https://github.com/ibchgenomic/pacbiohifi-read-analyzer

pacbiohifi read analyzer using recursion
https://github.com/ibchgenomic/pacbiohifi-read-analyzer

bioinformatics bioinformatics-tool pacbio pacbio-data pacbio-hifi-sequencing-reads pacbiohifi

Last synced: 2 months ago
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pacbiohifi read analyzer using recursion

• Host: GitHub
• URL: https://github.com/ibchgenomic/pacbiohifi-read-analyzer
• Owner: IBCHgenomic
• License: mit
• Created: 2024-08-17T19:53:47.000Z (9 months ago)
• Default Branch: main
• Last Pushed: 2024-08-17T19:55:19.000Z (9 months ago)
• Last Synced: 2025-03-11T23:15:34.899Z (2 months ago)
• Topics: bioinformatics, bioinformatics-tool, pacbio, pacbio-data, pacbio-hifi-sequencing-reads, pacbiohifi
• Language: Python
• Homepage:
• Size: 2.93 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# pacbio-polyATGC-trimmer-recursion

a shorter version after implementing a array recompile and storing the variables while running a subtle part of the recursion. Brian Haas told me to find it a way to make it shorter. I implemented a recursive recompile with in the code and remove all the if iterations. so the code is now only a block of code and not blocks of code. I stored the variables in an array and then put a recursive recompile on the array. 

```

longreadpolyATGCtrimmer("/Users/gauravsablok/Desktop/CodeCheck/fasta_sample_datasets/test_sample_short.fasta",

                              polyATGCstretch_type="G")

	ids	sequences	stretch_count	trimmed_sequences_new

0	>1	GCAGCGTACGTGGTTGGATCAATTAGTGGGGCACATTTGAATCCAG...	[27, 30]	GCAGCGTACGTGGTTGGATCAATTAGTGCACATTTGAATCCAGCTT...

1	>2	GCAGCGTACGTGGTTGGATCAATTAGTGGGGCACATTTGAATCCAG...	[27, 30]	GCAGCGTACGTGGTTGGATCAATTAGTGCACATTTGAATCCAGCTT...

2	>3	GCAGCGTACGTGGTTGGATCAATTAGTGGGGCACATTTGAATCCAG...	[27, 30]	GCAGCGTACGTGGTTGGATCAATTAGTGCACATTTGAATCCAGCTT...

3	>4	CGAAAATTACTTCGGTACAATGCTTGTATACATGGGCAAAGCACAC...	[33, 36]	CGAAAATTACTTCGGTACAATGCTTGTATACATCAAAGCACACGGT...

```

Gaurav Sablok \

University of Potsdam \

Potsdam,Germany