HTSeq 2.1.2__cp310-cp310-macosx_10_15_x86_64.whl

HTSeq/scripts/count_features/reads_stats.py

@@ -0,0 +1,92 @@
+import HTSeq
+import sys
+
+
+class ReadsStatistics(object):
+    """
+    For storing the read counts
+    """
+
+    def __init__(self, feature_attr, read_io_object):
+        '''Initialize storage for the read counts
+
+        Args:
+            feature_attr (list of str): Feature names
+            read_io_object (ReadsIO): Read processor
+        '''
+        self.read_io_obj = read_io_object
+
+        self.empty = 0
+        self.ambiguous = 0
+        self.notaligned = 0
+        self.lowqual = 0
+        self.nonunique = 0
+        self.num_reads_processed = 0
+        self.counts = {key: 0 for key in feature_attr}
+
+    def add_num_reads_processed(self):
+        self.num_reads_processed += 1
+
+    def add_empty_read(self, read_sequence):
+        self.empty += 1
+        self.read_io_obj.write_to_samout(read_sequence, "__no_feature")
+
+    def add_ambiguous_read(self, read_sequence, assignment):
+        self.ambiguous += 1
+        self.read_io_obj.write_to_samout(read_sequence, assignment)
+
+    def add_low_quality_read(self, read_sequence):
+        self.lowqual += 1
+        self.read_io_obj.write_to_samout(read_sequence, "__too_low_aQual")
+
+    def add_not_unique_read(self, read_sequence):
+        self.nonunique += 1
+        self.read_io_obj.write_to_samout(read_sequence, "__alignment_not_unique")
+
+    def add_not_aligned_read(self, read_sequence):
+        self.notaligned += 1
+        self.read_io_obj.write_to_samout(read_sequence, "__not_aligned")
+
+    def add_to_count(self, feature, value=1):
+        self.counts[feature] += value
+
+    def add_good_read_assignment(self, read_sequence, assignment):
+        self.read_io_obj.write_to_samout(read_sequence, assignment)
+
+    def print_progress(self, force_print=False):
+        """
+        Simple function to update the progress of reads processing.
+        Parameters
+        ----------
+        force_print : boolean
+            Whether to print progress regardless of number of reads processed
+            or not.
+        """
+
+        if force_print:
+            do_print = True
+        else:
+            do_print = (
+                self.num_reads_processed > 0 and self.num_reads_processed % 100000 == 0
+            )
+
+        if do_print:
+            sys.stderr.write(
+                "%d alignment record%s processed.\n"
+                % (
+                    self.num_reads_processed,
+                    "s" if not self.read_io_obj.pe_mode else " pairs",
+                )
+            )
+            sys.stderr.flush()
+
+    def get_output(self, isam):
+        return {
+            "isam": isam,
+            "counts": self.counts,
+            "empty": self.empty,
+            "ambiguous": self.ambiguous,
+            "lowqual": self.lowqual,
+            "notaligned": self.notaligned,
+            "nonunique": self.nonunique,
+        }