phoenix | Jetstream compatible workflow template | Genomics library

 by   tgen Python Version: v1.0.2 License: MIT

kandi X-RAY | phoenix Summary

kandi X-RAY | phoenix Summary

phoenix is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. phoenix has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. However phoenix build file is not available. You can download it from GitHub.

This workflow supports the analysis of human sequencing samples against the GRCh38 reference genome using ensembl version 98 gene models. The workflow is designed to support project level analysis that can include one or multiple types of data. Though not required the expectation is a project contains data from a single individual thus centralizing all data types in a standardized output structure. The workflow template supports a diverse array of analysis methods required to analyze DNA, RNA, and single cell data. Based on standardized variables it also supports integrated analysis between data types. For some processes multiple options are provided that can be individually enabled or disabled by configuration parameters. Like all JetStream (workflows developed at TGen this workflow is designed to facilitate our dynamic and time sensitive analysis needs while ensuring compute and storage resources are used efficiently. The primary input is a JSON record from the TGen LIMS but hand created inputs in the form of a JSON or EXCEL worksheet can also be provided when run manually or by submission to the related JetStream Centro (web portal. All required files defined the the pipeline.yaml can be created using code provided in the JetStream Resources repository (
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            kandi-support Support

              phoenix has a low active ecosystem.
              It has 8 star(s) with 3 fork(s). There are 6 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 34 open issues and 259 have been closed. On average issues are closed in 142 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of phoenix is v1.0.2

            kandi-Quality Quality

              phoenix has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              phoenix is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              phoenix releases are available to install and integrate.
              phoenix has no build file. You will be need to create the build yourself to build the component from source.
              Installation instructions, examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed phoenix and discovered the below as its top functions. This is intended to give you an instant insight into phoenix implemented functionality, and help decide if they suit your requirements.
            • Check for unique contigs
            • Uses samtools to get frags using samtools
            • Gets the number of reads in a region
            • Calculates the length of a cigar string
            • Extract data from a samtools markdown file
            • Add samples to a json object
            • Start processing
            • Process a single variant record
            • Return the index of a sample column in a given variant
            • Convert a bam file to a pandas dataframe
            • Add metrics to Picard
            • Extend the segments
            • Process VCF files and return new VCF records
            • Process command line arguments
            • Generate summary table
            • Parse arguments and validate them
            • Parse Picard stats from a Picard file
            • Write a new VCF file
            • Parse arguments
            • Extracts cellranger metrics data
            • Add histogram data to a dictionary
            • Make calls for a given sample
            • Extract histogram data from a Picard file
            • Verify BAM id extraction
            • Performs a HTTP request
            • Returns the location of the output file
            Get all kandi verified functions for this library.

            phoenix Key Features

            No Key Features are available at this moment for phoenix.

            phoenix Examples and Code Snippets

            Phoenix Workflow - A JetStream Workflow,Running from command line
            Pythondot img1Lines of Code : 112dot img1License : Permissive (MIT)
            copy iconCopy
            {
                "project": "",
                "study": "",
                "email": "",
                "hpcAccount": "",
                "isilonPath": "",
                "pipeline": "phoenix",
                "dataFiles": [],
                "dnaAlignmentStyle": "tgen",
                "email": "somebody@tgen.org",
                "isilonPath": "",
                "pipeline"  
            Phoenix Workflow - A JetStream Workflow,Required Configuration Variables
            Pythondot img2Lines of Code : 34dot img2License : Permissive (MIT)
            copy iconCopy
            "dataFiles": [
                {
                    "assayCode": "TPFWG",
                    "dnaRnaMergeKey": "GIAB_NA12878_1_CL_Whole",
                    "fastqCode": "R1",
                    "fastqPath": "/home/tgenref/homo_sapiens/control_files/giab/fastq/NA12878_140407_D00360_0016_ASUPERFQS01/Projec  
            Phoenix Workflow - A JetStream Workflow,Output Folder Structure
            Pythondot img3Lines of Code : 9dot img3License : Permissive (MIT)
            copy iconCopy
            Project
            |--GeneralLibaryType
            |  |--AnalysisType
            |  |  |--Tool
            |  |  |  |--SampleName
            |  |  |     |--ResultFiles
            |  |  |--Tool
            |  |--AnalysisType
            |--GeneralLibaryType
              

