metagraph | Scalable annotated de Bruijn graphs for DNA | Genomics library
kandi X-RAY | metagraph Summary
kandi X-RAY | metagraph Summary
Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly
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Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of metagraph
metagraph Key Features
metagraph Examples and Code Snippets
./metagraph transform_anno -v --linkage --greedy \
-o linkage.txt \
--subsample R \
-p NCORES \
primates.column.annodbg
./metagraph transform
./metagraph build -v --parallel 30 -k 20 --mem-cap-gb 10 \
-o /graph /*.fasta.gz \
2>&1 | tee /log.txt
./metagraph build -v --parallel 30 -k 20 --mem-cap-gb 10 --disk-swap \
-o /graph /*.fasta.
DATA="../tests/data/transcripts_1000.fa"
./metagraph build -k 12 -o transcripts_1000 $DATA
./metagraph annotate -i transcripts_1000.dbg --anno-filename -o transcripts_1000 $DATA
./metagraph query -i transcripts_1000.dbg -a transcripts_1000.column.
Community Discussions
Trending Discussions on metagraph
QUESTION
I am using a 3.5: TFT LCD display with an Arduino Uno and the library from the manufacturer, the KeDei TFT library. The library came with a bitmap font table that is huge for the small amount of memory of an Arduino Uno so I've been looking for alternatives.
What I am running into is that there doesn't seem to be a standard representation and some of the bitmap font tables I've found work fine and others display as strange doodles and marks or they display upside down or they display with letters flipped. After writing a simple application to display some of the characters, I finally realized that different bitmaps use different character orientations.
My questionWhat are the rules or standards or expected representations for the bit data for bitmap fonts? Why do there seem to be several different text character orientations used with bitmap fonts?
Thoughts about the questionAre these due to different target devices such as a Windows display driver or a Linux display driver versus a bare metal Arduino TFT LCD display driver?
What is the criteria used to determine a particular bitmap font representation as a series of unsigned char values? Are different types of raster devices such as a TFT LCD display and its controller have a different sequence of bits when drawing on the display surface by setting pixel colors?
What other possible bitmap font representations requiring a transformation which my version of the library currently doesn't offer, are there?
Is there some method other than the approach I'm using to determine what transformation is needed? I currently plug the bitmap font table into a test program and print out a set of characters to see how it looks and then fine tune the transformation by testing with the Arduino and the TFT LCD screen.
My experience thus farThe KeDei TFT library came with an a bitmap font table that was defined as
...ANSWER
Answered 2021-Jun-12 at 16:19Raster or bitmap fonts are represented in a number of different ways and there are bitmap font file standards that have been developed for both Linux and Windows. However raw data representation of bitmap fonts in programming language source code seems to vary depending on:
- the memory architecture of the target computer,
- the architecture and communication pathways to the display controller,
- character glyph height and width in pixels and
- the amount of memory for bitmap storage and what measures are taken to make that as small as possible.
A brief overview of bitmap fonts
A generic bitmap is a block of data in which individual bits are used to indicate a state of either on or off. One use of a bitmap is to store image data. Character glyphs can be created and stored as a collection of images, one for each character in the character set, so using a bitmap to encode and store each character image is a natural fit.
Bitmap fonts are bitmaps used to indicate how to display or print characters by turning on or off pixels or printing or not printing dots on a page. See Wikipedia Bitmap fonts
A bitmap font is one that stores each glyph as an array of pixels (that is, a bitmap). It is less commonly known as a raster font or a pixel font. Bitmap fonts are simply collections of raster images of glyphs. For each variant of the font, there is a complete set of glyph images, with each set containing an image for each character. For example, if a font has three sizes, and any combination of bold and italic, then there must be 12 complete sets of images.
A brief history of using bitmap fonts
The earliest user interface terminals such as teletype terminals used dot matrix printer mechanisms to print on rolls of paper. With the development of Cathode Ray Tube terminals bitmap fonts were readily transferable to that technology as dots of luminescence turned on and off by a scanning electron gun.
Earliest bitmap fonts were of a fixed height and width with the bitmap acting as a kind of stamp or pattern to print characters on the output medium, paper or display tube, with a fixed line height and a fixed line width such as the 80 columns and 24 lines of the DEC VT-100 terminal.
With increasing processing power, a more sophisticated typographical approach became available with vector fonts used to improve displayed text quality and provide improved scaling while also reducing memory required to describe the character glyphs.
In addition, while a matrix of dots or pixels worked fairly well for languages such as English, written languages with complex glyph forms were poorly served by bitmap fonts.
Representation of bitmap fonts in source code
There are a number of bitmap font file formats which provide a way to represent a bitmap font in a device independent description. For an example see Wikipedia topic - Glyph Bitmap Distribution Format
The Glyph Bitmap Distribution Format (BDF) by Adobe is a file format for storing bitmap fonts. The content takes the form of a text file intended to be human- and computer-readable. BDF is typically used in Unix X Window environments. It has largely been replaced by the PCF font format which is somewhat more efficient, and by scalable fonts such as OpenType and TrueType fonts.
Other bitmap standards such as XBM, Wikipedia topic - X BitMap, or XPM, Wikipedia topic - X PixMap, are source code components that describe bitmaps however many of these are not meant for bitmap fonts specifically but rather other graphical images such as icons, cursors, etc.
As bitmap fonts are an older format many times bitmap fonts are wrapped within another font standard such as TrueType in order to be compatible with the standard font subsystems of modern operating systems such as Linux and Windows.
However embedded systems that are running on the bare metal or using an RTOS will normally need the raw bitmap character image data in the form similar to the XBM format. See Encyclopedia of Graphics File Formats which has this example:
Following is an example of a 16x16 bitmap stored using both its X10 and X11 variations. Note that each array contains exactly the same data, but is stored using different data word types:
QUESTION
I want to create a graph with custom vertex names. Is this possible with MetaGraphs.jl ?
