metagraph | Scalable annotated de Bruijn graphs for DNA | Genomics library

 by   ratschlab C++ Version: v0.3.6 License: GPL-3.0

kandi X-RAY | metagraph Summary

kandi X-RAY | metagraph Summary

metagraph is a C++ library typically used in Artificial Intelligence, Genomics applications. metagraph has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly
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            kandi-support Support

              metagraph has a low active ecosystem.
              It has 75 star(s) with 12 fork(s). There are 13 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 1 open issues and 55 have been closed. On average issues are closed in 106 days. There are 12 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of metagraph is v0.3.6

            kandi-Quality Quality

              metagraph has no bugs reported.

            kandi-Security Security

              metagraph has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              metagraph is licensed under the GPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              metagraph releases are available to install and integrate.
              Installation instructions, examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
            Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of metagraph
            Get all kandi verified functions for this library.

            metagraph Key Features

            No Key Features are available at this moment for metagraph.

            metagraph Examples and Code Snippets

            Metagenome Graph Project,Typical workflow,Convert annotation to Multi-BRWT
            C++dot img1Lines of Code : 11dot img1License : Non-SPDX (NOASSERTION)
            copy iconCopy
            ./metagraph transform_anno -v --linkage --greedy \
                                       -o linkage.txt \
                                       --subsample R \
                                       -p NCORES \
                                       primates.column.annodbg
            
            ./metagraph transform  
            Metagenome Graph Project,Typical workflow,Build graph
            C++dot img2Lines of Code : 9dot img2License : Non-SPDX (NOASSERTION)
            copy iconCopy
            ./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.  
            Metagenome Graph Project,Typical workflow,Example
            C++dot img3Lines of Code : 9dot img3License : Non-SPDX (NOASSERTION)
            copy iconCopy
            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

            QUESTION

            differences in bitmap or rasterized font bitmaps and text display on 3.5" TFT LCD
            Asked 2021-Jun-12 at 16:19

            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 question

            What 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 question

            Are 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 far

            The KeDei TFT library came with an a bitmap font table that was defined as

            ...

            ANSWER

            Answered 2021-Jun-12 at 16:19

            Raster 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:

            Source https://stackoverflow.com/questions/67465098

            QUESTION

            Adding custom names for vertices
            Asked 2021-Mar-12 at 15:07

            I want to create a graph with custom vertex names. Is this possible with MetaGraphs.jl ?

            ...

            ANSWER

            Answered 2021-Mar-11 at 07:39

            From 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.

            Source https://stackoverflow.com/questions/66576244

            QUESTION

            error in conversion of keras model to tflite
            Asked 2020-Dec-10 at 17:36

            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 17:36

            You are trying to use converting method from saved_model protobuf with keras model. Your method is tf.lite.TFLiteConverter.from_keras_model(model):

            Source https://stackoverflow.com/questions/65216987

            QUESTION

            SavedModel file does not exist when using Tensorflow hub
            Asked 2020-Sep-28 at 06:15

            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 22:42

            So, just deleting that folder and running the hub.load() function again solves the issue

            Source https://stackoverflow.com/questions/63078695

            QUESTION

            Sentences similarity using tensorflow
            Asked 2020-Sep-12 at 21:19

            I am trying to determine semantic similarity between one sentence and others as follows:

            ...

            ANSWER

            Answered 2020-Sep-12 at 21:19

            The 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?

            Source https://stackoverflow.com/questions/63813264

            QUESTION

            Tensorflow object_detection: unable to find input and output tensors
            Asked 2020-May-26 at 09:41

            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 09:41

            In 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.

            Source https://stackoverflow.com/questions/45059162

            QUESTION

            Can a TensorFlow Hub module be used in TensorFlow 2.0?
            Asked 2020-Apr-07 at 23:12

            I tried running this code in TensorFlow 2.0 (alpha):

            ...

            ANSWER

            Answered 2019-Apr-13 at 20:45

            In 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

            Source https://stackoverflow.com/questions/55585079

            QUESTION

            Is there a way to figure out in which region a Google Cloud Storage bucket is hosted?
            Asked 2020-Jan-19 at 18:20

            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:

            1. 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?
            2. 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 18:32

            You 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.

            Source https://stackoverflow.com/questions/59791000

            QUESTION

            Getting imagenet model pnasnet_large with to work with hub.KerasLayer
            Asked 2019-Nov-22 at 11:11

            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 15:55

            At 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.

            Source https://stackoverflow.com/questions/57879330

            QUESTION

            Nested unions in Cypher/Neo4j
            Asked 2019-Nov-21 at 22:22

            I've this metagraph in Neo4j:

            ...

            ANSWER

            Answered 2017-Oct-11 at 12:51
            Using Periodic Collect

            In Cypher, you can break a query into steps with WITH, and you can join two lists by concatenating them together.

            Source https://stackoverflow.com/questions/46650175

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install metagraph

            To compile from source (e.g., for builds with custom alphabet or other configurations), see documentation online.
            Simple build
            Build with disk swap (use to limit the RAM usage)

            Support

            Online documentation is available at https://metagraph.ethz.ch/static/docs/index.html. Offline sources are here.
            Find more information at:

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