Diego Javier Zea

Bad PDF files which have junk characters before header and after EOF marker error unexpected character.

4

Hi! I found the `Unexpected character` error while parsing many of my PDFs. Here is one example of a PDF giving me that error: https://drive.google.com/file/d/1YXdN7TfwK87_5ekbUElYRFOkVLifKj1F/view?usp=sharing ```julia julia> pdDocOpen("/home/diego/Downloads/Vernon et al....

Lasso and mouse/keyboard zooming and panning are not working

1

Hi! I have found this issue using Immerse v1.0.1 in Julia 1.6.2 (Ubuntu 18.04): ```julia julia> using Immerse, Distributions Gtk-Message: 13:44:24.950: Failed to load module "canberra-gtk-module" Gtk-Message: 13:44:24.951: Failed to...

LocalAlignment find lower score than biopython/scikit-bio implementations

5

While I was benchmarking Julia's `pairalign` (318 μs) against BioPython (7310 µs) and scikit-bio (925 µs) implementation, I found that Julia's local alignment returns a solution with score 63 while...

DataInspector is failing with WGLMakie

2

Hi! With this code (using WGLMakie 0.4.6 and Julia 1.6.2): ```julia using WGLMakie x = 0:0.075:10 plt = lines(x, sin.(x), cos.(x)) DataInspector(plt.figure) ``` I get the following error: ```julia MethodError:...

Hi! I would be great if Lint.jl could catch situations where mutating functions are not named with the bang at the end. i.e. ```julia my_fill(x) = fill!(x, zero(eltype(x))) function add_one(x)...

