partis

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Welcome to the partis support group. The idea is to use this to send announcements, and to discuss topics (such as support requests) that don't fit well into specific issues or feature requests on github.

For specific issues with the software, e.g. bug reports and feature requests, please submit an issue. Additionally, since lots of topics are also discussed in the issues, you can search through them.

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Evan Li, Duncan Ralph6

Apr 25

HMM parameters (similar to what linearham is using)

Ah, ok that makes more sense. That is referring to the partis rearrangement/naive sequence viterbi

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HMM parameters (similar to what linearham is using)

Ah, ok that makes more sense. That is referring to the partis rearrangement/naive sequence viterbi

Apr 25

ape...@gmail.com, Duncan Ralph2

Apr 8

sequence and germline start

I'm not sure that I'm interpreting this correctly -- it might be safer to give an example.

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sequence and germline start

I'm not sure that I'm interpreting this correctly -- it might be safer to give an example.

Apr 8

Elizabeth Van Itallie, Duncan Ralph2

Mar 4

min-cluster-size in Linearham

I'm pretty sure that setting one or both of --min-selection-metric-cluster-size or --min-paired-

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min-cluster-size in Linearham

I'm pretty sure that setting one or both of --min-selection-metric-cluster-size or --min-paired-

Mar 4

Feb 21

Over the past few months I've been converting partis from python 2 to 3, and I've just pushed

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Over the past few months I've been converting partis from python 2 to 3, and I've just pushed

Feb 21

11/9/23

default clustering on large samples

I recently changed the default behavior such that when clustering large samples (>10k seqs) --fast

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default clustering on large samples

I recently changed the default behavior such that when clustering large samples (>10k seqs) --fast

11/9/23

Elizabeth Van Itallie, Duncan Ralph2

10/11/23

setting emission probabilities

First, here's some example hmm files (they'll be in the same relative location in any partis

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setting emission probabilities

First, here's some example hmm files (they'll be in the same relative location in any partis

10/11/23

Elizabeth Van Itallie, … Duncan Ralph3

7/28/23

inverted D annotation

It doesn't consider them, no, but you're correct that just adding reversed D sequences to the

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inverted D annotation

It doesn't consider them, no, but you're correct that just adding reversed D sequences to the

7/28/23

Evi Van Itallie, Duncan Ralph2

4/19/23

linearham run_bootstrap_asr_ess.R

I've never run that stuff in parallel, but our best guess is it might have to do with library

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linearham run_bootstrap_asr_ess.R

I've never run that stuff in parallel, but our best guess is it might have to do with library

4/19/23

Jesse Connell, Duncan Ralph7

3/3/23

Some general partis questions

Interesting. I'll try to narrow down a minimal example of the "all -inf" thing for you.

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Some general partis questions

Interesting. I'll try to narrow down a minimal example of the "all -inf" thing for you.

3/3/23

Jamie Oaks, Duncan Ralph3

1/27/23

Total (forward) probability of a receptor sequence

No apology necessary. Your detailed (and fast) response is very helpful. Much appreciated, thanks!

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Total (forward) probability of a receptor sequence

No apology necessary. Your detailed (and fast) response is very helpful. Much appreciated, thanks!

1/27/23

Evi Van Itallie, Duncan Ralph2

12/7/22

logprob ranking for partition returns

Whoops! Yes, you're completely right, "lowest" is incorrect, it should say "

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logprob ranking for partition returns

Whoops! Yes, you're completely right, "lowest" is incorrect, it should say "

12/7/22

11/7/22

Docker hub deprecation

Docker hub has gradually become unusable (at least on free tier) the last few years, so I am

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Docker hub deprecation

Docker hub has gradually become unusable (at least on free tier) the last few years, so I am

11/7/22

Jesse Connell, Duncan Ralph7

2/25/22

Proper format of input for paired case (and in general)

Not sure if my message a minute ago went through, so just to reiterate, it works now! Thanks. I get a

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Proper format of input for paired case (and in general)

Not sure if my message a minute ago went through, so just to reiterate, it works now! Thanks. I get a

2/25/22

9/3/21

There's a few new-ish features that I thought folks might be interested in or at least want to be

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There's a few new-ish features that I thought folks might be interested in or at least want to be

9/3/21

Lmar Babrak, Duncan Ralph2

1/14/21

Numbering scheme for partis?

