bumping to 1.5.1; adding the name column back to the PeakCalling.ye…

…ast.call_peaks output; updating docs API section

callingcardstools/PeakCalling/yeast/call_peaks.py

@@ -106,8 +106,8 @@ def call_peaks(
     background_data_path: str,
     background_orig_chr_convention: str,
     chrmap_data_path: str,
-    deduplicate_experiment: bool = True,
     unified_chr_convention: str = "ucsc",
+    deduplicate_experiment: bool = True,
 ) -> pd.DataFrame:
     """
     Call peaks for the given Calling Cards data.
@@ -190,7 +190,9 @@ def call_peaks(
     ).set_index("name", drop=True)
 
     promoter_hops_df = (
-        promoter_df.set_index("name", drop=True)
+        promoter_df
+        .drop("score", axis=1)
+        .set_index("name")
         .join(
             [experiment_hops_df, background_hops_df],
             how="left",
@@ -209,6 +211,7 @@ def call_peaks(
                 "experiment_total_hops": "int64",
             }
         )
+        .reset_index()
     )
 
     start_time = time.time()
@@ -333,6 +336,13 @@ def parse_args(
         "something else, eg 'mitochondrial' or 'plasmid'.",
         required=True,
     )
+    parser.add_argument(
+        "--unified_chr_convention",
+        type=str,
+        help="the chromosome naming convention to use in the output " "DataFrame.",
+        required=False,
+        default="ucsc",
+    )
     parser.add_argument(
         "--deduplicate_experiment",
         action="store_true",
@@ -341,13 +351,6 @@ def parse_args(
         "coordinate on different strands, only one of those records will be "
         "retained.",
     )
-    parser.add_argument(
-        "--unified_chr_convention",
-        type=str,
-        help="the chromosome naming convention to use in the output " "DataFrame.",
-        required=False,
-        default="ucsc",
-    )
     parser.add_argument(
         "--output_path",
         default="sig_results.csv",
@@ -395,8 +398,8 @@ def main(args: argparse.Namespace) -> None:
         args.background_data_path,
         args.background_orig_chr_convention,
         args.chrmap_data_path,
-        args.deduplicate_experiment,
         args.unified_chr_convention,
+        args.deduplicate_experiment
     )
 
     result_df.to_csv(

callingcardstools/PeakCalling/yeast/enrichment.py

@@ -1,4 +1,5 @@
 import logging
+import warnings
 
 logger = logging.getLogger(__name__)
 
@@ -25,6 +26,8 @@ def enrichment(total_background_hops: int,
     :return: The Calling Cards effect (enrichment) value.
     :rtype: float
     """
+    warnings.warn("This function is deprecated and will be removed in a future release. "
+                  "use the vectorized function instead")
 
     numerator = (experiment_hops / (total_experiment_hops + pseudocount))
     denominator = (background_hops / (total_background_hops + pseudocount))

callingcardstools/PeakCalling/yeast/hypergeom_pval.py

@@ -1,8 +1,11 @@
 import logging
+import warnings
+
 from scipy.stats import hypergeom
 
 logger = logging.getLogger(__name__)
 
+
 def hypergeom_pval(total_background_hops: int,
                    total_experiment_hops: int,
                    background_hops: int,
@@ -21,6 +24,8 @@ def hypergeom_pval(total_background_hops: int,
     :return: The hypergeometric p-value.
     :rtype: float
     """
+    warnings.warn("This function is deprecated and will be removed in a future release. "
+                  "use the vectorized function instead")
     # check input
     if total_background_hops < 0 or not isinstance(total_background_hops, int):
         raise ValueError(('total_background_hops must '