...ANSWER
Answered 2021-Mar-11 at 07:39From what I understand, one way to do that in MetaGraphs.jl
is to define an "indexing property", for instance :name
, which would contain :A
, :B
, etc.
Then, you can add an edge using the syntax add_edge!(gm, gm[:A, :name], gm[:B, :name])
if my memory serves me. As for plotting, you can simply retrieve the property with get_prop
.
QUESTION
I am using tensorflow version 2.3.1 and keras 2.4.3 I trained a keras model where after training I tried to convert it to tflite model using the following commands:
...ANSWER
Answered 2020-Dec-10 at 17:36You are trying to use converting method from saved_model
protobuf with keras model. Your method is tf.lite.TFLiteConverter.from_keras_model(model)
:
QUESTION
When trying to use the hub.load
function from tensorflow_hub
, I get an OSError: SavedModel file does not exist at:
error.
The weird thing is that it worked a few days ago, so I don't quite understand why I'm getting this error now.
Code to reproduce:
...ANSWER
Answered 2020-Jul-26 at 22:42So, just deleting that folder and running the hub.load() function again solves the issue
QUESTION
I am trying to determine semantic similarity between one sentence and others as follows:
...ANSWER
Answered 2020-Sep-12 at 21:19The reason of the problem seems to be that TF2 does not support hub Models.
It's simple, but have you tried to disable tensorflow version 2 behaivour?
QUESTION
I've successfully trained and saved a faster RCNN model for tensorflow using their object detection API. I'm now trying to run some inferences on the code, taking bits of code from this tutorial.
However, after I successfully restore the metagraph and the checkpoint, the system can't find the input and output nodes, I get the following error:
KeyError: "The name 'image_tensor:0' refers to a Tensor which does not exist. The operation, 'image_tensor', does not exist in the graph."
The checkpoint and metagraph were created by the train.py script, on my own data, following the instructions given here.
This is my code:
...ANSWER
Answered 2020-May-26 at 09:41In the train graph, the input/output nodes are not given those names. What you will need to do is to "export" your trained model via the export_inference_graph.py tool. I believe it currently exports it to a frozen graph or a SavedModel, but in future releases, it will export to ordinary checkpoint as well.
QUESTION
I tried running this code in TensorFlow 2.0 (alpha):
...ANSWER
Answered 2019-Apr-13 at 20:45In Tensorflow 2.0 you should be using hub.load()
or hub.KerasLayer()
.
[April 2019] - For now only Tensorflow 2.0 modules are loadable via them. In the future many of 1.x Hub modules should be loadable as well.
For the 2.x only modules you can see examples in the notebooks created for the modules here
QUESTION
NCBI (the National Center for Biotech Info) generously provided their data for 3rd parties to consume. The data is located in cloud buckets such as gs://sra-pub-run-1/
. I would like to read this data without incurring additional costs, which I believe can be achieved by reading it from the same region as where the bucket is hosted. Unfortunately, I can't figure out in which region the bucket is hosted (NCBI mentions in their docs that's in the US, but not where in the US). So my questions are:
- Is there a way to figure out in which region a bucket that I don't own, like
gs://sra-pub-run-1/
is hosted? - Is my understanding correct that reading the data from instances in the same region is free of charge? What if the GCS bucket is multi-region?
Doing a simple gsutil ls -b -L
either provides no information (when listing a specific directory within sra-pub-run-1
or I get a permission denied error if I try to list info on gs://sra-pub-run-1/
directly using:
gsutil -u metagraph ls -b gs://sra-pub-run-1/
ANSWER
Answered 2020-Jan-17 at 18:32You cannot specify a specific Compute Engine zone as a bucket location, but all Compute Engine VM instances in zones within a given region have similar performance when accessing buckets in that region.
Billing-wise, egressing data from Cloud Storage into a Compute Engine instance in the same location/region (for example, US-EAST1 to US-EAST1) is free, regardless of zone.
So, check the "Location constraint" of the GCS bucket (gsutil ls -Lb gs://bucketname
), and if it says "US-EAST1", and if your GCE instance is also in US-EAST1, downloading data from that GCS bucket will not incur an egress fee.
QUESTION
I am trying out various Tensorflow models from hub but I can't seem to get this one to work with KerasLayer:
"https://tfhub.dev/google/imagenet/pnasnet_large/feature_vector/3"
I am using the same procedure used within the examples in the documentation:
https://www.tensorflow.org/tutorials/images/hub_with_keras
feature_extractor = hub.KerasLayer(URL,
input_shape=(height, width,3))
even tried a few amendments such as including:
trainable=True, tags={"train"})
,
so it would look like this:
feature_extractor = hub.KerasLayer(URL,
input_shape=(height, width,3), trainable=True, tags={"train"})
)
because that's what it said to do in the docs.
However, I am still getting this error:
...ValueError: Importing a SavedModel with tf.saved_model.load requires a 'tags=' argument if there is more than one MetaGraph. Got 'tags=None', but there are 2 MetaGraphs in the SavedModel with tag sets [[], ['train']]. Pass a 'tags=' argument to load this SavedModel
ANSWER
Answered 2019-Sep-12 at 15:55At this time, hub.KerasLayer
only works for TF2-style models like https://tfhub.dev/google/tf2-preview/inception_v3/feature_vector/4.
Please stay tuned for more choice of TF2-style models as TensorFlow 2.0 is getting released.
QUESTION
I've this metagraph in Neo4j:
...ANSWER
Answered 2017-Oct-11 at 12:51In Cypher, you can break a query into steps with WITH, and you can join two lists by concatenating them together.
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