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        "author": "Noah Hoffman",
        "author_email": "noah.hoffman@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Operating System :: POSIX",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6"
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        "description": "=======\n alnvu\n=======\n\n``alnvu`` makes a multiple alignment of biological sequences more\neasily readable by condensing it and highlighting variability.\n\nProduces formatted multiple alignments in plain text, html, and pdf.\n\n.. image:: https://travis-ci.org/nhoffman/alnvu.svg?branch=master\n    :target: https://travis-ci.org/nhoffman/alnvu\n\nauthors\n=======\n\n * Noah Hoffman\n * Chris Small\n * Connor McCoy\n * Tim Holland\n\n\ndependencies\n============\n\nRequired:\n\n * Python 2.7, 3.5+\n * ``fastalite`` (https://github.com/nhoffman/fastalite)\n\nOptional:\n\n * ``reportlab`` (http://www.reportlab.com/software/opensource/) for pdf output.\n * ``biopython`` (http://biopython.org/) to sort alignments in tree order.\n * ``Jinja2`` (http://jinja.pocoo.org/) for rendering html templates.\n\ninstallation\n============\n\nInstallation is easiest using ``pip``::\n\n  pip install alnvu\n\nTo install from the sources on GitHub, first clone the repository.\n\nUsing ``setup.py``::\n\n  cd alnvu\n  python setup.py install\n\nUsing ``pip``::\n\n  cd alnvu\n  pip install .\n\n\nexamples\n========\n\n    % cd alnvu\n\nThe default output. Note that columns are numbered (column 8 is the first shown, column 122 is the last)::\n\n    % ./av -w 80 testfiles/aln.fasta | head -n 15\n         # 00000000000000000000000000000000000000000000000000000000000000000000000000000000\n         # 00000000000000000000000000000000000000000000000000000000000000000000000000000000\n         # 00111111111122222222223333333333444444444455555555556666666666777777777788888888\n         # 89012345678901234567890123456789012345678901234567890123456789012345678901234567\n     59735 agagtttgatcctggctcaggacgaacgcTGGCGGCgtGCTTAACACATGCAAGTCGAACGaTgAAgcggtGCTTgcacc\n     70875 --------------------------------------------------------------------------------\n     58095 agagtttgatcctggctcagagcgaacgcTGGCGGCatGCTTAACACATGCAAGTCGcACGGgtggtttcgGCcatc---\n     70854 -----------------------------TGGCGGCagGCcTAACACATGCAAGTCGAgCGGatgAcgggAGCTTgctcc\n     62024 agagtttgatcctggctcaggacgaacgcTGGCGGCgtGCTTAACACATGCAAGTCGAACGaTgAAgcctttCggggtgg\n     59895 ---------------------------------------------------AAGTCGAACGGTgAAagagAGCTTagctc\n     57728 -----------------------------------------------------------tt-------------------\n     10734 ---------------------------gcTGaCGGCgtGCTTAACACATGCAAGTCGAACGGgatccattAGCgcttttg\n     71041 --------------------------cgcTGGCGGCagGCTTAACACATGCAAGTCGAACGaTgAAgtctAGCTTgctag\n     6161O -----------------------------TGGCGGt-gGCcTAACACATGCAAGTCGAACGGatccttcggGaTT-----\n\nThe input file can be provided via stdin::\n\n   % cat testfiles/aln.fasta | av\n\nExercising some of the options (show sequence numbers and a consensus; show differences with first sequence, restrict to columns 200-280)::\n\n  % av testfiles/aln.fasta --number-sequences --consensus --range 200,280 --compare-to 59735\n\t\t  # 000000000000000000000000000000000000000000000000000000000000000000000000000000000\n\t\t  # 222222222222222222222222222222222222222222222222222222222222222222222222222222222\n\t\t  # 000000000011111111112222222222333333333344444444445555555555666666666677777777778\n\t\t  # 012345678901234567890123456789012345678901234567890123456789012345678901234567890\n   1 ==REF==> 59735 TGGGGtG-TTGGTgGAAAGCgttatgga------------GTGGTTTTAGATGGGCTCACGGCCTATCAGCTTGTTGGTGA\n   2          70875 gGGt----------GAAAGtGggggaccgcaaggcctc--acGcagcagGAgcGGCcgAtGtCtgATtAGCTaGTTGGTGg\n   3          58095 gGcc----------cAAAGCcgaAaG--------------GcGccTTTgGAgcGGCctgCGtCCgATtAGgTaGTTGGTGg\n   4          70854 gGGa----------GAAAGCaggggaccttcgggcctt--GcGcTaTcAGATGaGCctAgGtCggATtAGCTaGTTGGTGg\n   5          62024 TGGGa-c-ggGGTtaAAAGCtccg----------------GcGGTgaagGATGaGCcCgCGGCCTATCAGCTTGTTGGTGg\n   6          59895 TcttcaG-caGcTGGAAAGaaTT-----------------tcGGTcaggGATGaGCTCgCGGCCTATCAGCTTGTTGGTGA\n   7          57728 TcGaG-GaTaGaT-GAAAGgtggcctctacatgtaagctatcacTgaagGAgGGGaTtgCGtCtgATtAGCTaGTTGGaGg\n   8          10734 TGGGG-t-TgttgGGAAAGgtTTtTt--------------cTGGaTTggGATGGGCTCgCGGCtTATCAGCTTGTTGGTGg\n   9          71041 gaGa----------GAAAGgGggcTtttagctc-------tcGcTaaTAGATGaGCctAaGtCggATtAGCTaGTTGGTGg\n  10          6161O gGGG----------GAAAGatTTA----------------tcGccaTTgGAgcGGCcCgCGtCtgATtAGCTaGTTGGTGg\n  11      CONSENSUS xGGx------x-x-GAAAGxxxxxxx--------------xcGcTxxxgGATGGGCcxgCGtCxgATtAGCTaGTTGGTGg\n\n\nThe above alignment rendered as colored html (thanks @timholl)::\n\n  % av testfiles/aln.fasta --number-sequences --consensus --range 200,280 --compare-to 59735 -q --html aln.html\n\n.. image:: https://github.com/nhoffman/alnvu/raw/master/doc/html.png\n\nWrite a single-page pdf file::\n\n  % av testfiles/aln.fasta --pdf test.pdf --quiet --blocks-per-page=5\n\nAnd do you know about ``seqmagick``? If not, run, don't walk to\nhttps://github.com/fhcrc/seqmagick and check it out, so that you can\ndo this::\n\n    % seqmagick convert testfiles/ae_like.sto --output-format=fasta - | av -cx\n\t\t   # 000000000000000000000000000000000\n\t\t   # 445555555555566666666666666667777\n\t\t   # 990111111155813445566778888991122\n\t\t   # 791123678914209568907050235891215\n      GA05AQR01D2ULR ...............TTGGT.GT..AG...A..\n      GA05AQR01DFGSE ........................T.TAAGT..\n      GA05AQR01CI0QB ...........A.....................\n      GA05AQR01DW22X .TC..G.T.T.......................\n      GA05AQR01A5WF4 ....................A........-T..\n      GA05AQR01BUV2U ---..............................\n      GA05AQR01B1R8I .............T...............CT..\n      GA05AQR02JASPX ........A........................\n      GCX02B001AYSTJ .............................-TA.\n      GCX02B001DP9EQ ............A..........CA.......T\n      GCX02B001AFAY1 ..............G..................\n      GCX02B002J489C ...-......A......................\n      GLKT0ZE01EDLCP AT...ATT.T.......................\n      GLKT0ZE02I8LRD ---GA............................\n    -ref-> CONSENSUS TCTAGCGCGCGGGGACGAACGAGGCGCGCTGGA",
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