callingcardstools/PeakCalling/yeast/poisson_pval.py

@@ -1,4 +1,5 @@
 import logging
+import warnings
 
 from scipy.stats import poisson
 
@@ -27,6 +28,8 @@ def poisson_pval(total_background_hops: int,
     :return: The Poisson p-value.
     :rtype: float
     """
+    warnings.warn("This function is deprecated and will be removed in a future release. "
+                  "use the vectorized function instead")
     # check input
     if total_background_hops < 0 or not isinstance(total_background_hops, int):
         raise ValueError(('total_background_hops must '

docs/API/Analysis/yeast/chipexo_promoter_sig/chipexo_promoter_sig.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.chipexo_promoter_sig.chipexo_promoter_sig
+    handler: python

docs/API/Analysis/yeast/chipexo_promoter_sig/main.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.chipexo_promoter_sig.main
+    handler: python

docs/API/Analysis/yeast/chipexo_promoter_sig/parse_args.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.chipexo_promoter_sig.parse_args
+    handler: python

docs/API/Analysis/yeast/chipexo_promoter_sig/read_in_chipexo_data.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.chipexo_promoter_sig.read_in_chipexo_data
+    handler: python

docs/API/Analysis/yeast/rank_response/bin_by_binding_rank.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.rank_response.bin_by_binding_rank.bin_by_binding_rank
+    handler: python

docs/API/Analysis/yeast/rank_response/calculate_random_expectation.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.rank_response.calculate_random_expectation.calculate_random_expectation
+    handler: python

docs/API/Analysis/yeast/rank_response/compute_rank_response.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.rank_response.compute_rank_response.compute_rank_response
+    handler: python

docs/API/Analysis/yeast/rank_response/create_partitions.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.rank_response.create_partitions.create_partitions
+    handler: python

docs/API/Analysis/yeast/rank_response/create_rank_response_table.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.rank_response.create_rank_response_table.create_rank_response_table
+    handler: python

docs/API/Analysis/yeast/rank_response/find_min_responsive/find_min_responsive.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.rank_response.find_min_responsive.find_min_responsive
+    handler: python

docs/API/Analysis/yeast/rank_response/find_min_responsive/main.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.rank_response.find_min_responsive_main.main
+    handler: python

docs/API/Analysis/yeast/rank_response/find_min_responsive/parse_args.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.rank_response.find_min_responsive_main.parse_args
+    handler: python

docs/API/Analysis/yeast/rank_response/label_responsive_genes.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.rank_response.label_responsive_genes.label_responsive_genes
+    handler: python

docs/API/Analysis/yeast/rank_response/parse_binomtest_results.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.rank_response.parse_binomtest_results.parse_binomtest_results
+    handler: python

docs/API/Analysis/yeast/rank_response/rank_response_main/main.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.rank_response.rank_response_main.main
+    handler: python

docs/API/Analysis/yeast/rank_response/rank_response_main/parse_args.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.rank_response.rank_response_main.parse_args
+    handler: python

docs/API/Analysis/yeast/rank_response/rank_response_ratio_summarize.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.rank_response.rank_response_ratio_summarize.rank_response_ratio_summarize
+    handler: python

docs/API/Analysis/yeast/rank_response/read_in_data.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.rank_response.read_in_data.read_in_data
+    handler: python

docs/API/Analysis/yeast/rank_response/set_none_str_to_none.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.rank_response.set_none_str_to_none.set_none_str_to_none
+    handler: python

docs/API/Analysis/yeast/rank_response/validate_config.md

@@ -0,0 +1,2 @@
+::: callingcardstools.Analysis.yeast.rank_response.validate_config.validate_config
+    handler: python

docs/API/PeakCalling/yeast/call_peaks/add_metrics.md

@@ -0,0 +1,2 @@
+::: callingcardstools.PeakCalling.yeast.call_peaks.add_metrics
+    handler: python

docs/API/PeakCalling/yeast/call_peaks/call_peaks.md

@@ -0,0 +1,2 @@
+::: callingcardstools.PeakCalling.yeast.call_peaks.call_peaks
+    handler: python

