## Dark matter
A collection of Python tools for filtering and visualizing
[Next Generation Sequencing](https://en.wikipedia.org/wiki/DNA_sequencing#Next-generation_methods)
reads.
Runs under Python 2.7, 3.5, and 3.6. [Change log](CHANGELOG.md)
[](https://travis-ci.org/acorg/dark-matter)
## Installation
You should be able to install via
```sh
$ pip install dark-matter
```
Some additional information is available for
[Linux](doc/linux.md), [OS X](doc/mac.md), and [Windows](doc/windows.md).
## iPython Notebook
If you are using dark matter in an
[iPython Notebook](https://ipython.org/notebook.html), you should install
the requirements in `requirements-ipynb.txt`.
## Development
If you are using dark matter as a developer, you should install the
requirements in `requirements-dev.txt`.
PyPI 官网下载 | dark-matter-3.0.38.tar.gz
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PyPI 官网下载 | dark-matter-3.0.38.tar.gz （151个子文件） 
setup.cfg 38B README.md 875B PKG-INFO 738B PKG-INFO 738B test_reads.py 120KB reads.py 54KB test_fasta.py 46KB test_titles.py 41KB test_sam.py 39KB graphics.py 37KB test_proteins.py 36KB proteins.py 35KB aa.py 30KB test_aa.py 27KB sam.py 25KB test_dna.py 24KB test_features.py 23KB test_intervals.py 21KB fasta-identity-table.py 20KB titles.py 19KB fasta.py 18KB noninteractive-alignment-panel.py 18KB filter.py 17KB alignments.py 16KB mutations.py 16KB local_align.py 14KB test_filter.py 14KB conversion.py 13KB conversion.py 12KB features.py 12KB test_local_align.py 12KB alignments.py 11KB test_utils.py 11KB html.py 10KB test_summarize.py 10KB write-htcondor-job-spec.py 9KB alignments.py 9KB hsp.py 9KB filter-reads-alignments.py 8KB proteins-to-pathogens.py 8KB hsp.py 7KB compare-consensuses.py 7KB test_alignments.py 7KB hsp.py 7KB test_fasta_ss.py 7KB utils.py 6KB compare-sequences.py 6KB intervals.py 6KB dna.py 6KB split-fasta-by-adaptors.py 6KB filter-hits-to-fasta.py 6KB test_sequence.py 6KB test_btop.py 5KB test_hsp.py 5KB test_fastq.py 5KB test_analyze_reads.py 4KB test_mutations.py 4KB consensus.py 4KB get-reads.py 4KB filter-fasta-by-taxonomy.py 4KB summarize.py 4KB setup.py 4KB filter-sam.py 4KB fasta-split-by-id.py 4KB fasta_ss.py 4KB sam-to-fasta-alignment.py 3KB test_dimension.py 3KB filter-fasta.py 3KB filter-fasta-by-complexity.py 3KB check-fasta-json-blast-consistency.py 3KB fasta-base-indices.py 3KB sequence.py 3KB extract-ORFs.py 3KB summarize-fasta-bases.py 3KB orfs.py 3KB process.py 3KB test_html.py 2KB make-fasta-database.py 2KB btop.py 2KB taxonomy.py 2KB score.py 2KB get-features.py 2KB sam-reference-read-counts.py 2KB test_simplify.py 2KB fasta-to-phylip.py 2KB trim-primers.py 2KB params.py 2KB dna-to-aa.py 2KB test_score.py 2KB fasta-subset.py 2KB local-align.py 2KB convert-diamond-to-json.py 2KB newick-to-ascii.py 2KB distance.py 1KB fastq.py 1KB test_taxonomy.py 1KB analyze_reads.py 1KB aa-info.py 1KB codon-distance.py 1KB score.py 1KB共 151 条
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