bwamem 0.0.1__tar.gz

bwamem-0.0.1/LICENSE.md

@@ -0,0 +1,364 @@
+This Source Code Form is subject to the terms of the Mozilla Public
+License, v. 2.0. If a copy of the MPL was not distributed with this
+file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+(c) 2016 Oxford Nanopore Technologies Ltd.
+
+
+Mozilla Public License Version 2.0
+==================================
+
+### 1. Definitions
+
+**1.1. “Contributor”**  
+    means each individual or legal entity that creates, contributes to
+    the creation of, or owns Covered Software.
+
+**1.2. “Contributor Version”**  
+    means the combination of the Contributions of others (if any) used
+    by a Contributor and that particular Contributor's Contribution.
+
+**1.3. “Contribution”**  
+    means Covered Software of a particular Contributor.
+
+**1.4. “Covered Software”**  
+    means Source Code Form to which the initial Contributor has attached
+    the notice in Exhibit A, the Executable Form of such Source Code
+    Form, and Modifications of such Source Code Form, in each case
+    including portions thereof.
+
+**1.5. “Incompatible With Secondary Licenses”**  
+    means
+
+* **(a)** that the initial Contributor has attached the notice described
+    in Exhibit B to the Covered Software; or
+* **(b)** that the Covered Software was made available under the terms of
+    version 1.1 or earlier of the License, but not also under the
+    terms of a Secondary License.
+
+**1.6. “Executable Form”**  
+    means any form of the work other than Source Code Form.
+
+**1.7. “Larger Work”**  
+    means a work that combines Covered Software with other material, in 
+    a separate file or files, that is not Covered Software.
+
+**1.8. “License”**  
+    means this document.
+
+**1.9. “Licensable”**  
+    means having the right to grant, to the maximum extent possible,
+    whether at the time of the initial grant or subsequently, any and
+    all of the rights conveyed by this License.
+
+**1.10. “Modifications”**  
+    means any of the following:
+
+* **(a)** any file in Source Code Form that results from an addition to,
+    deletion from, or modification of the contents of Covered
+    Software; or
+* **(b)** any new file in Source Code Form that contains any Covered
+    Software.
+
+**1.11. “Patent Claims” of a Contributor**  
+    means any patent claim(s), including without limitation, method,
+    process, and apparatus claims, in any patent Licensable by such
+    Contributor that would be infringed, but for the grant of the
+    License, by the making, using, selling, offering for sale, having
+    made, import, or transfer of either its Contributions or its
+    Contributor Version.
+
+**1.12. “Secondary License”**  
+    means either the GNU General Public License, Version 2.0, the GNU
+    Lesser General Public License, Version 2.1, the GNU Affero General
+    Public License, Version 3.0, or any later versions of those
+    licenses.
+
+**1.13. “Source Code Form”**  
+    means the form of the work preferred for making modifications.
+
+**1.14. “You” (or “Your”)**  
+    means an individual or a legal entity exercising rights under this
+    License. For legal entities, “You” includes any entity that
+    controls, is controlled by, or is under common control with You. For
+    purposes of this definition, “control” means **(a)** the power, direct
+    or indirect, to cause the direction or management of such entity,
+    whether by contract or otherwise, or **(b)** ownership of more than
+    fifty percent (50%) of the outstanding shares or beneficial
+    ownership of such entity.
+
+
+### 2. License Grants and Conditions
+
+#### 2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+* **(a)** under intellectual property rights (other than patent or trademark)
+    Licensable by such Contributor to use, reproduce, make available,
+    modify, display, perform, distribute, and otherwise exploit its
+    Contributions, either on an unmodified basis, with Modifications, or
+    as part of a Larger Work; and
+* **(b)** under Patent Claims of such Contributor to make, use, sell, offer
+    for sale, have made, import, and otherwise transfer either its
+    Contributions or its Contributor Version.
