[allow_multiple_mappings] more than two mappings possible?

[antonkratz]

allow_multiple_mappings will default to 0 (false) if it is not included. To allow the same term to be mapped twice (only in the case that two possible mappings are mathematically equivalent), simply set this argument to 1.

Can I also search for more than two multiple mappings? Does 1 mean it allows multiple (more than two mappings) or only up to two ("twice")?

Basically, I want to ask for a very permissive mapping, where it is OK for one system to map to multiple systems; is that possible?

[mhk7]

Hi Anton,

allow_multiple_mappings actually allows for an unlimited number of mappings as long as they are mathematically equivalent. If there are any slight differences it will still just pick the best mapping. Hope that helps!

Michael

On Wed, Aug 24, 2022 at 5:35 PM Anton Kratz @.***> wrote:

allow_multiple_mappings will default to 0 (false) if it is not included. To allow the same term to be mapped twice (only in the case that two possible mappings are mathematically equivalent), simply set this argument to 1.

Can I also search for more than two multiple mappings? Does 1 mean it allows multiple (more than two mappings) or only up to two ("twice")?

Basically, I want to ask for a very permissive mapping, where it is OK for one system to map to multiple systems; is that possible?

— Reply to this email directly, view it on GitHub https://github.com/mhk7/alignOntology/issues/6, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4KDMJTAOGT5MKVW4QRNB3V22PUNANCNFSM57Q7PR7A . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[antonkratz]

Hi Anton, allow_multiple_mappings actually allows for an unlimited number of mappings as long as they are mathematically equivalent. If there are any slight differences it will still just pick the best mapping. Hope that helps! Michael …

Can I allow_multiple_mappings also in combination with calculateFDRs? According to the documentation, it looks like calculateFDRs does not accept it?! Thanks!

[mhk7]

I didn't implement that since I thought it added complexity and I didn't see a use case for it at the time, but if you'd like to try it all you have to do is edit the calculateFDRs script very slightly.

Just change the 0 to a 1 as the 5th argument in these two lines in the script and that should do it:

$DIR/alignOntology $ONT1 $GO_ONT $THRESHOLD $VER_MODE 0 1 $TERM_NAME > $RESULTS_DIR/alignment.out &

$DIR/alignOntology $RESULTS_DIR/rand_files/randont$ITER $GO_ONT $THRESHOLD $VER_MODE 0 1 $TERM_NAME > $RESULTS_DIR/randfiles/alignment$ITER &

Best, Michael

On Thu, Aug 25, 2022 at 11:55 AM Anton Kratz @.***> wrote:

Hi Anton, allow_multiplemappings actually allows for an unlimited number of mappings as long as they are mathematically equivalent. If there are any slight differences it will still just pick the best mapping. Hope that helps! Michael … <#m-9148387167393247921_> On Wed, Aug 24, 2022 at 5:35 PM Anton Kratz @.> wrote: allow_multiple_mappings will default to 0 (false) if it is not included. To allow the same term to be mapped twice (only in the case that two possible mappings are mathematically equivalent), simply set this argument to 1. Can I also search for more than two multiple mappings? Does 1 mean it allows multiple (more than two mappings) or only up to two ("twice")? Basically, I want to ask for a very permissive mapping, where it is OK for one system to map to multiple systems; is that possible? — Reply to this email directly, view it on GitHub <#6 https://github.com/mhk7/alignOntology/issues/6>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4KDMJTAOGT5MKVW4QRNB3V22PUNANCNFSM57Q7PR7A https://github.com/notifications/unsubscribe-auth/AB4KDMJTAOGT5MKVW4QRNB3V22PUNANCNFSM57Q7PR7A . You are receiving this because you are subscribed to this thread.Message ID: @.>

Can I allow_multiple_mappings also in combination with calculateFDRs? According to the documentation, it looks like calculateFDRs does not accept it?! Thanks!

— Reply to this email directly, view it on GitHub https://github.com/mhk7/alignOntology/issues/6#issuecomment-1227529616, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4KDMKUM2QRTRSC3JP7OQDV26QQTANCNFSM57Q7PR7A . You are receiving this because you commented.Message ID: @.***>