MGA | original version of MGA has been archived - please see | Data Visualization library
kandi X-RAY | MGA Summary
kandi X-RAY | MGA Summary
MGA is a quality control tool for high-throughput sequence data. It screens for contaminants by aligning sequence reads in FASTQ format against a series of reference genomes using Bowtie and against a set of adapter sequences using Exonerate. MGA samples a subset of the reads, by default 100000, prior to alignment against reference genome sequences and adapters. This reduces considerably the overall run time. In addition, the reads are trimmed to 36 bases by default, prior to alignment by Bowtie. This is to ensure consistency of the output mapping and error rates across runs of differing lengths. Exonerate alignment against adapters uses the full-length sequences.
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Top functions reviewed by kandi - BETA
- Run the FASTQ file
- Reads the next FASTQ entry from the current reader
- Construct a FASTQ formatted sequence from the given lines
- Writes the summary to XML file
- Parses the command line options
- Prints the usage information
- Prints an error message
- Runs the FASTQ file
- Returns the number of lines in a file
- Configures the command line options
- Returns a string representation of this dataset
- Validate the meta data
- Estimates the number of lines in the given file
- Returns a String representation of the parameters
- Parse the command - line options
- Runs the FASTQ sampling algorithm
- Build the command line options
- Writes the MGAS report
- Merge FASTQ files into chunks
- Parses the command line arguments
- Parses the app session configuration
- Parses the FASTQ file
- Setup the options for this FASTQ output
- Setup the default options for this sequence
- Runs the pipeline
- Runs the analysis
MGA Key Features
MGA Examples and Code Snippets
Community Discussions
Trending Discussions on MGA
QUESTION
I'm trying to import data from semicolon separated csv file into a SQL Server database. Here is the table structure
...ANSWER
Answered 2022-Mar-12 at 12:06The SQL Server import facilities are very intolerant of bad data and even just formatting variations or options. In my career, I have literally spent thousands of work-hours trying to develop and debug import procedures for customers. I can tell you right now, that trying to fix this with SQL alone is both difficult and time-consuming.
When you have this problem (bad data and/or inconsistent formatting) it is almost always easier to find or develop a more flexible tool to pre-process the data into the rigid standard that SQL expects. So I would say that if Excel can parse it then just use Excel automation to pre-process them and then use SQL to import the Excel output. If that's not practical for you, then I'd advise writing your own tool in some client language (C#, Vb, Java, Python, etc.) to pre-process the files.
You can do it in SQL (and I have done it many times), but I promise you that it is a long complicated trek.
SSIS has more flexible error-handling for problems like this, but if you are not already familiar and using it, it has a very steep learning curve and your first SSIS project is likely to be very time-consuming also.
QUESTION
I submitted all of my code below for a better understanding. The code is fine, my question is: How can I perfectly show multiple countries with their country name list? I mean: When I change the country name, then the flag image should be changed automatically, so users see the country name and image. I already put many links in my loadFlag() function in my js file, but this is not working. Please help me, how can i do it with my code? Thanks in advance and love from the top of my heart.
...ANSWER
Answered 2022-Mar-02 at 17:43You're loading country flags from flagcdn.com in which each png is named after a two-letter country code that you have in your country_code value.
You just need to update your loadFlag function to properly update the img tag's property values. See the working code snippet below.
QUESTION
Here's how I parse the xml response from this url
...ANSWER
Answered 2022-Feb-23 at 15:19Unfortunately, you have to deal with the namespace in the file. So try it this way:
QUESTION
this is json output:
{"query":{"apikey":"...","base_currency":"USD","timestamp":1635972203},"data":{"JPY":113.99127,"CNY":6.39464,"CHF":0.9114,"CAD":1.23881,"MXN":20.54423,"INR":74.44808,"BRL":5.57063,"RUB":71.80098,"KRW":1175.11443,"IDR":14295.1734,"TRY":9.63691,"SAR":3.75119,"SEK":8.52554,"NGN":410.22181,"PLN":3.94541,"ARS":99.81213,"NOK":8.49529,"TWD":27.78459,"IRR":42000.64577,"AED":3.67284,"COP":3827.77643,"THB":33.32047,"ZAR":15.23269,"DKK":6.40357,"MYR":4.15212,"SGD":1.34783,"ILS":3.11624,"HKD":7.78416,"EGP":15.7003,"PHP":50.65881,"CLP":811.73282,"PKR":169.4547,"IQD":1458.01958,"DZD":136.722,"KZT":428.93534,"QAR":3.6499,"CZK":21.94293,"PEN":4.0008,"RON":4.25921,"VND":22747.41599,"BDT":85.57148,"HUF":308.78687,"UAH":26.25062,"AOA":598.0065,"MAD":9.06226,"OMR":0.38491,"CUC":24.00026,"BYR":2.00003,"AZN":1.69502,"LKR":200.00259,"SDG":438.90856,"SYP":2511.07513,"MMK":1746.02836,"DOP":56.29093,"UZS":10690.31508,"KES":111.25137,"GTQ":7.73108,"URY":44.18107,"HRV":6.47553,"MOP":8.01811,"ETB":47.31305,"CRC":635.74442,"TZS":