parsenewick can parse Newick files with support values instead of node names

6

Hi! Readding files from PhyML and FastTree like the following one gives an error with Phylo when support values are duplicated in the tree: ``` (A9CIT6:0.59280764,P51981:0.55926221,(Q8A861:0.99105703,((Q81IL5:0.76431643,((((A1B198:0.94287572,(Q2U1E8:0.71410953,Q5LT20:0.55480466)0.975579:0.21734008)1.000000:0.55075633,(Q92YR6:1.11236546,(((Q13PB7:1.33807955,(Q161M1:1.17720944,A1AYL4:0.93440931)0.784619:0.18922325)0.878426:0.09769089,((((Q1ASJ4:1.28537785,(A8LS88:0.87558406,(C1DMY1:0.14671933,(P77215:0.02112667,Q8ZNF9:0.01593493)1.000000:0.35900384)1.000000:0.81055398)0.999947:0.27041496)0.403932:0.04809748,(A4YVM8:1.35286455,(Q9RKF7:0.83804265,((Q8ZL58:0.21550115,Q12GE3:0.23170031)1.000000:0.65091551,(Q7CU39:0.71681321,(Q8P3K2:0.27030998,(Q1GLV3:0.34268834,Q7L5Y1:0.42965239)0.843769:0.09133540)1.000000:1.04593860)0.978319:0.19792131)0.995516:0.18393058)0.684889:0.10148106)0.965570:0.12638685)0.999013:0.10597436,(((A0A0H3LM82:1.53892471,(O06741:1.56982104,(G0L7B8:0.68911617,A9CEQ8:0.63642012)0.999148:0.26000097)0.760390:0.07007390)0.534387:0.04760860,(A0A0H3LT39:0.95322505,(Q3HKK5:1.65509086,(A8H7M5:1.21743086,A8H9D1:0.47372214)0.711619:0.14571049)0.992889:0.20930969)0.824619:0.10359095)0.957749:0.09170993,(((Q8ZNH1:0.35062372,Q5NN22:0.45517287)1.000000:0.51175191,(Q7D1T6:0.17783006,Q63IJ7:0.15483880)1.000000:0.87953156)0.879253:0.11535090,(Q28RT0:1.01784576,(B9JNP7:1.11261669,(B2UCA8:0.76348582,(((A6M2W4:0.21565444,A4W7D6:0.17558479)1.000000:0.37879482,(D4GJ14:0.06604958,(C6CBG9:0.01850349,B5R541:0.03323447)0.999985:0.05738427)1.000000:0.29155266)1.000000:0.31191076,((C6D9S0:0.03964480,Q8FHC7:0.03209453)1.000000:0.13486764,((A4XF23:0.22295702,(Q1QT89:0.18122799,B3PDB1:0.14414146)0.999998:0.06015729)0.968272:0.04285536,(B0T0B1:0.05224760,Q9AAR4:0.07234240)1.000000:0.14812779)0.999678:0.08813897)1.000000:0.36147407)1.000000:0.47112287)0.928316:0.13341811)0.550875:0.06620266)0.961209:0.13640648)1.000000:0.27744895)0.988757:0.09058974)0.866782:0.06631759,(A9CL63:0.35266112,Q92ZS5:0.19783599)1.000000:1.18369094)0.402267:0.02752454)0.999888:0.19319607,(Q9F3A5:0.58548261,((Q3KB33:0.33553686,(A0R5B5:0.21484600,D6Y7Y6:0.27848012)1.000000:0.24287080)0.942008:0.15046146,(Q1QUN0:0.25266568,(C0WBB5:0.25833170,(P0AES2:0.09059530,A6VQF1:0.05673552)1.000000:0.13075826)0.999738:0.14696003)1.000000:0.81155149)1.000000:0.47139015)1.000000:0.50975221)0.966695:0.13031427)0.863808:0.08043994)0.973288:0.08656638,(Q5P025:0.97873157,(C5CFI0:1.08126948,((A0A0H3KH80:0.00000001,(A0A0H2WWB5:0.00000001,Q53635:0.00000001)-1.000000:0.00000001)-1.000000:1.77379709,((Q838J7:0.42816989,Q927X3:0.43775742)1.000000:0.24306201,(Q5SJX8:0.32151423,Q9RYA6:0.31040549)1.000000:0.38120655)0.761411:0.11121216)0.449066:0.07920285)1.000000:0.65145569)0.934431:0.11633312)0.809578:0.05916034,(A0QTN8:1.01771865,((Q8DJP8:2.14313928,(Q8NN12:0.75309341,(P05404:0.60462842,(Q4K9X1:0.32854393,A6T9N5:0.34558716)1.000000:0.22924230)0.999793:0.18933082)0.610131:0.11821100)0.811426:0.14174769,(A8HTB8:0.54448819,(Q5LM96:0.23356964,Q28SI7:0.15669417)1.000000:0.47534595)1.000000:0.49079583)0.999955:0.20013288)0.717358:0.06863833)0.729022:0.08518511)0.998543:0.11833475,(Q607C7:1.08575204,(((O34508:0.48939847,B0TZW0:1.11933860)0.879395:0.12702564,(Q9WXM1:0.80769788,(A9B055:0.36657533,(A5UXJ3:0.34547016,A9GEI3:0.26128229)0.974762:0.12479711)1.000000:0.52751375)1.000000:0.33586771)0.610795:0.07157613,(Q11T61:0.92177095,Q834W6:0.44934225)0.999732:0.14429535)0.996719:0.09875344)0.787853:0.04813874)0.983918:0.24536033)1.000000:0.66916649); ```  Cheers,

Add depthfirst to TraversalOrder to help with plotting

4

That will help when creating Arrays for plotting node attributes, such as adding names/labels to internal nodes. Cheers

Add function to save/write a tree in Newick format

1

I think it will be useful, particularly to share the tree between sessions and programs.

Incorrect link on docs

4

Hi! I am trying to learn to use Flux, and I found this link error in the tutorial: https://fluxml.ai/Flux.jl/stable/tutorials/logistic_regression/#Dataset In particular, _"(see Performance tips)"_ links to https://fluxml.ai/Flux.jl/stable/tutorials/logistic_regression/tutorials/@ref%20man-performance-tips instead of linking...

corspearman when all the values are NaNs

8

It looks like an `tiedrank`'s error: ``` julia julia> corspearman([1.,2.,3.,4.,5.,6.], [NaN, NaN, NaN, NaN, NaN, NaN]) 1.0 julia> rank([NaN, NaN, NaN, NaN, NaN, NaN]) ERROR: MethodError: `rank` has no method...