docs/API/PeakCalling/yeast/call_peaks/count_hops.md

@@ -0,0 +1,2 @@
+::: callingcardstools.PeakCalling.yeast.call_peaks.count_hops
+    handler: python

docs/API/PeakCalling/yeast/call_peaks/main.md

@@ -0,0 +1,2 @@
+::: callingcardstools.PeakCalling.yeast.call_peaks.main
+    handler: python

docs/API/PeakCalling/yeast/call_peaks/parse_args.md

@@ -0,0 +1,2 @@
+::: callingcardstools.PeakCalling.yeast.call_peaks.parse_args
+    handler: python

docs/API/PeakCalling/yeast/enrichment_vectorized.md

@@ -0,0 +1,2 @@
+::: callingcardstools.PeakCalling.yeast.enrichment_vectorized.enrichment_vectorized
+    handler: python

docs/API/PeakCalling/yeast/hypergeom_pval_vectorized.md

@@ -0,0 +1,2 @@
+::: callingcardstools.PeakCalling.yeast.hypergeom_pval_vectorized.hypergeom_pval_vectorized
+    handler: python

docs/API/PeakCalling/yeast/poisson_pval_vectorized.md

@@ -0,0 +1,2 @@
+::: callingcardstools.PeakCalling.yeast.poisson_pval_vectorized.poisson_pval_vectorized
+    handler: python

docs/API/PeakCalling/yeast/read_in_data/qbed_df_to_pyranges.md

@@ -0,0 +1,2 @@
+::: callingcardstools.PeakCalling.yeast.read_in_data.qbed_df_to_pyranges
+    handler: python

docs/API/PeakCalling/yeast/read_in_data/read_in_background_data.md

@@ -0,0 +1,2 @@
+::: callingcardstools.PeakCalling.yeast.read_in_data.read_in_background_data
+    handler: python

docs/API/PeakCalling/yeast/read_in_data/read_in_chrmap.md

@@ -0,0 +1,3 @@
+::: callingcardstools.PeakCalling.yeast.read_in_data.read_in_chrmap
+
+    handler: python

docs/API/PeakCalling/yeast/read_in_data/read_in_experiment_data.md

@@ -0,0 +1,2 @@
+::: callingcardstools.PeakCalling.yeast.read_in_data.read_in_experiment_data
+    handler: python

docs/API/PeakCalling/yeast/read_in_data/read_in_promoter_data.md

@@ -0,0 +1,2 @@
+::: callingcardstools.PeakCalling.yeast.read_in_data.read_in_promoter_data
+    handler: python

docs/API/PeakCalling/yeast/read_in_data/relabel_chr_column.md

@@ -0,0 +1,2 @@
+::: callingcardstools.PeakCalling.yeast.read_in_data.relabel_chr_column
+    handler: python

docs/home/changelog.md

@@ -4,6 +4,13 @@
 
 ### Changes
 
+- Needed to keep `name` in the output of PeakCalling.yeast.call_peaks
+- adding Analysis and PeakCalling modules to the documentation API section
+
+## Version 1.5.0
+
+### Changes
+
 - overhaul of the PeakCalling/yeast module to address memory usage.
   adding pyranges as a depedency as a result. removed `consider_strand`
   and added a argument to deduplicate the experiment qbeds based on

