arendsee / synder Goto Github PK

Trace intervals between genomes using a synteny map

License: Other

C++ 58.34% R 41.66%

synteny bioinformatics orthology-inference interval-tree

synder's Introduction

Synder

Map intervals on one genome to search spaces on another genome using
a synteny map

Citation

If you use this tool, please cite:

Zebulun Arendsee, Andrew Wilkey, Urminder Singh, Jing Li, Manhoi Hur, and Eve Wurtele. "synder: inferring genomic orthologs from synteny maps." BioRxiv (2019).

Funding

This work is funded by the National Science Foundation grant:

NSF-IOS 1546858 Orphan Genes: An Untapped Genetic Reservoir of Novel Traits

Installation

In an R session

library(devtools)
install_github('arendsee/synder')

To build the vignettes in an R shell run

library(devtools)
devtools::build_vignettes()

If you use RStudio, then there is probably some button for this (GUIs are too volatile for me to say anything terribly helpful).

Troubleshooting

If you get an error during install saying:

** preparing package for lazy loading                                                              
Error : object 'extract' not found whilst loading namespace 'R.utils'
ERROR: lazy loading failed for package ‘synder’                                
* removing ‘/home/<username>/R/x86_64-pc-linux-gnu-library/3.4/synder’           
Error: Command failed (1)

Try removing the packages R.oo and R.utils and then, in a vanilla setting without magrittr loaded, reinstall them. Then try installing synder.

If you get weird errors in the data, for example data(toy) and then see a lot of hash marks in the GFF files. Then start a new session, load GenomicRanges and Biostrings. Then try reloading synder.

Documentation

First read the "intro" vignette

library(synder)
vignette("intro", package="synder")

Other vignettes can be listed with vignette(package="synder").

Information on specific command is available through normal channels:

library(synder)
?synder::search
?synder::anon_search

synder's People

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mhhur amupitan lijing28101

synder's Issues

Segfaults on certain 9th column GFF values

When I search this GFF file

Gm01    phytozomev9_0   gene    27355   28320   .   -   .   Name=Glyma.01g000100;ID=1;Alias=Glyma.01g000100.Wm82.a2.v1;agi_genecode=magnesium%20ion%20binding%2Cthiamin%20pyrophosphate%20binding%2Chydro-lyases%2Ccatalytics%2C2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid%20synthases;ancestorIdentifier=Glyma01g00210.v1.1;Dbxref=AGI_GeneCode:AT1G68890.1

with this synteny map

Gm01 336 562 KN643195.1 5697 5923 0.747788 +
Gm01 172767 172964 KN645832.1 1444871 1445068 0.497462 +
Gm01 254499 254749 KN645832.1 1415869 1416119 0.640000 +
Gm01 620173 620377 KN645832.1 673645 673849 0.504902 +
Gm01 698546 698755 KN645832.1 657432 657641 0.559809 +

and the command

synder search -i a.gff -s b.syn

I get the error message

SKIPPING ENTRY: Synteny map has no contig names 'nding%2Chydro-lyases%2Ccatalytics%2C2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid%20synthases;ancestorIdentifier=Glyma01g00210.v1.1;Dbxref=AGI_GeneCode:AT1G68890.1'
ERROR: Failed to open synteny map ''

I am using Synder v0.17.3

Here is my system info

Linux xxx 3.10.0-327.22.2.el7.x86_64 #1 SMP EDT 2016 x86_64 x86_64 x86_64 GNU/Linux

question in output

Hi @arendsee, I used the example ty1 data in your package.
search(ty1$syn$Saccharomyces_arboricola,ty1$gff)
The score column in output is NA, and inbetween is FALSE.
I also tried to set the offset to 011111, and change the trans to d, but thees two column in the output are the same. Why it has no score?
And how to understand the last three column? What condition means the query gene has similar sequence in the target genome?

broken link

For a practical introduction to synder, read introduction vignette. the intro link is broken

can't load vignettes in terminal

After installing Synder in commandline, I couldn't load vignettes using the command line given. Is there a particular way I can do it?

common communications -Zeb- reply directly to this issue

confirm everything you receive by replying to it directly (in this case, in github issues). after the first few weeks we should have China-US communications figured out to a T.

Pick a single repository to be communicating in so that the whole group can be aware of the various issues and progress.
(core orphan/PMR group=Manhoi, Arun, Priyanka, Urminder, Jing, Ananth, Eve, Zeb) (we should add Kevin, Pramesh, Tianlong into the group after we get it going)
Zeb, each week report to the group what you have done, via the issues channel. You can just reference code or whatever. You are at the center of the orphan coding hub at present.

failed to install

I tried to install synder with the suggestion, but it raised the error:

> library(devtools)
> install_github('arendsee/synder')
Downloading GitHub repo arendsee/synder@master
from URL https://api.github.com/repos/arendsee/synder/zipball/master
Installation failed: error in running command

Do you have any idea about that?

Thanks
Raymond

Mac Installation

I'm working on a iMac (21.5-inch, Late 2015) OS X El Capitan. Having some trouble with installation. I can fetch the code fine but compiling is giving some errors...

git clone https://github.com/arendsee/synder.git
cd synder
make

and I get...

cd src && /Applications/Xcode.app/Contents/Developer/usr/bin/make
gcc -c -Wall -g -O2 test.[ch]
In file included from test.c:7:
./itree/search.h:49:1: error: unknown type name 'uint'; did you mean 'int'?
uint count_point_overlaps(uint pnt, IntervalTree * tree);
^~~~
int
./itree/search.h:49:27: error: unknown type name 'uint'; did you mean 'int'?
uint count_point_overlaps(uint pnt, IntervalTree * tree);
                          ^~~~
                          int
./itree/search.h:57:1: error: unknown type name 'uint'; did you mean 'int'?
uint count_interval_overlaps(Interval * interval, IntervalTree * tree);
^~~~
int
./itree/search.h:72:43: error: unexpected type name 'IntervalTree': expected identifier
IntervalResult * get_point_overlaps(uint, IntervalTree *);
                                          ^
./itree/search.h:72:56: error: expected ')'
IntervalResult * get_point_overlaps(uint, IntervalTree *);
                                                       ^
./itree/search.h:72:36: note: to match this '('
IntervalResult * get_point_overlaps(uint, IntervalTree *);
                                   ^
./itree/search.h:72:37: error: a parameter list without types is only allowed in a function definition
IntervalResult * get_point_overlaps(uint, IntervalTree *);
                                    ^
6 errors generated.
make[1]: *** [test.o] Error 1
make: *** [all] Error 2

My gcc version is

$ gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.3.0 (clang-703.0.31)
Target: x86_64-apple-darwin15.6.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

Error in fetch(key)

In R studio
after install the synder package, click on
Packages ->synder -> any of these as.data.frame.DumpResult, as.data.frame.GFF, etc. got
this error message
Error in fetch(key) : lazy-load database '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/synder/help/synder.rdb' is corrupt

Cannot load vignettes

After I install and library synder in RStudio, I run the code vignette("intro",package = "synder").
The error message is "vignette ‘intro’ not found".
My R version is 3.3.3, RStudio is 0.99.903.