            Community Discussions

            QUESTION

            ignore local computer time and get date and time from timezone using momentjs
            Asked 2021-Jun-14 at 13:35

            I'm trying to use moment.js to get the correct date and time of a user ignoring the date and time from the local computer which I'm thinking the user might change sometime. It's there a way to achieve this, I'm currently using the code below but it's not getting me the results I need

            ...

            ANSWER

            Answered 2021-Jun-14 at 13:35

            An easy way of doing this is using an external service to return a time that you want, either by creating an api yourself or using an existing one.

            If you want something fast and easy you can try TimeAPI.

            Source https://stackoverflow.com/questions/67968554

            QUESTION

            Pass data from tableView cell is tap to second tableView
            Asked 2021-Jun-14 at 08:17

            I'm trying to pass data from a tableView when the cell is tap to a detailTableView. I'm not getting any errors when the detail tableView is loaded. The segue is being performed, however, the tableView remains blank. My goal to add the color to the textLabel in the cell and add the zord in the detailTextLabel within the same cell. Can someone tell me what I'm doing wrong

            ...

            ANSWER

            Answered 2021-Jun-14 at 08:17

            May be order here matters performSegue should be before deselectRow for if let index_path = self.table_View.indexPathForSelectedRow { to have a value

            Source https://stackoverflow.com/questions/67966703

            QUESTION

            Javascript Sort Date and time from String
            Asked 2021-Jun-12 at 11:59

            I have a list of objects named rides and I want to get the time and date fields and want to sort the data in ascending order

            ...

            ANSWER

            Answered 2021-Jun-12 at 11:56

            You can use Array#sort and parse the date and time of each element in a Date object for comparison:

            Source https://stackoverflow.com/questions/67948567

            QUESTION

            Logic edits all existing rows instead of adding new when using Save stored procedure
            Asked 2021-Jun-07 at 18:02

            I have an issue regarding SQL stored procedures. I have connected my SQL Server db to my ASP.NET Web Forms app and have created a button that uses Stored Procedures to Save data inside the db.

            I only want to use two fields on my front-end, namely Name and Surname. I do not want other moderators to input the Id (which is the primary key), so the stored procedure must increment it by itself once they add some Name and Surname.

            However, once data has been put in the fields, all rows get populated with that data?

            Example database.

            Id Name Surname 1 Alex Smith 2 Bob Phoenix 3 Correy Lollas

            After clicking on the Insert button I have created populating Name and Surname (Id is supposed to autoincrement)

            Id Name Surname 1 Test Name 2 Test Name 3 Test Name

            Stored procedure, although I think the problem is in the logic.

            ...

            ANSWER

            Answered 2021-Jun-07 at 13:58

            The answer was to change @Id int = NULL to @Id int and also just WHERE ([Id] = @Id). Now everything is working as it should.

            Full:

            Source https://stackoverflow.com/questions/67872264

            QUESTION

            Uncaught (in promise) TypeError: states.filter is not a function at searchStates
            Asked 2021-Jun-07 at 13:42

            ...

            ANSWER

            Answered 2021-Jun-07 at 13:42

            The expected JSON result from your question is not the same as the JSON from the API!

            You can use states.items.filter instead of states.filter but the API linked has no property abbr so it will return undefined:

            Source https://stackoverflow.com/questions/67872675

            QUESTION

            How to position google autocomplete predictions?
            Asked 2021-Jun-06 at 18:45

            I have a table with a list of contacts as seen in the image. I also have an event that gets triggered when a row is clicked so it can show the selected contact detail (I am using angular NGIF directive to show and hide the detail)

            The thing is because my google input is placed inside an NGIF block, when user expands the contact detail and tries to type in it, the predictions (pac-container) is showing on the row that I clicked (within the table) rather than underneath the google input autocomplete search box.