mkdocs.yml

@@ -37,11 +37,52 @@ nav:
     - SummaryParser: 'API/Alignment/SummaryParser.md'
     - mammals:
       - Qbed: 'API/Alignment/mammals/Qbed.md'
+  - Analysis:
+    - yeast:
+      - rank_response:
+        - bin_by_binding_rank: 'API/Analysis/yeast/rank_response/bin_by_binding_rank.md'
+        - calculate_random_expectation: 'API/Analysis/yeast/rank_response/calculate_random_expectation.md'
+        - compute_rank_response: 'API/Analysis/yeast/rank_response/compute_rank_response.md'
+        - create_partitions: 'API/Analysis/yeast/rank_response/create_partitions.md'
+        - create_rank_response_table: 'API/Analysis/yeast/rank_response/create_rank_response_table.md'
+        - label_responsive_genes: 'API/Analysis/yeast/rank_response/label_responsive_genes.md'
+        - parse_binomtest_results: 'API/Analysis/yeast/rank_response/parse_binomtest_results.md'
+        - rank_response_ratio_summarize: 'API/Analysis/yeast/rank_response/rank_response_ratio_summarize.md'
+        - read_in_data: 'API/Analysis/yeast/rank_response/read_in_data.md'
+        - set_none_str_to_none: 'API/Analysis/yeast/rank_response/set_none_str_to_none.md'
+        - validate_config: 'API/Analysis/yeast/rank_response/validate_config.md'
+        - find_min_responsive:
+          - find_min_responsive: 'API/Analysis/yeast/rank_response/find_min_responsive/find_min_responsive.md'
+          - parse_args: 'API/Analysis/yeast/rank_response/find_min_responsive/parse_args.md'
+          - main: 'API/Analysis/yeast/rank_response/find_min_responsive/main.md'
+        - chipexo_promoter_sig:
+          - read_in_chipexo_data: 'API/Analysis/yeast/chipexo_promoter_sig/read_in_chipexo_data.md'
+          - chipexo_promoter_sig: 'API/Analysis/yeast/chipexo_promoter_sig/chipexo_promoter_sig.md'
+          - parse_args: 'API/Analysis/yeast/chipexo_promoter_sig/parse_args.md'
+          - main: 'API/Analysis/yeast/chipexo_promoter_sig/main.md'
   - BarcodeParser:
     - mammals:
       - BarcodeCounterQc: 'API/BarcodeParser/mammals/BarcodeCounterQc.md'
     - yeast:
       - BarcodeCounterQc: 'API/BarcodeParser/yeast/BarcodeCounterQc.md'
+  - PeakCalling:
+    - yeast:
+      - read_in_data:
+        - qbed_df_to_pyranges: "API/PeakCalling/yeast/read_in_data/qbed_df_to_pyranges.md"
+        - read_in_background_data: "API/PeakCalling/yeast/read_in_data/read_in_background_data.md"
+        - read_in_chrmap: "API/PeakCalling/yeast/read_in_data/read_in_chrmap.md"
+        - read_in_experiment_data: "API/PeakCalling/yeast/read_in_data/read_in_experiment_data.md"
+        - read_in_promoter_data: "API/PeakCalling/yeast/read_in_data/read_in_promoter_data.md"
+        - relabel_chr_column: "API/PeakCalling/yeast/read_in_data/relabel_chr_column.md"
+      - enrichment_vectorized: "API/PeakCalling/yeast/enrichment_vectorized.md"
+      - hypergeom_pval_vectorized: "API/PeakCalling/yeast/hypergeom_pval_vectorized.md"
+      - poisson_pval_vectorized: "API/PeakCalling/yeast/poisson_pval_vectorized.md"
+      - call_peaks:
+        - count_hops: 'API/PeakCalling/yeast/call_peaks/count_hops.md'
+        - add_metrics: 'API/PeakCalling/yeast/call_peaks/add_metrics.md'
+        - call_peaks: 'API/PeakCalling/yeast/call_peaks/call_peaks.md'
+        - parse_args: 'API/PeakCalling/yeast/call_peaks/parse_args.md'
+        - main: 'API/PeakCalling/yeast/call_peaks/main.md'
   - QC:
     - create_status_coder: 'API/QC/create_status_coder.md'
     - StatusFlags: 'API/QC/StatusFlags.md'

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "callingCardsTools"
-version = "1.5.0"
+version = "1.5.1"
 description = "A collection of objects and functions to work with calling cards sequencing tools"
 authors = ["chase mateusiak <[email protected]>"]
 license = "MIT"