Work on this project continues on forked repository.
- gcc with support of c++11
Use git clone https://github.com/rikiel/traveler to download project
cd traveler/src
make build
The binaries will be copied into traveler/bin. To navigate there from the src directory use: cd ../bin
traveler [-h|--help]
traveler [OPTIONS] <STRUCTURES>
STRUCTURES:
<-gs|--target-structure> DBN_FILE
<-ts|--template-structure [--file-format FILE_FORMAT]> IMAGE_FILE DBN_FILE
DBN_FILE (Varna/DotBracketNotation) is in format like in example below
IMAGE_FILE* - visualization of template molecule, type of file can be specified by FILE_FORMAT argument
OPTIONS:
[-a|--all] [--overlaps] OUT_PREFIX
# computes mapping (TED) and outputs target leayout as both .ps and .svg image to files with prefix OUT_PREFIX
# with the optional --overlaps argument, overlaps in the layout are identified and highlited
[-t|--ted <FILE_MAPPING_OUT>]
# runs mapping (TED) only and saves mapping table to FILE_MAPPING_OUT file
[-d|--draw] [--overlaps] FILE_MAPPING_IN OUT_PREFIX
# use mapping in FILE_MAPPING_IN and outputs layout as both .ps and .svg image to files with prefix OUT_PREFIX
# if optional argument --overlaps is present overlaps in the layout are identified and highlighted
COLOR CODING:
Traveler uses the following color coding of nucleotides:
* Red - inserted bases
* Green - edited bases - e.g. the template has an adenosine at a position while the target has a cytosine at the same position and therefore cytosine will be colored green in the resulting layout)
* Blue - reinserted bases - happens when traveler needs to redraw simple structures like hairpins (for example due to the change in the number of bases)
* Brown - rotated parts - similar situation to reinserted bases, but takes place when redrawing a multibranch loop (in that case all branches need to be rotated to lie on a circle)
Two types of template IMAGE_FILE are currectly supported by Traveler:
Other extractors of RNA structure can be implemented and specified by the FILE_FORMAT argument.
$ mkdir 18S/
$ cd 18S/
$ wget --recursive --no-directories --no-parent \
http://richard.ba30.eu/traveler/img/input/18S/
In other examples, we will use 18S/ directory as INDIR, OUTDIR will be /tmp/
$ cat $INDIR/mouse.fasta
>mouse
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAG
UGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAU
. . .
...(((((.......))))).((((((((((.(((((((((.....(((.(((..((...(((....((..........)
)...)))))......(((......((((..((..((....(((..................((((....(((((((....
. . .
FASTA (Varna/DBN) file should contain line starting with '>' and name of molecule, without any blank character
other lines are filled with LABELS and BRACKETS in dot-bracket notation of secondary structure pairing
match-tree must contain both LABELS and BRACKETS, templated-tree need only BRACKETS
Example 1: Visualize mouse 18S rRNA using human 18S rRNA as template using CRW ps image as the template layout.
$ ./build/traveler \
--target-structure $INDIR/mouse.fasta \
--template-structure $INDIR/human.ps $INDIR/human.fasta \
--all $OUTDIR/mouse_draw-to_human
Example 2: Compute TED distance and mapping between human 18S rRNA (template) and mouse 18S rRNA (target).
$ ./build/traveler \
--target-structure $INDIR/mouse.fasta \
--template-structure $INDIR/human.ps $INDIR/human.fasta \
--ted $OUTDIR/mouse_draw-to_human.map
$ ./build/traveler \
--target-structure $INDIR/mouse.fasta \
--template-structure $INDIR/human.ps $INDIR/human.fasta \
--draw --overlaps $OUTDIR/mouse_draw-to_human.map $OUTDIR/mouse_draw-to_human
$ # generates 4 files - .svg and .ps files, both with/without colored bases (see COLOR CODING section)
$ # checks also if output molecule has overlaps and draws them in output image
Options --ted and --draw serve for separatation of mapping and visualization since TED computation and on the other hand, Traveler allows for multiple output visualization (coloring, overlaps).
As we said, we support two types of input images - crw and varna. There are three steps you need to satisfy, when you want to support other image types.
- You need to implement
extractorinterface and it's methodextract. Method should obtain all nucleotides (the primary structure) and their position in image (points) from given file. - In the class, you need to implement method
get_type, that should only return extractor's type that is used in IMAGE_FILE argument. - Adds your new extractor to method
extractor.get_all_extractors()
For more ideas, how it should be implemented, see usage of crw_extractor and varna_extractor.