Comments (5)
ewachtel
commented on August 14, 2024
All suboptimal alignments are reported up to the specified distance
criteria in the arguments described in the help section. Note that if a
query is very long, shorter alignments that have a high probability of
occurring randomly will not be reported.
Regards,
Ed
Ed Wachtel
(917) 573-7591
…On Fri, Mar 18, 2022 at 10:19 PM Mehdi Borji ***@***.***> wrote:
Is there a way to report all alignments up to the distance requested? For
example if I have an alignment with distance of 1 in the beginning of a
query I prefer than to an alignment with distance of 0 somewhere else. The
solution I can think of is have moving window across the query however I
believe these suboptimal alignments are already found but just not
reported. Something like would be very useful for trimming trailing or
leading strings from a longer one.
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mehdiborji
commented on August 14, 2024
Thank you @ewachtel for your response. Is this feature also part of the python wrapper?
Here's an example where I introduce one mismatch in my query and edlib fails to report it because a perfect alignment exists elsewhere:
C='GTGTGCTCTTCCGATCT'
V='TCTTCAGCGTTCCCGAGA'
my_string=2*C+V+C+'A'+V[1:]+C
edlib.align(V, my_string,'HW','locations',1)
{'editDistance': 0,
'alphabetLength': 4,
'locations': [(34, 51)],
'cigar': None}
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ewachtel
commented on August 14, 2024
I was thinking of a different project. Actually, I am not the right person
to discuss edlib (I did not author it)
Ed Wachtel
(917) 573-7591
…On Sun, Mar 20, 2022 at 2:16 PM Mehdi Borji ***@***.***> wrote:
Thank you @ewachtel <https://github.com/ewachtel> for your response. Is
this feature also part of the python wrapper?
Here's an example where I introduce one mismatch in my query and edlib
fails to report it because a perfect alignment exists elsewhere:
C='GTGTGCTCTTCCGATCT'
V='TCTTCAGCGTTCCCGAGA'
my_string=2*C+V+C+'A'+V[1:]+C
edlib.align(V, my_string,'HW','locations',1)
{'editDistance': 0,
'alphabetLength': 4,
'locations': [(34, 51)],
'cigar': None}
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cherryamme
commented on August 14, 2024
Did you find anyway to solve this problem? @mehdiborji
I want result to report all possible site too
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Martinsos
commented on August 14, 2024
Hey @cherryamme @mehdiborji !
So edlib (C version) does return multiple locations: either just their ends, or their ends + starts, depends on what you tell it to do.
When returning alignment, it does it only for one of those however.
It has been some time since I have worked on edlib so I can't remember 100%, but I believe alignments for other end locations could probably also be obtained. However Edlib doesn't do that at the moment, and it would require some changes to the codebase. I currently don't have time to work on this, but if somebody wants to take it on I can try to help.
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Related Issues (20)
- Is there a suffix mode? HOT 3
- align two arrays of strings HOT 7
- anchored alignment HOT 2
- Error when query or target is the empty string and task='path'
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- Mention Perl binding in Readme HOT 2
- Cigar results interpretation
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- [Documentation] (1) mention ruby-bindings and (2) mention "why use edlib" in the main README HOT 1
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- Wheels for macos python 3.11 HOT 1
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- How to report all possibale positions not only the best one ? HOT 1
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