biopython-1.80.patch: add; migrate away from Bio.SubsMat.
This patch fixes build time test failures with Biopython 1.80 caused
by removal of Bio.SubsMat in favor of Bio.Align.substitution_matrices.
Closes: 1024835
Etienne Mollier
1 year, 4 months ago
| 0 | Description: port python-pauvre to python-biopython 1.80. | |
| 1 | Author: Étienne Mollier <emollier@debian.org> | |
| 2 | Bug: https://github.com/conchoecia/pauvre/issues/45 | |
| 3 | Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1024835 | |
| 4 | Forwarded: https://github.com/conchoecia/pauvre/pull/46 | |
| 5 | Last-Update: 2022-12-18 | |
| 6 | --- | |
| 7 | This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ | |
| 8 | --- python-pauvre.orig/pauvre/browser.py | |
| 9 | +++ python-pauvre/pauvre/browser.py | |
| 10 | @@ -49,7 +49,6 @@ | |
| 11 | ||
| 12 | # Biopython stuff | |
| 13 | from Bio import SeqIO | |
| 14 | -import Bio.SubsMat.MatrixInfo as MI | |
| 15 | ||
| 16 | ||
| 17 | class PlotCommand: | |
| 18 | --- python-pauvre.orig/pauvre/synplot.py | |
| 19 | +++ python-pauvre/pauvre/synplot.py | |
| 20 | @@ -43,7 +43,7 @@ | |
| 21 | ||
| 22 | # Biopython stuff | |
| 23 | from Bio import SeqIO | |
| 24 | -import Bio.SubsMat.MatrixInfo as MI | |
| 25 | +from Bio.Align import substitution_matrices | |
| 26 | ||
| 27 | # following this tutorial to install helvetica | |
| 28 | # https://github.com/olgabot/sciencemeetproductivity.tumblr.com/blob/master/posts/2012/11/how-to-set-helvetica-as-the-default-sans-serif-font-in.md | |
| 29 | @@ -171,8 +171,9 @@ | |
| 30 | def black_colormap(): | |
| 31 | zeroone = np.linspace(0, 1, 100) | |
| 32 | colorrange = [(0,0,0,x) for x in zeroone] | |
| 33 | - minblosum = min(MI.blosum62.values()) | |
| 34 | - maxblosum = max(MI.blosum62.values()) | |
| 35 | + blosumvals = substitution_matrices.load("BLOSUM62").values() | |
| 36 | + minblosum = int(min(blosumvals)) | |
| 37 | + maxblosum = int(max(blosumvals)) | |
| 38 | colormap = {i: colorrange[int(translate(i, minblosum, maxblosum, 0, 99))] | |
| 39 | for i in range(minblosum, maxblosum + 1, 1)} | |
| 40 | return colormap | |
| 41 | @@ -479,7 +480,9 @@ | |
| 42 | # this needs to be increased by the bar_thickness (0.9 * track_width in this case, or 0.09) | |
| 43 | y2 = len(optGFFs) - 2 - i | |
| 44 | myPatches = plot_synteny(seq1, ind1, seq2, ind2, y1, y2, | |
| 45 | - featType, MI.blosum62, cm, seqname) | |
| 46 | + featType, | |
| 47 | + substitution_matrices.load("BLOSUM62"), | |
| 48 | + cm, seqname) | |
| 49 | for patch in myPatches: | |
| 50 | allPatches.append(patch) | |
| 51 |