inScan | Region based insertion detection from long reads | Genomics library

by Nextomics Python Version: Current License: GPL-3.0

X-Ray Key Features Code Snippets Community Discussions(2)Vulnerabilities Install Support

kandi X-RAY | inScan Summary

inScan is a Python library typically used in Artificial Intelligence, Genomics applications. inScan has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. However inScan build file is not available. You can download it from GitHub.

inScan is devoloping for finding genomic insertion variation from long reads(from both Pacbio and Nanopore sequencing). inScan differs from the published state of art Structure Variation detecting tools(Sniffles and NanoSV) for long reads sequencing technology in two ways. First, inScan can find complex insertions when the insert sequence mapped to another chromosome. Second, inScan detects insertions in a given region, therefore useful for quickly checking if there are insertions in the region(Short Tandem Repeat region for example) of interest.

Support

Quality

Security

License

Reuse

Support

inScan has a low active ecosystem.

It has 3 star(s) with 0 fork(s). There are 6 watchers for this library.

It had no major release in the last 6 months.

inScan has no issues reported. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of inScan is current.

Quality

inScan has 0 bugs and 0 code smells.

Security

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

inScan code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

inScan 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.

Reuse

inScan releases are not available. You will need to build from source code and install.

inScan 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.

It has 272 lines of code, 24 functions and 5 files.

It has medium code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed inScan and discovered the below as its top functions. This is intended to give you an instant insight into inScan implemented functionality, and help decide if they suit your requirements.

Calculates the number of insertions in the read fragment
Calculate the length of the reference sequence
Return the distance between two sequences
Check if two fragments are in the same ref
Get all regions in a BED file
Return a dictionary of reads that are in scan
The overlap between two ranges
Return the end of the query end
Return the query length

Get all kandi verified functions for this library.

inScan Key Features

No Key Features are available at this moment for inScan.

inScan Examples and Code Snippets

No Code Snippets are available at this moment for inScan.

Community Discussions

Trending Discussions on inScan

Display JSON Response specific keys/values using PHP

Printing a snake pattern in java using an array

QUESTION

Display JSON Response specific keys/values using PHP

Asked 2020-Jul-23 at 20:12

I want to display specific keys and values from the following JSON Response I am using API to fetch the JSON values:

...

ANSWER

Answered 2020-Jul-23 at 20:12

$js = json_decode($response, true);

foreach($js as $return){    
    echo $return['tracking_data']['track_status'];
    foreach($return['tracking_data']['shipment_track'] as $st){
        echo $st['pickup_date'];
    }

    foreach($return['tracking_data']['shipment_track_activities'] as 
       $sta){
       echo $sta['date'];
       echo $sta['status'];
    }
} ?>

Source https://stackoverflow.com/questions/63060905

QUESTION

Printing a snake pattern in java using an array

Asked 2020-Apr-11 at 03:36

I'm having trouble with an assignment where we are required to print out this array:

1 10 11 20 21

2 9 12 19 22

3 8 13 18 23

4 7 14 17 24

5 6 15 16 25

My code is somewhat correct but it is not printing 10 and 19 where it should be.

My output:

Choose a number for the rows from 0 to 16. 5 Choose a number for the columns from 0 to 16 5 1 0 10 0 19
2 9 11 18 20
3 8 12 17 21
4 7 13 16 22
5 6 14 15 23

My code:

...

ANSWER

Answered 2020-Apr-11 at 01:20

Idk if this is exactly what you're asking for, but this will generate the "snaking" pattern you described.

It could be simplified with ternary but this makes it more readable I think

It would be interesting to find a more clever way about it though, if anyone finds a better way pls comment

Source https://stackoverflow.com/questions/61150845

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

Vulnerabilities

No vulnerabilities reported

Install inScan

inScan takes three positional arguments, a bam file, a bed file, a output file name. inScan has been tested using NGMLR, BWA mem, Minimap2 output bam files. Generally, inScan will work for a bam file with "SA" tag. bed file contains the regions to be tested.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

Find more information at: