Installation

.github/workflows/test.yml

@@ -9,19 +9,14 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         PIP_FLAGS: [""]
         MINIMUM_REQUIREMENTS: [0]
         include:
           - platform_id: manylinux_x86_64
             python-version: 3.7
             MINIMUM_REQUIREMENTS: 1
             OPTIONS_NAME: "min"
-          - platform_id: manylinux_x86_64
-            python-version: 3.9
-            PIP_FLAGS: "--pre"
-            # test pre-releases
-            OPTIONS_NAME: "pre"
 
     steps:
       - name: Checkout 🛎️

MANIFEST.in

@@ -1,3 +1,3 @@
 recursive-include iced *.c *.h *.py
-recursive-include *.matrix *.bed
+recursive-include iced *.matrix *.bed *.mat
 include pyproject.toml

iced/normalization/_normalization_.pyx

@@ -1,4 +1,4 @@
-import numpy as np
+#import numpy as np
 cimport cython
 cimport numpy as np
 

iced/scripts/ice.py

@@ -0,0 +1,127 @@
+#! /usr/bin/env python
+from __future__ import print_function
+import sys
+import argparse
+import numpy as np
+from scipy import sparse
+
+import iced
+from iced.io import load_counts, savetxt, write_counts
+
+def main():
+    parser = argparse.ArgumentParser("ICE normalization")
+    parser.add_argument('filename',
+                        metavar='File to load',
+                        type=str,
+                        help='Path to file of contact counts to load')
+    parser.add_argument("--results_filename",
+                        "-r",
+                        type=str,
+                        default=None,
+                        help="results_filename")
+    parser.add_argument("--filtering_perc", "-f",
+                        type=float,
+                        default=None,
+                        help="Percentage of reads to filter out")
+    parser.add_argument("--filter_low_counts_perc",
+                        type=float,
+                        default=0.02,
+                        help="Percentage of reads to filter out")
+    parser.add_argument("--filter_high_counts_perc",
+                        type=float,
+                        default=0,
+                        help="Percentage of reads to filter out")
+    parser.add_argument("--remove-all-zeros-loci", default=False,
+                        action="store_true",
+                        help="If provided, all non-interacting loci will be "
+                            "removed prior to the filtering strategy chosen.")
+    parser.add_argument("--max_iter", "-m", default=100, type=int,
+                        help="Maximum number of iterations")
+    parser.add_argument("--eps", "-e", default=0.1, type=float,
+                        help="Precision")
+    parser.add_argument("--dense", "-d", default=False, action="store_true")
+    parser.add_argument("--output-bias", "-b", default=False, help="Output the bias vector")
+    parser.add_argument("--verbose", "-v", default=False, type=bool)
+    parser.add_argument("--base", default=None, type=int,
+                        help="Indicates whether the matrix file is 0 or 1-based")
+
+
+    args = parser.parse_args()
+    filename = args.filename
+
+    # Deprecating filtering_perc option
+    filter_low_counts = None
+    if "--filtering_perc" in sys.argv:
+        DeprecationWarning(
+            "Option '--filtering_perc' is deprecated. Please use "
+            "'--filter_low_counts_perc' instead.'")
+        # And print it again because deprecation warnings are not displayed for
+        # recent versions of python
+        print("--filtering_perc is deprecated. Please use filter_low_counts_perc")
+        print("instead. This option will be removed in ice 0.3")
+        filter_low_counts = args.filtering_perc
+    if "--filter_low_counts_perc" in sys.argv and "--filtering_perc" in sys.argv:
+        raise Warning("This two options are incompatible")
+    if "--filtering_perc" is None and "--filter_low_counts_perc" not in sys.argv:
+        filter_low_counts_perc = 0.02
+    elif args.filter_low_counts_perc is not None:
+        filter_low_counts_perc = args.filter_low_counts_perc
+
+    if args.base is None:
+        base = 1
+        print("Assuming the file is 1-based. If this is not the desired option, "
+            "set option --base to 0")
+    else:
+        base = args.base
+
+    if args.verbose:
+        print("Using iced version %s" % iced.__version__)
+        print("Loading files...")
+
+    # Loads file as i, j, counts
+    counts = load_counts(filename, base=base)
+
+
+    if args.dense:
+        counts = np.array(counts.todense())
+    else:
+        counts = sparse.csr_matrix(counts)
+
+    if args.verbose:
+        print("Normalizing...")
+
+    if filter_low_counts_perc != 0:
+        counts = iced.filter.filter_low_counts(counts,
+                                            percentage=filter_low_counts_perc,
+                                            remove_all_zeros_loci=args.remove_all_zeros_loci,
+                                            copy=False, sparsity=False, verbose=args.verbose)
+    if args.filter_high_counts_perc != 0:
+        counts = iced.filter.filter_high_counts(
+            counts,
+            percentage=args.filter_high_counts_perc,
+            copy=False)
+
+    counts, bias = iced.normalization.ICE_normalization(
+        counts, max_iter=args.max_iter, copy=False,
+        verbose=args.verbose, eps=args.eps, output_bias=True)
+
+    if args.results_filename is None:
+        results_filename = ".".join(
+            filename.split(".")[:-1]) + "_normalized." + filename.split(".")[-1]
+    else:
+        results_filename = args.results_filename
+
+    counts = sparse.coo_matrix(counts)
+
+    if args.verbose:
+        print("Writing results...")
+
+    #write_counts(results_filename, counts)
+    write_counts(
+        results_filename,
+        counts, base=base)
+
+
+
+    if args.output_bias:
+        np.savetxt(results_filename + ".biases", bias)