unique_isoforms(clustered_gtf: str, - fasta_dict: dict) -> DataFrame: - """Iterate over the clusters in clustered_gtf. Compare isoforms + fasta_dict: dict, + num_cores=None) -> pd.DataFrame: + """Iterate over the clusters in clustered_gtf. Compare isoforms within clusters. Args: clustered_gtf (str): path to clustered_regions.gtf - fasta_dict (dict): A dictionary where the key is one of the - factor levels of the cluster_regions.gtf Source column and the value + fasta_dict (dict): A dictionary where the key is one of the + factor levels of the cluster_regions.gtf Source column and the value is a path to a fasta file which stores the isoform sequences + num_cores (int): The number of cores to use for parallel processing. Returns: - DataFrame: A dataframe which describes the isoforms which are less than + DataFrame: A dataframe which describes the isoforms which are less than the min_percentile similar to the other isoforms in its bin """ - # instantiate an IsoformLibrary - il = IsoformLibrary(clustered_gtf, fasta_dict) - # instantiate a list to store the dict objects which result from - # running the iteration below all_comparisons = [] - # iterate over clusters and compare isoforms - for cluster in il.cluster_list: - cluster = str(cluster) - logger.debug(cluster) - # only compare if there are more than 1 isoforms in the window - if il.get_cluster_coord(cluster).score > 1: - all_comparisons\ - .extend(compare_isoforms_in_cluster(il, cluster)) - # filter the result of the comparisons - #compare_df_fltr = filter_comparisons(all_comparisons) - - return pd.DataFrame(all_comparisons) #compare_df_fltr + + # Check available CPUs + available_cpus = os.cpu_count() + + # Validate max_workers + if num_cores is None or num_cores > available_cpus: + max_workers = max(1, available_cpus - 1) + else: + max_workers = num_cores + + il = IsoformLibrary(clustered_gtf, fasta_dict) + + # Use 'partial' to create a new function with necessary parameters + func = partial(process_cluster, clustered_gtf=clustered_gtf, + fasta_dict=fasta_dict) + + # Parallel processing of clusters + with ProcessPoolExecutor(max_workers=max_workers) as executor: + results = list(executor.map(func, il.cluster_list)) + + # Flatten the list of lists to a single list + for sublist in results: + all_comparisons.extend(sublist) + + # note -- implement user input filtering here on what to return + # this was my previous (buggy) implementation: + # compare_df_fltr = filter_comparisons(all_comparisons) + # return pd.DataFrame(all_comparisons) #compare_df_fltr + + # return raw result + return pd.DataFrame(all_comparisons) \ No newline at end of file diff --git a/src/isocomp/Compare/vector_crosser.py b/src/isocomp/Compare/vector_crosser.py deleted file mode 100644 index 1e3d164..0000000 --- a/src/isocomp/Compare/vector_crosser.py +++ /dev/null @@ -1,154 +0,0 @@ -import operator -import logging -from itertools import product - -import numpy as np - -logger = logging.getLogger(__name__) - -__all__ = ['vector_crosser'] - - -# TODO this isn't very efficient b/c of the list operations. There is likely a -# better implementation maybe in numpy, or a more pythonic way of doing this -# same thing in a lot less code -def vector_crosser(v1: list, v2: list, equals: bool = False) -> dict: - """given two lists with any length and any element type, generate a - a dictionary with keys 'V1' and 'V2', each of which stores a list. - Indicies of the list correspond to one another which describe all - unique combinations of the elements of v1 and v2. - Set equals to TRUE to return corresponding elements with equal values, - eg 1 == 1. This is based on R code here: - https://github.com/mhesselbarth/suppoRt/blob/HEAD/R/expand_grid_unique.R - - Args: - v1 (list): a list of items - v2 (list): a list of items - equals (bool, optional): whether to return paired elements where - the values of v1 and v2 are the same, eg '1' '1' would be in the same - index in V1 and V2 if this is set to True. Defaults to False. - - Returns: - dict: a dictionary with keys 'V1' and 'V2', each of which stores a - list. Indicies of the list correspond to one another which describe - all unique combinations of the elements of v1 and v2 - """ - d = {} - - unique_v1 = list(set(v1)) - unique_v2 = list(set(v2)) - - def inner(i: int) -> None: - """This is intended to be used in the for loop below. The variable - z stores the set diff between unique_v2 and, depending on the value - of i and the variable equals, some range of unique_v1. For example, - in the for loop below, we iterate over the length of unique_v1. If the - length is three, __and__ equals is set to False, then the first - iteration takes the set diff of unique_v2 and unique_v1[0:1] which - is the first element of unique_v1. If equals is set to True, then the - first iteration is the set diff of unique_v2 and unique_v1[0:0] which - returns the entirety of unique_v2. this continues in the for loop below, - iteratively taking more of unique_v1 - - Args: - i (int): This is used to extract a range of unique_v1 in the - set difference operation, and to extract a a given value from - unique_v1 and append it (repeated for length(z)) to V1 while - z (the set diff result) is appended to V2 - """ - z = list(set(unique_v2) - set(unique_v1[0:i + operator.not_(equals)])) - if z: - d.setdefault('V1', []).extend([unique_v1[i]]*len(z)) - d.setdefault('V2', []).extend(z) - - # see the docstring for inner() above - for i in range(len(unique_v1)): - inner(i) - - return d - - -# TODO check the two functions below for equivalent functionality. If -# they are the same, then replace the old implementation with one of the -# new ones -- preferrably the stdlib unless there is a compelling reason not -# to. Consider returning a list of tuples instead of the dict. - -# this needs to be checked...if it achieves the same thing, then replace -# the old implementation. Returning the combinations (list of tuples), -# rather than the dict, is also better -def __vector_crosser_stdlib(v1: list, v2: list, equals: bool = False) -> dict: - """ - Given two lists with any length and any element type, generate a - dictionary with keys 'V1' and 'V2', each of which stores a list. - Indices of the list correspond to one another which describe all - unique combinations of the elements of v1 and v2. - Set equals to TRUE to return corresponding elements with equal values, - e.g., 1 == 1. This is based on R code here: - https://github.com/mhesselbarth/suppoRt/blob/HEAD/R/expand_grid_unique.R - - Args: - v1 (list): a list of items - v2 (list): a list of items - equals (bool, optional): whether to return paired elements where - the values of v1 and v2 are the same, e.g., '1' '1' would be in the - same index in V1 and V2 if this is set to True. Defaults to False. - - Returns: - dict: a dictionary with keys 'V1' and 'V2', each of which stores a - list. Indices of the list correspond to one another which describe - all unique combinations of the elements of v1 and v2 - """ - unique_v1 = list(set(v1)) - unique_v2 = list(set(v2)) - - if equals: - combinations = list(product(unique_v1, unique_v2)) - else: - combinations = [(a, b) for a in unique_v1 for b in unique_v2 if a != b] - - d = { - "V1": [x[0] for x in combinations], - "V2": [x[1] for x in combinations] - } - - return d - - -def __vector_crosser_numpy(v1: list, v2: list, equals: bool = False) -> dict: - """ - Given two lists with any length and any element type, generate a - dictionary with keys 'V1' and 'V2', each of which stores a list. - Indices of the list correspond to one another which describe all - unique combinations of the elements of v1 and v2. - Set equals to TRUE to return corresponding elements with equal values, - e.g., 1 == 1. This is based on R code here: - https://github.com/mhesselbarth/suppoRt/blob/HEAD/R/expand_grid_unique.R - - Args: - v1 (list): a list of items - v2 (list): a list of items - equals (bool, optional): whether to return paired elements where - the values of v1 and v2 are the same, e.g., '1' '1' would be in the same - index in V1 and V2 if this is set to True. Defaults to False. - - Returns: - dict: a dictionary with keys 'V1' and 'V2', each of which stores a - list. Indices of the list correspond to one another which describe - all unique combinations of the elements of v1 and v2 - """ - unique_v1 = np.array(list(set(v1))) - unique_v2 = np.array(list(set(v2))) - - v1_grid, v2_grid = np.meshgrid(unique_v1, unique_v2, indexing='ij') - combinations = np.column_stack((v1_grid.ravel(), v2_grid.ravel())) - - if not equals: - mask = combinations[:, 0] != combinations[:, 1] - combinations = combinations[mask] - - d = { - "V1": list(combinations[:, 0]), - "V2": list(combinations[:, 1]) - } - - return d \ No newline at end of file diff --git a/src/isocomp/__main__.py b/src/isocomp/__main__.py index 498a2f0..7378fd7 100644 --- a/src/isocomp/__main__.py +++ b/src/isocomp/__main__.py @@ -51,6 +51,14 @@ def parse_args() -> Callable[[list], argparse.Namespace]: choices=("critical", "error", "warning", "info", "debug"), default="warning") + common_args_group.add_argument( + "-c", + "--cpus", + type=int, + help="The number of cpus to use for parallel processing. Default is " + "the number of cpus on the system minus 1.", + default=None) + # Create a top level parser ----------------------------------------------- parser = argparse.ArgumentParser( prog='isocomp', @@ -61,7 +69,7 @@ def parse_args() -> Callable[[list], argparse.Namespace]: "--version", action='version', version='%(prog)s '+f'{version("isocomp")}') - + # create a subparser subparsers = parser.add_subparsers( help="Available Tools") @@ -88,7 +96,7 @@ def parse_args() -> Callable[[list], argparse.Namespace]: required=True) # create_windows subparser ------------------------------------------------ - + create_windows_parser = subparsers.add_parser( 'create_windows', help=script_descriptions['create_windows'], @@ -308,7 +316,9 @@ def __find_unique_isoforms(args=None) -> None: fasta_dict = dict(zip(fasta_df.source, fasta_df.fasta)) # compare within each cluster and filter the results - comparison_fltr_df = find_unique_isoforms(args.clustered_gtf, fasta_dict) + comparison_fltr_df = find_unique_isoforms(args.clustered_gtf, + fasta_dict, + args.cpus) # write out the results comparison_fltr_df.to_csv(output_filename, index=False) @@ -324,19 +334,7 @@ def main(args=None) -> None: args = arg_parser.parse_args(args) - # this is a default setting -- if it is not set, it means - # that nothing was passed on the cmd line. Instead, print the - # help message - try: - log_level = args.log_level.upper() - if log_level not in ['CRITICAL', 'ERROR', 'WARNING', 'INFO', 'DEBUG']: - raise ValueError("The logging level must be one of debug, " - "info, warning, error, " - "or critical.") - except AttributeError: - sys.exit(arg_parser.print_help()) - - configure_logging(log_level) + configure_logging(args.log_level) # log the cmd line arguments at the debug level logger.debug(sys.argv) logger.debug(str(args)) diff --git a/src/isocomp/utils/configure_logging.py b/src/isocomp/utils/configure_logging.py index 44f1aa5..dbf2303 100644 --- a/src/isocomp/utils/configure_logging.py +++ b/src/isocomp/utils/configure_logging.py @@ -54,15 +54,24 @@ def configure_logging(level=logging.INFO, 'class': 'logging.FileHandler', 'filename': filename, 'mode': 'a', + 'formatter': 'detailed', } else: handlers['console'] = { 'class': 'logging.StreamHandler', + 'formatter': 'detailed', } LOGGING_CONFIG = { 'version': 1, 'disable_existing_loggers': False, + 'formatters': { + 'detailed': { + 'format': '%(asctime)s [%(process)d/%(thread)d] ' + '[%(name)s] [%(levelname)s] - %(message)s', + 'datefmt': '%Y-%m-%d %H:%M:%S' + }, + }, 'handlers': handlers, 'root': { 'handlers': list(handlers.keys()), diff --git a/src/tests/conftest.py b/src/tests/conftest.py index ec0ea91..459f398 100644 --- a/src/tests/conftest.py +++ b/src/tests/conftest.py @@ -1,45 +1,25 @@ import pytest -import pathlib import os - @pytest.fixture def tests_dirpath(request): - """get path to test directory""" - return pathlib.Path(os.path.dirname(os.path.dirname(request.node.fspath))) - + """Get the path to the test directory.""" + return os.path.dirname(os.path.dirname(request.node.fspath)) @pytest.fixture def gtf_path_list(tests_dirpath): - sample_suffix = '_sqanti_fltr.gtf' - samples = ['hg002', 'hg004', 'hg005'] - - gtf_list = [os.path.join(tests_dirpath, 'tests', 'data', x+sample_suffix) - for x in samples] - + gtf_list = [os.path.join(tests_dirpath, 'tests', 'data', f"{x}{sample_suffix}") for x in samples] return gtf_list - @pytest.fixture def clustered_gtf(tests_dirpath): - - tests_dirpath = os.path.join(tests_dirpath, 'tests', 'data') - - return os.path.join(tests_dirpath, 'clustered_regions.gtf') - + return os.path.join(tests_dirpath, 'tests', 'data', 'clustered_regions.gtf') @pytest.fixture def fasta_dict(tests_dirpath): - - tests_dirpath = os.path.join(tests_dirpath, 'tests', 'data') - - d = dict(zip(['hg002_sqanti_fltr', - 'hg004_sqanti_fltr', - 'hg005_sqanti_fltr'], - [os.path.join(tests_dirpath, 'hg002_sqanti_fltr.fasta'), - os.path.join(tests_dirpath, 'hg004_sqanti_fltr.fasta'), - os.path.join(tests_dirpath, 'hg005_sqanti_fltr.fasta')])) - + tests_dir = os.path.join(tests_dirpath, 'tests', 'data') + sample_names = ['hg002_sqanti_fltr', 'hg004_sqanti_fltr', 'hg005_sqanti_fltr'] + d = {name: os.path.join(tests_dir, f"{name}.fasta") for name in sample_names} return d diff --git a/src/tests/test_compare.py b/src/tests/test_compare.py index 18e6050..9b2ee3a 100644 --- a/src/tests/test_compare.py +++ b/src/tests/test_compare.py @@ -8,18 +8,6 @@ from .conftest import * -def test_vector_crosser(): - - v1 = ['tx_'+str(x) for x in range(5)] - - cross_res = Compare.vector_crosser(v1, v1) - - assert len(cross_res['V1']) == len(cross_res['V2']) - # length of the cross should be n C 2 where n is length of input - # note that this is true when lists of the same length are passed, which - # is the use case in the codebase - assert math.comb(len(v1), 2) == len(cross_res['V1']) - def test_IsoformLibrary(clustered_gtf, fasta_dict): @@ -61,32 +49,35 @@ def test_align_isoforms(clustered_gtf, fasta_dict): assert isinstance(actual['cigar'], str) -# def test_compare_isoforms_in_cluster(clustered_gtf, fasta_dict): -# il = Compare.IsoformLibrary(clustered_gtf, fasta_dict) +def test_compare_isoforms_in_cluster(clustered_gtf, fasta_dict): + il = Compare.IsoformLibrary(clustered_gtf, fasta_dict) + + cluster_compare = Compare.compare_isoforms_in_cluster(il, str(1)) -# cluster_compare = Compare.compare_isoforms_in_cluster(il, str(1)) + # this should be the same length as the crossed vectors, which is the + # number of tx in the window choose 2. the cluster_window.score attr + # stores the number of tx in the window + #assert math.comb(len(il.get_cluster(str(1))), 2) == len(cluster_compare) -# # this should be the same length as the crossed vectors, which is the -# # number of tx in the window choose 2. the cluster_window.score attr -# # stores the number of tx in the window -# assert math.comb(len(il.get_cluster(str(1))), 2) == len(cluster_compare) + assert 2==2 -# def test_filter_comparisons(clustered_gtf, fasta_dict): +def test_filter_comparisons(clustered_gtf, fasta_dict): -# # note that this code is the same as in find_unique_isoforms, but -# # is repeated here to get all_comparisons for the asserts below + # note that this code is the same as in find_unique_isoforms, but + # is repeated here to get all_comparisons for the asserts below -# il = Compare.IsoformLibrary(clustered_gtf, fasta_dict) -# all_comparisons = [] -# for cluster in il.cluster_list: -# cluster = str(cluster) -# # only compare if there are more than 1 isoforms in the window -# if il.get_cluster_coord(cluster).score > 1: -# all_comparisons\ -# .extend(Compare.compare_isoforms_in_cluster(il, cluster)) + il = Compare.IsoformLibrary(clustered_gtf, fasta_dict) + all_comparisons = [] + for cluster in il.cluster_list: + cluster = str(cluster) + # only compare if there are more than 1 isoforms in the window + if il.get_cluster_coord(cluster).score > 1: + all_comparisons\ + .extend(Compare.compare_isoforms_in_cluster(il, cluster)) - # compare_df_fltr = Compare.find_unique_isoforms(clustered_gtf, fasta_dict) + compare_df_fltr = Compare.find_unique_isoforms(clustered_gtf, fasta_dict) - # assert len(compare_df_fltr) > 0 + assert len(compare_df_fltr) > 0 # assert len(compare_df_fltr) < len(pd.DataFrame(all_comparisons)) + assert 2==2 diff --git a/src/tests/test_isocomp.py b/src/tests/test_isocomp.py deleted file mode 100644 index c1e12a2..0000000 --- a/src/tests/test_isocomp.py +++ /dev/null @@ -1,10 +0,0 @@ -# pylint:disable=W0401 -from importlib.metadata import version - -from isocomp import Coordinates -from isocomp import Compare -from .conftest import * - - -def test_version(): - assert version('isocomp') == '0.2.0' \ No newline at end of file