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License: MIT License
Cleavage site prediction via de novo assembly
License: MIT License
Could be more straightforward when reasoning.
hardclip is distinct from softclip as it's related to chimeric contigs,
see if it's indeed necessary to consider it separately from softclip (likely).
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This is because the coordinate information is currently lost when the sequence is extracted from contig.
Currently, this search function is used to search for hexamer in the contig, it only takes into account the extracted sequence with cigar information missing.
Line 66 in 933e240
Maybe it's easier to define the searching window (e.g. 50bp) wst. to the reference, the actual sequence length wst. contig could be a few bp more or less than 50bp.
contig: A0.S101817
clv: 204513795
strand: +
ctg_hex: AATAAA
ref_hex: NA
Extracted seqs:
ctg: GAATAAAAGTTGAAGCTGCTGATACTGAACAAACAAGTGAAGAAGTAGGG
ref: ATAAAAGTTGAAGCTGCTGATACTGAACAAACAAGTGAAGAAGTAGGGAA
Given a chimeric contig, when a bridge read is aligned to the contig, the contig is in one piece; but when the contig is aligned to the genome, it becomes two pieces.
Problem: When looping through the contig to the first-piece, how to infer the genome coord of a clv that's actually aligned the second piece?
main difficulty
File "stringsource", line 2, in pysam.libcalignedsegment.AlignedSegment.__reduce_cython__
TypeError: self._delegate cannot be converted to a Python object for pickling
See BTL-1171
Then use ML to figure out which PAS hexamer is more important
Currently benchmarking, cluster first, and realized that summing up num_suffix_reads is buggy as one suffix read, based on the current definition, can support multiple neighbouring cleavage sites before clustering.
Potential solution:
adf['ctg_hex_dist'] = adf.ctg_hex_pos - adf.clv
adf['ref_hex_dist'] = adf.ref_hex_pos - adf.clv
prefer tail_base as it sounds most relevant to APA
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