+
+#### 2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+#### 2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+* **(a)** for any code that a Contributor has removed from Covered Software;
+    or
+* **(b)** for infringements caused by: **(i)** Your and any other third party's
+    modifications of Covered Software, or **(ii)** the combination of its
+    Contributions with other software (except as part of its Contributor
+    Version); or
+* **(c)** under Patent Claims infringed by Covered Software in the absence of
+    its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+#### 2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+#### 2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+#### 2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+#### 2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+
+### 3. Responsibilities
+
+#### 3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+#### 3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+* **(a)** such Covered Software must also be made available in Source Code
+    Form, as described in Section 3.1, and You must inform recipients of
+    the Executable Form how they can obtain a copy of such Source Code
+    Form by reasonable means in a timely manner, at a charge no more
+    than the cost of distribution to the recipient; and
+
+* **(b)** You may distribute such Executable Form under the terms of this
+    License, or sublicense it under different terms, provided that the
+    license for the Executable Form does not attempt to limit or alter
+    the recipients' rights in the Source Code Form under this License.
+
+#### 3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+#### 3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+#### 3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+
+### 4. Inability to Comply Due to Statute or Regulation
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: **(a)** comply with
+the terms of this License to the maximum extent possible; and **(b)**
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+
+### 5. Termination
+
+**5.1.** The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated **(a)** provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and **(b)** on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+**5.2.** If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+**5.3.** In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+
+### 6. Disclaimer of Warranty
+
+> Covered Software is provided under this License on an “as is”
+> basis, without warranty of any kind, either expressed, implied, or
+> statutory, including, without limitation, warranties that the
+> Covered Software is free of defects, merchantable, fit for a
+> particular purpose or non-infringing. The entire risk as to the
+> quality and performance of the Covered Software is with You.
+> Should any Covered Software prove defective in any respect, You
+> (not any Contributor) assume the cost of any necessary servicing,
+> repair, or correction. This disclaimer of warranty constitutes an
+> essential part of this License. No use of any Covered Software is
+> authorized under this License except under this disclaimer.
+
+### 7. Limitation of Liability
+
+> Under no circumstances and under no legal theory, whether tort
+> (including negligence), contract, or otherwise, shall any
+> Contributor, or anyone who distributes Covered Software as
+> permitted above, be liable to You for any direct, indirect,
+> special, incidental, or consequential damages of any character
+> including, without limitation, damages for lost profits, loss of
+> goodwill, work stoppage, computer failure or malfunction, or any
+> and all other commercial damages or losses, even if such party
+> shall have been informed of the possibility of such damages. This
+> limitation of liability shall not apply to liability for death or
+> personal injury resulting from such party's negligence to the
+> extent applicable law prohibits such limitation. Some
+> jurisdictions do not allow the exclusion or limitation of
+> incidental or consequential damages, so this exclusion and
+> limitation may not apply to You.
+
+
+### 8. Litigation
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+
+### 9. Miscellaneous
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+
+### 10. Versions of the License
+
+#### 10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+#### 10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+#### 10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+#### 10.4. Distributing Source Code Form that is Incompatible With Secondary Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+## Exhibit A - Source Code Form License Notice
+
+    This Source Code Form is subject to the terms of the Mozilla Public
+    License, v. 2.0. If a copy of the MPL was not distributed with this
+    file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+## Exhibit B - “Incompatible With Secondary Licenses” Notice
+
+    This Source Code Form is "Incompatible With Secondary Licenses", as
+    defined by the Mozilla Public License, v. 2.0.
+
+

bwamem-0.0.1/MANIFEST.in

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+include README.md
+include LICENSE.md
+include pyproject.toml
+include setup.py
+include MANIFEST.in
+recursive-include bwa *.h *.c *.a *.o
+recursive-include bwamem *.py *.c
+recursive-include tests *.py
+global-exclude *.pyc
+global-exclude __pycache__
+global-exclude .git*

bwamem-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: bwamem
+Version: 0.0.1
+Summary: Bindings to bwa aligner
+Author-email: Chang Ye <yech1990@gmail.com>
+Maintainer-email: Chang Ye <yech1990@gmail.com>
+License-Expression: MPL-2.0
+Project-URL: Homepage, https://github.com/y9c/bwamem
+Project-URL: Repository, https://github.com/y9c/bwamem
+Project-URL: Documentation, https://y9c.github.io/bwamem/
+Project-URL: Bug Tracker, https://github.com/y9c/bwamem/issues
+Keywords: bioinformatics,alignment,bwa,genomics
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: MacOS
+Classifier: Programming Language :: C
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: cffi>=1.0.0
+Provides-Extra: dev
+Requires-Dist: pytest>=6.0; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Dynamic: license-file
+
+bwamem
+======
+
+Python bindings to `bwa mem` aligner; sufficient to load and index and perform
+alignments of sequences to the index to obtain basic statistics.
+
+These python bindings are licensed under Mozilla Public License 2.0, bwa is licenced
+under GNU General Public License v3.0.
+
+Documentation can be found at https://y9c.github.io/bwamem/.
+
+Installation
+------------
+
+The git source repository contains bwa as a submodule. The repository should therefore
+be cloned using the recursive option.
+
+The package `setup.py` script requires `libbwa.a` to have been built in the submodule
+directory before running. This can be performed via the `libbwa.a` target, which first
+makes some amendments to the bwa/Makefile. To build and install the package one should
+therefore run:
+
+    git clone --recursive https://github.com/y9c/bwamem.git
+    cd bwamem
+    make bwa/libbwa.a 
+    python setup.py install
+
+
+Building BWA Indexes
+--------------------
+
+The `BwaIndexer` class provides a pythonic interface to build BWA indexes from
+FASTA files. It supports different BWT construction algorithms:
+
+```python
+from bwamem import BwaIndexer
+
+# Create indexer with default settings (auto algorithm)
+indexer = BwaIndexer()
+
+# Build index from FASTA file
+index_path = indexer.build_index('reference.fa')
+print(f'Index built at: {index_path}')
+
+# Use specific algorithm
+indexer = BwaIndexer(algorithm='is')  # or 'rb2', 'bwtsw', 'auto'
+index_path = indexer.build_index('reference.fa', prefix='my_index')
+```
+
+Available algorithms:
+- `auto`: Automatically choose algorithm based on genome size
+- `rb2`: RB2 algorithm (good for medium genomes)
+- `bwtsw`: BWT-SW algorithm (good for large genomes)
+- `is`: IS algorithm (good for small genomes)
+
+Performing Alignments
+---------------------
+
+The `BwaAligner` class provides a pythonic interface to `bwa mem` aligner. It
+takes as input a bwa index fileset on construction and can then be used to find
+alignments of sequences given as strings.
+
+### Single-End Alignment
+
+For single-end reads, use the `align()` method with one sequence:
+
+```python
+from bwamem import BwaAligner, Alignment
+index = 'path/to/index' # the path given to bwa index
+seq = 'ACGATCGCGATCGA'
+
+aligner = BwaAligner(index)
+alignments = aligner.align(seq)  # Returns tuple of Alignment objects
+print('Found {} alignments.'.format(len(alignments)))
+for aln in alignments:
+    print(f'  {aln.rname}:{aln.pos} {aln.orient} {aln.cigar} (mapq={aln.mapq}, score={aln.score})')
+```
+
+### Paired-End Alignment
+
+For paired-end reads, use the `align()` method with two sequences:
+
+```python
+from bwamem import BwaAligner, PairedAlignment
+index = 'path/to/index'
+read1 = 'ACGATCGCGATCGA'
+read2 = 'TTCGATCGATCGAT'
+
+aligner = BwaAligner(index)
+paired_alignments = aligner.align(read1, read2)  # Returns tuple of PairedAlignment objects
+print('Found {} paired alignments.'.format(len(paired_alignments)))
+for pe_aln in paired_alignments:
+    print(f'  Read1: {pe_aln.read1.rname}:{pe_aln.read1.pos} {pe_aln.read1.orient}')
+    print(f'  Read2: {pe_aln.read2.rname}:{pe_aln.read2.pos} {pe_aln.read2.orient}')
+    print(f'  Proper pair: {pe_aln.is_proper_pair}, Insert size: {pe_aln.insert_size}')
+```
+
+### Custom Insert Size Distribution
+
+For paired-end reads, you can specify the expected insert size distribution:
+
+```python
+# With custom insert size parameters
+paired_alignments = aligner.align(read1, read2, insert_size=500, insert_std=50)
+```
+
+### Data Structures
+
+**Alignment** (for single-end reads):
+```python
+Alignment(rname='chr1', orient='+', pos=1000, mapq=60, cigar='100M', NM=0, score=100, is_primary=True)
+```
+
+**PairedAlignment** (for paired-end reads):
+```python
+PairedAlignment(read1=Alignment(...), read2=Alignment(...), is_proper_pair=True, insert_size=500)
+```
+
+### Alignment Parameters
+
+Alignment parameters can be given as they are on the `bwa mem` command line:
+
+```python
+from bwamem import BwaAligner
+index = 'path/to/index'
+options = '-x ont2d -A 1 -B 0'
+aligner = BwaAligner(index, options=options)
+```
+
+The package now supports all BWA MEM options including paired-end specific parameters like insert size distribution (`-I` option).
