SigProfilerExtractor 1.2.2__tar.gz → 1.2.3__tar.gz

{sigprofilerextractor-1.2.2/SigProfilerExtractor.egg-info → sigprofilerextractor-1.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SigProfilerExtractor
-Version: 1.2.2
+Version: 1.2.3
 Summary: Extracts mutational signatures from mutational catalogues
 Home-page: https://github.com/AlexandrovLab/SigProfilerExtractor.git
 Author: S Mishu Ashiqul Islam
@@ -130,7 +130,7 @@ sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37",
 |  | **output** | String | The name of the output folder. The output folder will be generated in the current working directory.  |
 |  | **input_data** | String | <br>Path to input folder for input_type:<ul><li>`vcf`</li><li>`bedpe`</li></ul>Path to file for input_type:<ul><li>`matrix`</li><li>`seg:TYPE`</li></ul> |
 |  | **reference_genome** | String | The name of the reference genome (default: `"GRCh37"`). This parameter is applicable only if the `input_type` is `"vcf"`. |
-|  | **opportunity_genome** | String | The build or version of the reference genome for the reference signatures (default: `"GRCh37"`). When the input_type is `"vcf"`, the opportunity_genome automatically matches the input reference genome value. Only the genomes available in COSMIC are supported (`GRCh37`, `GRCh38`, `mm9`, `mm10`, and `rn6`). If a different opportunity genome is selected, the default genome `GRCh37` will be used. |
+|  | **opportunity_genome** | String | The build or version of the reference genome for the reference signatures (default: `"GRCh37"`). When the input_type is `"vcf"`, the opportunity_genome automatically matches the input reference genome value. Only the genomes available in COSMIC are supported (`GRCh37`, `GRCh38`, `mm9`, `mm10`, `mm39`, `rn6`, and `rn7`). If a different opportunity genome is selected, the default genome `GRCh37` will be used. |
 |  | **context_type** | String | Mutation context name(s), separated by commas (`,`), that define the mutational contexts for signature extraction (default: `"96,DINUC,ID"`). In the default value, `96` represents the SBS96 context, `DINUC` represents the dinucleotide context, and `ID` represents the indel context. |
 |  | **exome** | Boolean | Defines if the exomes will be extracted (default: `False`). |
 | **NMF Replicates** |  |  |  | 

{sigprofilerextractor-1.2.2 → sigprofilerextractor-1.2.3}/README.md

@@ -97,7 +97,7 @@ sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37",
 |  | **output** | String | The name of the output folder. The output folder will be generated in the current working directory.  |
 |  | **input_data** | String | <br>Path to input folder for input_type:<ul><li>`vcf`</li><li>`bedpe`</li></ul>Path to file for input_type:<ul><li>`matrix`</li><li>`seg:TYPE`</li></ul> |
 |  | **reference_genome** | String | The name of the reference genome (default: `"GRCh37"`). This parameter is applicable only if the `input_type` is `"vcf"`. |
-|  | **opportunity_genome** | String | The build or version of the reference genome for the reference signatures (default: `"GRCh37"`). When the input_type is `"vcf"`, the opportunity_genome automatically matches the input reference genome value. Only the genomes available in COSMIC are supported (`GRCh37`, `GRCh38`, `mm9`, `mm10`, and `rn6`). If a different opportunity genome is selected, the default genome `GRCh37` will be used. |
+|  | **opportunity_genome** | String | The build or version of the reference genome for the reference signatures (default: `"GRCh37"`). When the input_type is `"vcf"`, the opportunity_genome automatically matches the input reference genome value. Only the genomes available in COSMIC are supported (`GRCh37`, `GRCh38`, `mm9`, `mm10`, `mm39`, `rn6`, and `rn7`). If a different opportunity genome is selected, the default genome `GRCh37` will be used. |
 |  | **context_type** | String | Mutation context name(s), separated by commas (`,`), that define the mutational contexts for signature extraction (default: `"96,DINUC,ID"`). In the default value, `96` represents the SBS96 context, `DINUC` represents the dinucleotide context, and `ID` represents the indel context. |
 |  | **exome** | Boolean | Defines if the exomes will be extracted (default: `False`). |
 | **NMF Replicates** |  |  |  | 

{sigprofilerextractor-1.2.2 → sigprofilerextractor-1.2.3}/SigProfilerExtractor/sigpro.py

@@ -1094,25 +1094,19 @@ def sigProfilerExtractor(
         devopts["make_decomposition_plots"] = make_decomposition_plots
 
