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