Hi, We use IMGT numbering, with the caveats: 1) positions in partis output files all use 0-based

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Numbering scheme for partis?

Hi, We use IMGT numbering, with the caveats: 1) positions in partis output files all use 0-based

1/14/21

5/16/20

per-base mutation rates for simulation

I just pushed a change to master that changes default behavior for simulation, so wanted to make sure

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per-base mutation rates for simulation

I just pushed a change to master that changes default behavior for simulation, so wanted to make sure

5/16/20

nbst...@gmail.com, Duncan Ralph5

5/1/20

Give partis count information for input seqs

In case anyone was using the info in this thread, it's now out of date. We now do use

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Give partis count information for input seqs

In case anyone was using the info in this thread, it's now out of date. We now do use

5/1/20

5/1/20

predicting affinity with partis

We've just added a new feature to partis: predicting the affinity of each sequence. Given an

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predicting affinity with partis

We've just added a new feature to partis: predicting the affinity of each sequence. Given an

5/1/20

Ayelet Peres, Duncan Ralph2

4/2/20

Yeah running 'cache-parameters' will be the fastest way to run only allele inference. You

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Yeah running 'cache-parameters' will be the fastest way to run only allele inference. You

4/2/20

JP, … Duncan Ralph4

11/14/19

Memory consumption

Yes, in almost all real repertoires the cluster size distribution is dominated by small clusters. As

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Memory consumption

Yes, in almost all real repertoires the cluster size distribution is dominated by small clusters. As

11/14/19

12/7/18

So I probably should have done this a while ago, but it just occurred to me to add some documentation

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So I probably should have done this a while ago, but it just occurred to me to add some documentation

12/7/18

Kristian Davidsen, … Duncan Ralph9

11/20/18

Custom germline database

Yes! That's exactly right, what I needed to add was the biocore channel, which has a much newer

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Custom germline database

Yes! That's exactly right, what I needed to add was the biocore channel, which has a much newer

11/20/18

zacand...@gmail.com, Duncan Ralph2

10/26/18

Understanding the naming scheme for inferred alleles

oops, missed hitting reply all. Also may as well add: I just learned yesterday that the macaque

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Understanding the naming scheme for inferred alleles

oops, missed hitting reply all. Also may as well add: I just learned yesterday that the macaque

10/26/18

7/11/18

yaml output files

I just merged into master the new default yaml output file format. This is a big simplification,

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yaml output files

I just merged into master the new default yaml output file format. This is a big simplification,

7/11/18

GrubaK, Duncan Ralph2

7/11/18

Differences in assigning

re-sending to the list email, since I apparently missed hitting reply-all when I originally replied

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Differences in assigning

re-sending to the list email, since I apparently missed hitting reply-all when I originally replied

7/11/18

Jakub Otwinowski, … Duncan Ralph8

1/17/18

cdr3 boundaries

I just added an option --extra-annotation-columns so you can specify non-default annotation columns

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cdr3 boundaries

I just added an option --extra-annotation-columns so you can specify non-default annotation columns

1/17/18

nbst...@gmail.com, … Duncan Ralph5

11/30/17

Get bounds for all regions: CDRs and FWRs

Here's an old email from someone with details on the --presto-output and some attached aligned

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Get bounds for all regions: CDRs and FWRs

Here's an old email from someone with details on the --presto-output and some attached aligned

11/30/17

nbst...@gmail.com, Duncan Ralph4

11/27/17

CDR3 seq column for partis annotate?

Yeah, it looks like it inferred a new allele in your sample, so it needs the germline info directory

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CDR3 seq column for partis annotate?

Yeah, it looks like it inferred a new allele in your sample, so it needs the germline info directory

11/27/17

nbst...@gmail.com, Duncan Ralph2

11/17/17

Cannot allocate memory, OSError

That does seem like a lot of memory, although it's hard to put exact numbers on what to expect.

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Cannot allocate memory, OSError

That does seem like a lot of memory, although it's hard to put exact numbers on what to expect.

11/17/17

nbst...@gmail.com, Duncan Ralph4

11/17/17

error when 'looking for new alleles'

Thanks Ralph. I updated my scipy and it fixed this problem. On Thu, Nov 16, 2017 at 10:47 AM, Duncan

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error when 'looking for new alleles'

Thanks Ralph. I updated my scipy and it fixed this problem. On Thu, Nov 16, 2017 at 10:47 AM, Duncan

11/17/17

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