gogleva / secretsanta Goto Github PK

Error:
Error in S4Vectors:::normalize_names_replacement_value(value, x) :
attempt to set too many names (1) on GroupedIRanges object of length 0

The same error persists even in the fasta extrcated with getOutfasta method

1. Vignette: fix typos and grammar.
2. Vignette: figure numbering.
3. Vignette: Fig 1: typo in target
4. Incorporate installation script
5. Run mode - not very intuitive argument, make Boolean and piper by default.
6. Further work: higher level of abstraction for individual functions -> virtual wrapper.

• Travis-CI post-build hook?

sp2 outputs something weird as Cpos in the NN results: values > 100
so we will use a different line to extract cleavage position:

'Max cleavage site probability:' - should work for both signalp2 and signalp3 outputs

• add prediction_type argument to specify HMM or NN predictions
• adopt parser

Alternative method for TM-prediction.
Stand-alone version lives here:
https://github.com/ElofssonLab/TOPCONS2

paper:
https://www.ncbi.nlm.nih.gov/pubmed/25969446

Initialising site -----------------------------------------------------------------------------------
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Copying '/home/anna/R/x86_64-pc-linux-gnu-library/3.4/pkgdown/assets/pkgdown.js'
Building home ---------------------------------------------------------------------------------------
Error in xml2::xml_contents(heading)[[1]] : subscript out of bounds

• try with UniprotKB may be
• use GO-terms?
• map 'secreted' for already known proteins/functions ~ applies for model species

• try to put all the dependencies in a docker container
• licence issue --> ask developers once again

upd examples, take into account all the new parameters and added functionality

convention for status messages:

• start with a small letter
• end with ...

convention for error messages:

• start with capital letter
• end with .

Have been trying to run the example for signalp4 and it seems to run well, except the result is not returned, gor the same error with targetp.

step1_sp4 <- signalp(inp, version = 4,
organism = 'euk',
run_mode = "starter")

Output=

"Version used ... signalp4
Running signalp locally ...
2 sequences need to be truncated ...
Ok for single processing.
Submitted sequences... 100
Candidate sequences with signal peptides ... 3
Error in .wrap_in_length_one_list_like_object(value, names(x)[[i]], x) :
failed to coerce 'list(value)' to a AAStringSetList object of length 1"

update dependencies?

isolate helper functions and source all of them (e.g crop_names)

• add 'sensitive mode' when running SignalP 4.1
• may be specify some more options?

minimal documentation

include more default arguments

Error in names(sp) <- c("gene_id", "Cmax", "Cpos", "Ymax", "Ypos", "Smax", :
'names' attribute [12] must be the same length as the vector [5]

currently parallel version of tmhmm is slower that the native tmhmm -> profile this

Run_mode - not very intuitive argument, make boolean and piper by default (?)

revise examples, current example does not contain 'Signal peptide field'

Very nice package. Much appreciated.
There are third-party tools dependencies.
Do you plan to deliver a docker? Containers look like the natural solution for these package architectures.

Bests,
-A

• "[KRHQSA]-[DENQ]-E-L>" (http://prosite.expasy.org/PDOC00014)
• ELM as "[KRHQSAP][DENQT]EL$" (http://elm.eu.org/elms/TRG_ER_KDEL_1)
• provide a choice of ER-retention motifs
• set reasonable default options

on top of default options for possible reverse functionality

Alternative method for TM-prediction.
Stand-alone version lives here:
https://github.com/ElofssonLab/TOPCONS2

paper:
https://www.ncbi.nlm.nih.gov/pubmed/25969446

• imports for dependencies
• exports for objects?

when running the targetp function, when the backend is pointing to targetp v2.0c, the code fails with the message:

flag provided but not defined: -N
Usage of targetp:
...usage statement for targetp...
Error in checkForRemoteErrors(val) :
one node produced an error: 'names' attribute [7] must be the same length as the vector [1]

Is this because SecretSanta will only work with the older version of targetp (v1.1)? I would have just tried that before posting here but I haven't been able to find an old version of targetp. Their website only provides v2.0c as far as I can see.

bring the slow integration test back

• what works, what does not, could it be overcomed?

(internal links) => might improve readability

Higher level of abstraction for individual functions -> virtual wrapper/closure -> framework for integration of new tools? Would it make documentation more complex?

not safe currently:

• rm -rf
• add comments
• add warnings

vignettes: check that citations are correct and adequately formatted
missing entries?

• make it inherit from Biostrings::AAStringSetList --> to use all AAStringSetList methods

Error in checkForRemoteErrors(val) :
2 nodes produced errors; first error: subscript contains invalid names