2298.03956,"TMT":3.49009,"TND":2.80635,"PAB":1.00002,"LBP":1505.5263,"RSD":101.16202,"LYD":4.54568,"GHS":6.00013,"YER":249.956,"BOB":6.82018,"BHD":0.377,"CDF":1999.22628,"PYG":6875.19435,"UGX":3550.05822,"SVC":8.7497,"TTD":6.74137,"AFN":90.84208,"NPR":119.13277,"HNL":24.06657,"BIH":1.68483,"BND":1.34753,"ISK":129.16264,"KHR":4060.117,"GEL":3.14003,"MZN":63.22108,"BWP":11.45513,"PGK":3.5113,"JMD":153.22216,"XAF":564.86281,"NAD":15.2189,"ALL":105.53113,"SSP":391.0052,"MUR":42.90097,"MNT":2830.04693,"NIO":35.21094,"LAK":10330.27262,"MKD":53.08156,"AMD":474.80501,"MGA":3928.06091,"XPF":102.48118,"TJS":11.26034,"HTG":98.0013,"BSD":1.00003,"MDL":17.41883,"RWF":1018.02194,"KGS":84.77099,"GNF":9510.20822,"SRD":21.40242,"SLL":10779.18736,"XOF":568.81159,"MWK":807.36713,"FJD":2.06806,"ERN":15.05028,"SZL":15.21372,"GYD":207.78611,"BIF":1980.25293,"KYD":0.82002,"MVR":15.42042,"LSL":15.23032,"LRD":146.80405,"CVE":94.95278,"DJF":177.50237,"SCR":14.42749,"SOS":575.00647,"GMD":52.15123,"KMF":424.6543,"STD":21.11031,"XRP":0.83002,"AUD":1.34372,"BGN":1.68394,"BTC":0.0159,"JOD":0.70801,"GBP":0.73402,"ETH":0.00022,"EUR":0.86112,"LTC":0,"NZD":1.40184}}
The data section contains many key value pairs, but their number and names vary according to base_currency. (For example if i send request with USD there is no USD key or if i send request with CNY there is no CNY key in data section)
So what kind of data class should I create so that I can use it with the retrofit and gsoncreator libraries. (I am also trying to use and learn jetpack android libraries if this is important)
i use that data classes: (I am not using gson annotations because i believe my variables names are correct and i try that it doesn't help)
data class ResponseFromApi(val data: Data,val query: Query)
data class Query(val apikey: String, val base_currency: String, val timestamp: Int)
data class Data(val hashmapForData: HashMap) (i suspect some values are integer but i am not sure)
it doesn't work. Maybe that's not the problem. I don't know but least i need to know, Are these classes correct? What is the proper way to do this.
And i don't know how to get error message from retrofit object so i can identify the problem. But this is another question.
...ANSWER
Answered 2021-Nov-04 at 09:37Arpit Shukla's answer is correct.
QUESTION
I have recently started to work with airborne LiDAR data that has a compound coordinate reference system consisting of a horizontal (projected) and vertical component. An example, with code to create a compound CRS object from a WKT description, is shown below.
I'm deriving various raster layers from the LiDAR point cloud and I want to assign just the horizontal component of the compound CRS to each of these (EPSG:7856 in the example). Does anyone know of an existing package function that will extract the horizontal PROJCRS component reliably, i.e. allowing for a variety of old and new CRS definitions?
Update 2021-11-01: Tweaked the original example of a WKT string to provide code to create a compound CRS object in R.
...ANSWER
Answered 2021-Nov-01 at 08:42After much trawling through the R spatial jungle I haven't yet found an existing function to extract the horizontal CRS component. The function below is my attempt to write one. I've tested it with old and new LiDAR data, where the older data has a simple (just horizontal) CRS and the new data has a compound CRS.
I'm sure there must be an existing and better way.
Update 2021-11-01: Tweaked the function to accept any spatial object compatible with the sf::st_crs() function.
QUESTION
I have a static website repo hosted with Github Pages. The javascript must load two text files (.yml files more precisely) stored in that same repo in a data folder. The functions used to load the two files are the following:
ANSWER
Answered 2021-Aug-16 at 08:19Alright I found the problem. It actually comes from the syntax used in the yaml files. The first characters in the file seem to matter. I experimented with the content of a YAML file and here are the results when loaded through the hosted github page:
- Simplest content: loads correctly
QUESTION
have scraped data from this website and now I wanat to turn the data into a Pandas dataframe. The data looks like this:
...ANSWER
Answered 2021-Jul-06 at 18:52You have a Json string, so parse it before creating a dataframe:
QUESTION
I have a text file that I am trying to extract data from using regular expressions, here is a sample of the text file :
...ANSWER
Answered 2021-Jun-09 at 19:38You can just break that one capture group into 2 and separate them out with whitespaces:
QUESTION
I have a field that looks like this :
...ANSWER
Answered 2021-May-31 at 14:39You can match anything except whitespace and digits with the following expression:
QUESTION
I have an API that return data that looks like this :
...ANSWER
Answered 2021-Mar-30 at 14:01Probably MatchTransactions.onlyInFile1 is undefined, so when the ngFor directive tries to access MatchTransactions.onlyInFile1[0] you get that error.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install MGA
You can use MGA like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the MGA component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .
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