         # Check if genome_build is available in COSMIC, if not reset to GRCh37
-        if (
-            genome_build == "GRCh37"
-            or genome_build == "GRCh38"
-            or genome_build == "mm9"
-            or genome_build == "mm10"
-            or genome_build == "rn6"
-        ):
+        if genome_build in ["GRCh37", "GRCh38", "mm9", "mm10", "mm39", "rn6", "rn7"]:
             genome_build = genome_build
         else:
             sysdata = open(out_put + "/JOB_METADATA.txt", "a")
             sysdata.write(
-                "\n[{}] The selected opportunity genome is {}. COSMIC signatures are available only for GRCh37/38, mm9/10 and rn6 genomes. So, the opportunity genome is reset to GRCh37.\n".format(
+                "\n[{}] The selected opportunity genome is {}. COSMIC signatures are available only for GRCh37/38, mm9/10/39 and rn6/7 genomes. So, the opportunity genome is reset to GRCh37.\n".format(
                     str(datetime.datetime.now()).split(".")[0], str(genome_build)
                 )
             )
             print(
                 "The selected opportunity genome is "
                 + str(genome_build)
-                + ". COSMIC signatures are available only for GRCh37/38, mm9/10 and rn6 genomes. So, the opportunity genome is reset to GRCh37."
+                + ". COSMIC signatures are available only for GRCh37/38, mm9/10/39 and rn6/7 genomes. So, the opportunity genome is reset to GRCh37."
             )
             sysdata.close()
             genome_build = "GRCh37"

sigprofilerextractor-1.2.3/SigProfilerExtractor/version.py

@@ -0,0 +1,7 @@
+
+# THIS FILE IS GENERATED FROM SIGPROFILEREXTRACTOR SETUP.PY
+short_version = '1.2.3'
+version = '1.2.3'
+Update = 'v1.2.3: Add support for rn7 and mm39 genomes'
+    
+    

{sigprofilerextractor-1.2.2 → sigprofilerextractor-1.2.3/SigProfilerExtractor.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SigProfilerExtractor
-Version: 1.2.2
+Version: 1.2.3
 Summary: Extracts mutational signatures from mutational catalogues
 Home-page: https://github.com/AlexandrovLab/SigProfilerExtractor.git
 Author: S Mishu Ashiqul Islam
@@ -130,7 +130,7 @@ sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37",
 |  | **output** | String | The name of the output folder. The output folder will be generated in the current working directory.  |
 |  | **input_data** | String | <br>Path to input folder for input_type:<ul><li>`vcf`</li><li>`bedpe`</li></ul>Path to file for input_type:<ul><li>`matrix`</li><li>`seg:TYPE`</li></ul> |
 |  | **reference_genome** | String | The name of the reference genome (default: `"GRCh37"`). This parameter is applicable only if the `input_type` is `"vcf"`. |
-|  | **opportunity_genome** | String | The build or version of the reference genome for the reference signatures (default: `"GRCh37"`). When the input_type is `"vcf"`, the opportunity_genome automatically matches the input reference genome value. Only the genomes available in COSMIC are supported (`GRCh37`, `GRCh38`, `mm9`, `mm10`, and `rn6`). If a different opportunity genome is selected, the default genome `GRCh37` will be used. |
+|  | **opportunity_genome** | String | The build or version of the reference genome for the reference signatures (default: `"GRCh37"`). When the input_type is `"vcf"`, the opportunity_genome automatically matches the input reference genome value. Only the genomes available in COSMIC are supported (`GRCh37`, `GRCh38`, `mm9`, `mm10`, `mm39`, `rn6`, and `rn7`). If a different opportunity genome is selected, the default genome `GRCh37` will be used. |
 |  | **context_type** | String | Mutation context name(s), separated by commas (`,`), that define the mutational contexts for signature extraction (default: `"96,DINUC,ID"`). In the default value, `96` represents the SBS96 context, `DINUC` represents the dinucleotide context, and `ID` represents the indel context. |
 |  | **exome** | Boolean | Defines if the exomes will be extracted (default: `False`). |
 | **NMF Replicates** |  |  |  | 

{sigprofilerextractor-1.2.2 → sigprofilerextractor-1.2.3}/setup.py

@@ -8,7 +8,7 @@ import subprocess
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = "1.2.2"
+VERSION = "1.2.3"
 
 
 with open("README.md") as f:
@@ -21,7 +21,7 @@ def write_version_py(filename="SigProfilerExtractor/version.py"):
 # THIS FILE IS GENERATED FROM SIGPROFILEREXTRACTOR SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
-Update = 'v1.2.2: Add mutation count and stability to 4608 plots in All_Solutions and a stop parameter'
+Update = 'v1.2.3: Add support for rn7 and mm39 genomes'
     
     """
     fh = open(filename, "w")

sigprofilerextractor-1.2.2/SigProfilerExtractor/version.py

@@ -1,7 +0,0 @@
-
-# THIS FILE IS GENERATED FROM SIGPROFILEREXTRACTOR SETUP.PY
-short_version = '1.2.2'
-version = '1.2.2'
-Update = 'v1.2.2: Add mutation count and stability to 4608 plots in All_Solutions and a stop parameter'
-    
-