Runtime &results on example

[mbosio85]

Hello,

I tried your tool on the example dataset and it died tue to timeout in the pairwise alignment phase.
I extended the value to 300 but still it died for this line :

"ENSMUSP00000009538 ENSMUSP00000009538 ENSMUSP00000016664"

In this other line an error pops up due to the alignment did not output any value ('[]'),
Is it expected ?

ENSMUSP00000100212 ENSMUSP00000100212 ENSMUSP00000137424

Should I switch to the commented code in the alignment part and use localmd vs globalmd? would it affect the performances ?
alignments = align(isoform_seq, main_iso_seq, ratio)#pairwise2.align.localmd(isoform_seq, main_iso_seq, 5, -4, -100, -10, -10 * ratio, -1.5)

Then I just wanted to ask you what is the expected classification for the example cases [1,0] so that I know that that the output I am getting is the correct one.

One final question, looking in the extract_features.py
n_termini = 1 if sum(s2[:20] == '-') == 0 else (-1 if sum(s2[:20] == '-') > 12 else 0)
This would output 1 if she sum is '0', 0 if it is >0 and <= 12 :, and 2 if the sum is > 12.
Is this the expected behavior?

Thanks for your help!

Mattia

[AlexandrNP]

Hello Mattia, We are sorry for inconveniences. We are currently updating Alt-In Tool. There were issues with BioPython and we have addressed them already by switching to EMBOSS alignment. Because we are trying to make a standalone version of tool we discarded requirement for InterProScan but we need a very specific set of scripts from superfamily. For your convenience we offer to use a docker image with all installed prerequisites. You can run test examples simply by executing following commands. Please note that instation of docker is required. docker run -it narykov/alt-in:latest bash cd .. python altintool.py test/interactors.tsv test/diabetes_ensembl_protein.fa test/string_protein.fa test/results.txt If you have further questions or need more assistance to work with our code please feel free to contact me using this email or my university email onarykov@wpi.edu Best regards, Oleksandr Narykov

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On Thu, Jan 24, 2019 at 10:41 AM Mattia Bosio ***@***.***> wrote: Hello, I tried your tool on the example dataset and it died tue to timeout in the pairwise alignment phase. I extended the value to 300 but still it died for this line : "ENSMUSP00000009538 ENSMUSP00000009538 ENSMUSP00000016664" In this other line an error pops up due to the alignment did not output any value ('[]'), Is it expected ? ENSMUSP00000100212 ENSMUSP00000100212 ENSMUSP00000137424 Should I switch to the commented code in the alignment part and use *localmd* vs *globalmd*? would it affect the performances ? alignments = align(isoform_seq, main_iso_seq, ratio)#pairwise2.align.localmd(isoform_seq, main_iso_seq, 5, -4, -100, -10, -10 * ratio, -1.5) Then I just wanted to ask you what is the expected classification for the example cases [1,0] so that I know that that the output I am getting is the correct one. One final question, looking in the extract_features.py n_termini = 1 if sum(s2[:20] == '-') == 0 else (-1 if sum(s2[:20] == '-') > 12 else 0) This would output *1* if she sum is '0', *0* if it is >0 and <= 12 :, and *2* if the sum is > 12. Is this the expected behavior? Thanks for your help! Mattia — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADfnOkZmFqy9SF_qw-eNuK2VDHyr9SFIks5vGdQlgaJpZM4aRIs7> .