metient 0.1.1.dev3__tar.gz → 0.1.1.dev4__tar.gz

{metient-0.1.1.dev3 → metient-0.1.1.dev4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.0
 Name: metient
-Version: 0.1.1.dev3
+Version: 0.1.1.dev4
 Summary: UNKNOWN
 Home-page: https://github.com/divyakoyy/metient.git
 Author: UNKNOWN

{metient-0.1.1.dev3 → metient-0.1.1.dev4}/README.md

@@ -11,14 +11,14 @@ pip install metient
 ```
 
 ## Tutorial
-A tutorial for running calibrate mode is available [here](https://github.com/divyakoyy/metient/blob/main/metient_calibrate_tutorial.ipynb)
+A tutorial for running calibrate mode is available [here](https://github.com/divyakoyy/metient/blob/main/tutorial/metient_calibrate_tutorial.ipynb)
 
 
 ## Inputs
 There are two required inputs, a tsv file with the reference and variant counts for each sample and mutation, and a txt file specifying the edges of the clone tree.
 
 ### 1. **Tsv file**
-Each row in the tsv should correspond to the reference and variant read counts at a single locus in a single tumor sample. 
+Each row in the tsv should correspond to the reference and variant read counts at a single locus in a single tumor sample.  
 
 The required fields for the tsv file:
 | Column name | Description |
@@ -30,7 +30,7 @@ The required fields for the tsv file:
 | **cluster_index** | If using a clustering method, the cluster index that this mutation belongs to. NOTE: this must correspond to the indices used in the tree txt file. Rows with the same anatomical site index and cluster_index will get pooled together.|
 | **ref** | The number of reads that map to the reference allele for this mutation or mutation cluster in this anatomical site. |
 | **var** | The number of reads that map to the variant allele for this mutation or mutation cluster in this anatomical site. |
-| **site_category** | Must be one of `primary` or `metastasis`. If multiple primaries are specified (i.e., the true primary is not known), we will run Metient multiple times with each primary used as the true primary. Output files are saved with the suffix `_{anatomical_site_label}` to indicate which primary was used in that run. |
+| **site_category** | Must be one of `primary` or `metastasis`. If multiple primaries are specified, such that the `primary` label is used for multiple different anatomical site indices (i.e., the true primary is not known), we will run Metient multiple times with each primary used as the true primary. Output files are saved with the suffix `_{anatomical_site_label}` to indicate which primary was used in that run. |
 | **var_read_prob** | This gives Metient the ability to correct for the effect copy number alterations CNAs) have on the relationship between VAF (i.e., the proportion of alleles bearing the mutation) and subclonal frequency (i.e., the proportion of cells bearing the mutation). Let j = character_index. This is the probabilty of observing a read from the variant allele for mutation at j in a cell bearing the mutation. Thus, if mutation at j occurred at a diploid locus, this should be 0.5. In a haploid cell (e.g., male sex chromosome), this should be 1.0. If a CNA duplicated the reference allele in the lineage bearing mutation j prior to j occurring, there will be two reference alleles and a single variant allele in all cells bearing j, such that var_read_prob = 0.3333. If using a CN caller that reports major and minor CN: `var_read_prob = (p*maj)/(p*(maj+min)+(1-p)*2)`, where `p` is tumor purity, `maj` is major CN, `min` is minor CN, and we're assuming the variant allele has major CN. For more information, see S2.2 of [PairTree's supplementary info](https://aacr.silverchair-cdn.com/aacr/content_public/journal/bloodcancerdiscov/3/3/10.1158_2643-3230.bcd-21-0092/9/bcd-21-0092_supplementary_information_suppsm_sf1-sf21.pdf?Expires=1709221974&Signature=dJH6~Dg-6gEb-S88i0wDGW28QZn16keQj34Vo2tAvJL2cUJrQo48afpHPp-a2zAwQa~ET6SDgw3hb3ITacB06GDUc3GYCdCgYtfPMjFGwygFj-Q9xf-c44VAvwiyliwsBXK1shZmURlFMwSjzkwRwasuWu50sMNmeJSoVyX3nQ-rRBlK93aDR5s9c0l-p4aGvTi6QmfKJPsxXaHB4Lz5yXSl3Xd~JPK-Y~ltC14epDRb~MiSPWUFCAiYetUXcQ7J7vd6b4XQKT9PnYkjQtUq55tLSoUkOGe5JkJ32NXCeoT~l-XD97pCeDYVDOYzAuOkAG0tDYrPebEh2TGTA3fnbA__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA) for more details. |
 
 

{metient-0.1.1.dev3 → metient-0.1.1.dev4}/metient.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.0
 Name: metient
-Version: 0.1.1.dev3
+Version: 0.1.1.dev4
 Summary: UNKNOWN
 Home-page: https://github.com/divyakoyy/metient.git
 Author: UNKNOWN

{metient-0.1.1.dev3 → metient-0.1.1.dev4}/setup.py

@@ -4,4 +4,4 @@ with open('requirements.txt') as f:
     requirements = f.read().splitlines()
     #print(requirements)
 
-setup(name='metient', version='0.1.1.dev3', url="https://github.com/divyakoyy/metient.git", packages=['metient', 'metient.util', 'metient.lib'], install_requires=requirements,)
+setup(name='metient', version='0.1.1.dev4', url="https://github.com/divyakoyy/metient.git", packages=['metient', 'metient.util', 'metient.lib'], install_requires=requirements,)