MartGro

## Chatterjees_Xi.ipynb

      
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                MartGro
                / Chatterjees_Xi.ipynb
            
            
              Created
              December 26, 2021 19:55
            
              
                Quick demonstration of a new coefficient of correlation
              
          
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## installing rmats
https://bioconda.github.io/recipes/rmats/README.html

1) install it via conda
conda install rmats -c bioconda

2) check
which rmats.py


## IQ Samples
Places where you can find recordings of radio signals with different modulations:

https://www.sdrangel.org/iq-files/
https://www.sdrplay.com/iq-demo-files/
https://lucasteske.dev/satcom-projects/sample-baseband-files

## build.log
cpanm (App::cpanminus) 1.7044 on perl 5.030003 built for x86_64-linux
Work directory is /home/stud/ga42vor/.cpanm/work/1591284525.30081
You have make /usr/bin/make
You have LWP 6.44
You have /bin/tar: tar (GNU tar) 1.29
Copyright © 2015 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

## conda_dependencies.txt
# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
_libgcc_mutex=0.1=main
_openmp_mutex=5.1=1_gnu
argcomplete=3.1.1=pypi_0
argh=0.27.2=pypi_0
biopython=1.79=pypi_0
ca-certificates=2023.7.22=hbcca054_0
certifi=2016.9.26=py36_0

## RSP1_instructions.md

      
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                MartGro
                / RSP1_instructions.md
            
            
              Last active
              February 12, 2023 08:44
            
              
                Getting the RSP1 to run under Ubuntu 20.04
              
          
Get the Driver

Download the driver from the following link:
https://www.sdrplay.com/dlfinishs/

Follow the Instructions of CubicSDR

For instructions on how to build CubicSDR on Linux, refer to the following link:

  
## napari_image_display_widget.py
import sys
from PyQt5.QtWidgets import QApplication, QLabel
from PyQt5.QtGui import QPixmap

class ImageWidget(QLabel):
    """
    A QLabel widget that displays an image from a file
    """
    def __init__(self, parent=None):
        """

## How to align long sequences with BWA
Aligning > 1MB long sequences (e.g. long DNA sequences) can take quite long with Needleman Wunsch

An alternative is using the BWA:
http://bioinformatics-core-shared-training.github.io/cruk-bioinf-sschool/Day1/Sequence%20Alignment_July2015_ShamithSamarajiwa.pdf

#1 Create index:
../bwa-0.7.17/bwa index -p index_path -a bwtsw dna_reference.fasta


./bwa-0.7.17/bwa mem -t 16 index_path dna_of_interest.fasta | ./samtools-1.16.1/samtools sort -o output.bam -

## extract_roi.py
# This relies on the read-roi library from here: https://github.com/hadim/read-roi
# Additionally, it requires shapely for the polygons
# And ray for parallelizing

from read_roi import read_roi_zip
import glob

#find all roi zip files
all_zip_path = glob.glob("your_folder/*.zip")

## HowTo Run flatCAM
1) Download FlatCAM_beta_8.994_sources

2) Python 3.8

3) Manually install gdal from conda

4) Bug fixes:
- Vector bug fix
	https://bioconda.github.io/recipes/rmats/README.html

	1) install it via conda
	conda install rmats -c bioconda

	2) check
	which rmats.py
	Places where you can find recordings of radio signals with different modulations:

	https://www.sdrangel.org/iq-files/
	https://www.sdrplay.com/iq-demo-files/
	https://lucasteske.dev/satcom-projects/sample-baseband-files
	cpanm (App::cpanminus) 1.7044 on perl 5.030003 built for x86_64-linux
	Work directory is /home/stud/ga42vor/.cpanm/work/1591284525.30081
	You have make /usr/bin/make
	You have LWP 6.44
	You have /bin/tar: tar (GNU tar) 1.29
	Copyright © 2015 Free Software Foundation, Inc.
	License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
	This is free software: you are free to change and redistribute it.
	There is NO WARRANTY, to the extent permitted by law.
	# This file may be used to create an environment using:
	# $ conda create --name <env> --file <this file>
	# platform: linux-64
	_libgcc_mutex=0.1=main
	_openmp_mutex=5.1=1_gnu
	argcomplete=3.1.1=pypi_0
	argh=0.27.2=pypi_0
	biopython=1.79=pypi_0
	ca-certificates=2023.7.22=hbcca054_0
	certifi=2016.9.26=py36_0
	import sys
	from PyQt5.QtWidgets import QApplication, QLabel
	from PyQt5.QtGui import QPixmap

	class ImageWidget(QLabel):
	"""
	A QLabel widget that displays an image from a file
	"""
	def __init__(self, parent=None):
	"""
	Aligning > 1MB long sequences (e.g. long DNA sequences) can take quite long with Needleman Wunsch

	An alternative is using the BWA:
	http://bioinformatics-core-shared-training.github.io/cruk-bioinf-sschool/Day1/Sequence%20Alignment_July2015_ShamithSamarajiwa.pdf

	#1 Create index:
	../bwa-0.7.17/bwa index -p index_path -a bwtsw dna_reference.fasta


	./bwa-0.7.17/bwa mem -t 16 index_path dna_of_interest.fasta \| ./samtools-1.16.1/samtools sort -o output.bam -
	# This relies on the read-roi library from here: https://github.com/hadim/read-roi
	# Additionally, it requires shapely for the polygons
	# And ray for parallelizing

	from read_roi import read_roi_zip
	import glob

	#find all roi zip files
	all_zip_path = glob.glob("your_folder/*.zip")
	1) Download FlatCAM_beta_8.994_sources

	2) Python 3.8

	3) Manually install gdal from conda

	4) Bug fixes:
	- Vector bug fix