+
+Complete Workflow Example
+-------------------------
+
+Here's a complete example showing how to build an index and perform both single-end and paired-end alignments:
+
+```python
+from bwamem import BwaIndexer, BwaAligner, Alignment, PairedAlignment
+
+# Step 1: Build index from FASTA file
+indexer = BwaIndexer(algorithm='auto')
+index_path = indexer.build_index('reference.fa')
+print(f'Index built at: {index_path}')
+
+# Step 2: Create aligner with the index
+aligner = BwaAligner(index_path)
+
+# Step 3a: Single-end alignment
+print("Single-end alignments:")
+se_sequences = ['ACGATCGCGATCGA', 'GCTAGCTAGCTAG']
+for i, seq in enumerate(se_sequences, 1):
+    alignments = aligner.align(seq)
+    print(f'Found {len(alignments)} alignments for sequence {i}')
+    for aln in alignments:
+        print(f'  {aln.rname}:{aln.pos} {aln.orient} {aln.cigar} (mapq={aln.mapq})')
+
+# Step 3b: Paired-end alignment
+print("\nPaired-end alignments:")
+pe_reads = [
+    ('ACGATCGCGATCGA', 'TTCGATCGATCGAT'),
+    ('GCTAGCTAGCTAG', 'CGATCGATCGATC')
+]
+for i, (read1, read2) in enumerate(pe_reads, 1):
+    paired_alignments = aligner.align(read1, read2)
+    print(f'Found {len(paired_alignments)} paired alignments for read pair {i}')
+    for pe_aln in paired_alignments:
+        print(f'  Read1: {pe_aln.read1.rname}:{pe_aln.read1.pos} {pe_aln.read1.orient}')
+        print(f'  Read2: {pe_aln.read2.rname}:{pe_aln.read2.pos} {pe_aln.read2.orient}')
+        print(f'  Proper pair: {pe_aln.is_proper_pair}, Insert size: {pe_aln.insert_size}')
+
+# Step 3c: Paired-end with custom insert size
+print("\nPaired-end with custom insert size:")
+pe_alignments = aligner.align('ACGATCGCGATCGA', 'TTCGATCGATCGAT', 
+                             insert_size=500, insert_std=50)
+print(f'Found {len(pe_alignments)} alignments with custom insert size')
+```
+
+### Advanced Paired-End Features
+
+```python
+# Filter for proper pairs only
+proper_pairs = [pe for pe in pe_alignments if pe.is_proper_pair]
+print(f'Found {len(proper_pairs)} proper pairs')
+
+# Access individual read alignments
+for pe_aln in pe_alignments:
+    read1_aln = pe_aln.read1
+    read2_aln = pe_aln.read2
+    if read1_aln.is_primary and read2_aln.is_primary:
+        print(f'Primary alignment: {read1_aln.rname}:{read1_aln.pos}-{read2_aln.pos}')
+
+```