Christoph Mayer

Use tabs instead of spaces in result.txt file

1

I have file names that contain spaces. I try to avoid them, but its not always my choice. Now if I split the lines in the result files using a...

root label not handled in tree.write()

1

I assign node labels to all nodes, including inner nodes: I traverse the tree with for n in t.traverse(): n.name = something This assigns a name also to the root,...

This example code fails: http://etetoolkit.org/docs/latest/_downloads/face_grid.py It contains this line: f.margin_border.width = 1 which causes an error. It works with f.border.width = 1 Does this lead to the same behaviour as...

Genetic code start codon variation

1

Some genetic codes such as the Vertebrate Mitochondrial Code allow potentially different start codons / start amino acids. Is it possible to take this into account in diamond, e.g. by...

Error: Gap penalty settings are not supported for this scoring matrix.

1

I am doing a blastx search using default parameters except --gapopen N, since I think the default parameter should be lowered for my application. This gives me the error message:...

[ Bug] sg.WIN_CLOSED event is not generated, after catching mouse down events in same window for read_all_windows calls

4

### Type of Issue (Enhancement, Error, Bug, Question) Bug ---------------------------------------- #### Operating System MacOs 10.14.6 #### PySimpleGUI Port (tkinter, Qt, Wx, Web) tkinter ---------------------------------------- ## Versions Version information can be...

Order of clustering steps can differ on different machines, even in reruns

1

Running PF in rcluster mode can result in different orders of the clustering steps. I have started PF on one machine. Eventually it turned out that RAM was insufficient. In...

Unclear effect of the protein2genome model

1

The manual says: "protein2genome This model allows alignment of a protein sequence to genomic DNA. This is similar to the protein2dna model, with the addition of modelling of introns and...

Especially in vertebrate genome projects it is common that the same gene name is used in different species, but Orthograph does not seem to be able to handle this. If...