            I tried to manipulate the css of the class pac-container but I couldn't figure out a way to override the css of that class.

            Here is my the html of my autocomplete search box

            ...

            ANSWER

            Answered 2021-Jun-06 at 18:45

            I had to go with a DOM Manipulation way using JS.. so I added a (keyUp) event handler on google search box with a method to calculate the position like the following:

            Source https://stackoverflow.com/questions/67846670

            QUESTION

            How do I plot weather data from two data sets on one bar graph using python?
            Asked 2021-May-29 at 19:32

            Python newbie here. I'm looking at some daily weather data for a couple of cities over the course of a year. Each city has its own csv file. I'm interested in comparing the count of daily average temperatures between two cities in a bar graph, so I can see (for example) how often the average temperature in Seattle was 75 degrees (or 30 or 100) compared to Phoenix.

            I'd like a bar graph with side-by-side bars with temperature on the x-axis and count on the y-axis. I've been able to get a bar graph of each city separately with this data, but don't know how to get both cities on the same bar chart with with a different color for each city. Seems like it should be pretty simple, but my hours of search haven't gotten me a good answer yet.

            Suggestions please, oh wise stackoverflow mentors?

            Here's what I've got so far:

            ...

            ANSWER

            Answered 2021-May-29 at 19:32

            You can concat DataFrames, assigning city as a column, and then use histplot in seaborn:

            Source https://stackoverflow.com/questions/67753461

            QUESTION

            Is there a way to get the modified data from within a EEx template
            Asked 2021-May-27 at 23:17

            I'm using EEx template engine to render HTML pages (no Phoenix here). I'm passing the connection (Plug.Conn) conn to the template along with extracted parameter list (params) and the session map (session) with : body = EEx.eval_file(path, conn: conn, params: conn.params, session: session). params and session are provided just for convenience as they also are in the connection.

            If the page modifies the session (configured with cookies), say with something like <% Plug.Conn.put_session(conn, "reply", 42) %>), this modifies the connection but this also remains local to the page and is not propagated.

            Is there a way to retrieve this modified version of the connection from the EEx engine ?

            NB: I'm talking about the connection (Plug.Conn), but it could be any variable that is modified or created by the template engine, just a similar way Code.eval_string("a=1\n b=2\n c=a+b") does : {3, [a: 1, b: 2, c: 3]}.

            ...

            ANSWER

            Answered 2021-May-25 at 15:13

            EEx.eval_file and EEx.eval_string both return a String type, they do not return the updated bindings (as, like you say, Code.eval_string does).

            I think the reasoning behind this is that you want a render function to have no side-effects (like database calls or session modification).

            You don't want business-logic in your templates, you want to put that in your controller or data layer (with the advantage that you can test it in isolation).

            Maybe offtopic, but if you're coming from a PHP background (where you can put all your code in one file that looks like an HTML template) this might be the source of the confusion.

            Update

            This could work though:

            Source https://stackoverflow.com/questions/67685731

            QUESTION

            wxPython - can't call class method within __init__
            Asked 2021-May-27 at 15:39

            I know this is probably a basic question, but I'm just getting into GUI building and haven't needed to dabble much in classes for that matter. I have some code (see below) to handle the GUI portion of the program (the CLI version is already running perfectly, but management runs for the hills whenever they see a CLI...), but I can't quite get it to work out. FYI running python 3.9.1 and wxPython 4.1.1 Phoenix (though wx.version also spits out wxWidgets 3.1.5, if that's relevant) on Windows 10

            A lot of the code was based around examples / other folks asking stuff here, and unfortunately I can't find the original posts to credit them, but this is really just for learning and once I have a grasp of what I'm doing I'll be writing everything from scratch. So to the original authors, I apologize, but I thank you enormously!

