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Cluster.fit command #415

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mothur-westcott opened this issue Jan 22, 2018 · 4 comments
Closed

Cluster.fit command #415

mothur-westcott opened this issue Jan 22, 2018 · 4 comments
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Enhancement
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Version 1.41.0

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@mothur-westcott
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mothur-westcott commented Jan 22, 2018 •
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Fit sequences to existing dataset model.

  • Calc distances needed - Within new data and from new data to model
  • Initialize dataset model - sens.spec on existing data model, place new data in singletons
  • Move new data sequences around until optimal fit is found
  • Create new list file

Simple Example:
Old Data:
otu1 otu2 otu3 otu4 otu5
A,B,C,D,E F,G,H,I J,K L M

New Data:
N O P Q R

New List:
otu2 otu4 otu5
O,Q,R N P
@mothur-westcott mothur-westcott added this to the Version 1.40.0 milestone Jan 22, 2018
mothur-westcott added a commit that referenced this issue Jan 29, 2018
@mothur-westcott
Creates sensspeccalc class
ea7b75d 
#240 #415
mothur-westcott added a commit that referenced this issue Jan 29, 2018
@mothur-westcott
Adds cluster.fit command
6619081 
#415
@mothur-westcott
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Required: model list, fasta and count file as well as the fasta file to fit.
Optional: model’s distance matrix to save the calc time, name or count file for fit data.
Outputs: Clustered fit data in a list file with OTUlabels from your model data. If sequences are not fitted to the existing OTUS they are outputted in an *unfitted.list file.

mothur-westcott added a commit that referenced this issue Jan 29, 2018
@mothur-westcott
Updates screen output
8313cd3 
#415
mothur-westcott added a commit that referenced this issue Jan 30, 2018
@mothur-westcott
Updates project file
419f4dc 
#415
mothur-westcott added a commit that referenced this issue May 3, 2018
@mothur-westcott
WIP Cluster.fit
a58c974 
#415
mothur-westcott added a commit that referenced this issue May 11, 2018
@mothur-westcott
Refactor opti code
703346a 
#415
mothur-westcott added a commit that referenced this issue May 17, 2018
@mothur-westcott
WIP optifit
ad592a1 
#415
mothur-westcott added a commit that referenced this issue May 17, 2018
@mothur-westcott
Fixes cluster.fit read and initialize
94dbbdc 
#415
mothur-westcott added a commit that referenced this issue May 31, 2018
@mothur-westcott
Working on optifit initialization
08f5d71 
#415
mothur-westcott added a commit that referenced this issue Jun 3, 2018
@mothur-westcott
Adds function to extract unfitted reads
df05f72 
#415
mothur-westcott added a commit that referenced this issue Jun 4, 2018
@mothur-westcott
Autobuild fix
43ebf72 
#415
mothur-westcott added a commit that referenced this issue Jun 5, 2018
@mothur-westcott
WIP clustering unfitted
ab39abd 
#415
mothur-westcott added a commit that referenced this issue Jun 8, 2018
@mothur-westcott
Adds open method
6cc572b 
#415
mothur-westcott added a commit that referenced this issue Jun 8, 2018
@mothur-westcott
Fixes issues with unfitted extraction
0a9da89 
#415
mothur-westcott added a commit that referenced this issue Jun 11, 2018
@mothur-westcott
WIP cluster.fit open/close
a4b23d0 
#415
mothur-westcott added a commit that referenced this issue Jun 12, 2018
@mothur-westcott
Adds refphylip parameter
b833fdd 
#415
mothur-westcott added a commit that referenced this issue Jun 12, 2018
@mothur-westcott
Updates cluster.fit outputs
0c2927d 
#415
mothur-westcott added a commit that referenced this issue Jun 14, 2018
@mothur-westcott
Prep functions to take self reference
fb2c1da 
#415
mothur-westcott added a commit that referenced this issue Jun 14, 2018
@mothur-westcott
Adds tag to reference otus
121c425 
#415
mothur-westcott added a commit that referenced this issue Jun 15, 2018
@mothur-westcott
Adds sensspec function
dd258d1 
#415
mothur-westcott added a commit that referenced this issue Jun 15, 2018
@mothur-westcott
WIP cluster.fit denovo
cb89ac6 
#415
mothur-westcott added a commit that referenced this issue Jul 5, 2018
@mothur-westcott
Improves optiref class for denovo
335d145 
#415
mothur-westcott added a commit that referenced this issue Jul 16, 2018
@mothur-westcott
Adds denovoiters parameter
fb759de 
#415
@krmaas
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krmaas commented Sep 17, 2018

I"m sooooo excited for this option!!!!

@pschloss
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shhhh! don't tell anyone, it's ultra-top secret 😄

mothur-westcott added a commit that referenced this issue Sep 18, 2018
@mothur-westcott
Adjusted screen output for cluster.fit
4d47ee2 
#415
mothur-westcott added a commit that referenced this issue Sep 25, 2018
@mothur-westcott
Adds criteria parameter to cluster.fit
d961118 
The criteria parameter allows you to indicate which metric will influence the fitting. Options are fit, combo and both. Default=both.
Using fit means a sequence will be fitted to an OTU if the fit makes the metric for the fitted sequences better (only considers metric value generated by fit seqs).
Using combo means a sequence will be fitted to an OTU if the fit makes the metric for the fitted and the reference sequences better (considers metric value generated by all reference and fit sequences).
Using both means a sequence will be fitted to an OTU if it makes the metric for the fitted sequences better (fit) or the metric for the combo better (combo)

#415
mothur-westcott added a commit that referenced this issue Sep 25, 2018
@mothur-westcott
Adds printer parameter to cluster.fit
40c1446 
The printref parameter allows to indicate whether you want the reference seqs printed with the fit seqs. For example, if you are trying to see how a new patient's data changes the clustering, you want to set printref=t so the old patient and new patient OTUs are printed together. If you want to see how your data would fit with a reference like silva, setting printref=f would output only your sequences to the list file. By default printref=t for denovo clustering and printref=f when using a reference.

#415
mothur-westcott added a commit that referenced this issue Oct 8, 2018
@mothur-westcott
Fixes bug in cluster.fit with singleton calc
dd65c8e 
WIP Biom update

#415 #178
@mothur-westcott
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Add accnos parameter to assign reference sequences.

mothur-westcott added a commit that referenced this issue Dec 18, 2018
@mothur-westcott
Adds accnos parameter to cluster.fit
51b3034 
The accnos parameter allows you to assign reference sequences by name. This can save time by allowing you to provide a distance matrix containing all the sequence distances rather than a sample matrix and reference matrix and mothur calculating the distances between the sample and reference.

#415
@mothur-westcott mothur-westcott mentioned this issue Dec 18, 2018
Merged
mothur-westcott added a commit that referenced this issue May 27, 2020
@mothur-westcott
Modifies cluster.fit so reflist can be used with denovo
9ecf3f1 
#705 #415
mothur-westcott added a commit that referenced this issue May 27, 2020
@mothur-westcott
#415 #705
0b0cb43
mothur-westcott added a commit that referenced this issue May 27, 2020
@mothur-westcott
#415 Update comments
d15f931
mothur-westcott added a commit that referenced this issue Mar 29, 2021
@mothur-westcott
Removes criteria parameter from cluster.fit
d558360 
#769 #415
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@pschloss @mothur-westcott @krmaas