            The program is to display a "start" screen (frame), with just a title and single button. On clicking the button, a modal file dialog box opens where the user selects the .csv data file to use, the start frame disappears, and a new frame appears with a view of the data in the right pane (in a grid sizer) and some drop downs and radio buttons in the left pane. The last drop-down (self.inputNum) will be bound to an event handler which will add a number of additional drop-downs for the user to select the different targets to analyze (the number of course being determined by their selection in the self.inputNum combobox). However, when running the script, I get an error

            ...

            ANSWER

            Answered 2021-Apr-28 at 17:12

            Sorry folks, my pre-coffee brain was calling CreateGrid() when the function is defined as createGrid(). There were a few other mistakes in the code (event handlers that referred to buttons that I no longer had implemented, calling StartFrame.makeMenuBar from a different class without also importing the functions StartFrame.makeMenuBar called, etc).

            But still feel free to point out inefficiencies and redundancies and other various un-pythonic things I'm doing. Still learning :)

            Source https://stackoverflow.com/questions/67303430

            QUESTION

            Is there a way to setup 2 frontends in phoenix app?
            Asked 2021-May-27 at 14:51

            In the project I have phoenix web app which serves its own frontend (webpack 5, served on "/")

            ...

            ANSWER

            Answered 2021-May-27 at 14:51

            Did you tried the following structure for your Nuxt app?

            Source https://stackoverflow.com/questions/67723979

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

            Vulnerabilities

            No vulnerabilities reported

            Install phoenix

            Please see the wiki for a detailed install guide.

            Support

            TGen [tgen] (default) Fastq files are chunked to 40M reads Chunks are aligned with BWA, processed with samtools fixmate and samtools sort Individual chunks are merged with samtools merge PCR duplicates and platform (optical) duplicates are marked with samtools markdupGATK Best Paractices [broad]("Like" - does not support uBAM inputs) Fastq files are chunked to 40M reads Chunks are aligned with BWA, and converted to BAM files with samtools view In one step individual chunks are merged and PCR or platform (optical) duplicates are marked with GATK/Picard markduplicates Alignment records are sorted using GATK/Picard SortSAMClinical [ashion] Fastq files are concatenated In one step reads are aligned with BWA, duplicates are marked with samblaster, converted to BAM and sorted using sambambaBase Recalibration (optional, off by default) chunked baserecalibration using GATKBAM to CRAM (enabled by default) samtools viewVariant Discovery (SNV/INDEL) Deepvariant (Only calls on primary contigs 1-22, X, Y) requires a GPU compute resource GATK HaplotypeCaller (gVCF mode) gVCF generation single sample calling using genotypeGVCFs and CNNscroreVariant Freebayes Strelka2 (Germline mode) Octopus (Individual) (Only calls on primary contigs 1-22, X, Y)Structural Variant Detection MantaCopy Number Analysis iCHOR (operates on genomes only)Variant Discovery (SNV/INDEL) Strelka2 (Somatic mode) Mutect2 Lancet Currently NOT enabled for genomes by default VarDictJava Octopus (Only calls on primary contigs 1-22, X, Y)Structural Variant Detection Manta DellyCopy Number Analysis GATK CNV iCHOR (operates on genomes only)RNA Alignment STAR 2-pass mode outputs unsorted BAM by default option to output TranscriptomeSAM unsorted BAM is processed with samtools fixmate and samtools sort to output a sorted BAM PCR duplicates and platform duplicates (optical) are optionally marked as a QC step samtools markdup GATK/Picard MarkDuplicates (default recommendation)Gene and Transcript Expression Estimates Salmon Star-count - Recommended count method HtSeq FeatureCountsFusion Transcript Detection Star-Fusion10x Genomics Cell Ranger Supports 3' and 5' assays Supports VDJ analysisstarSOLO Supports 3' and 5' assays
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