telometer 0.74__tar.gz → 0.76__tar.gz

{telometer-0.74 → telometer-0.76}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: telometer
-Version: 0.74
+Version: 0.76
 Summary: a simple regular expression based method for measuring individual, chromosome-specific telomere lengths from long-read sequencing data
 Author: Santiago E Sanchez
 Author-email: ses94@stanford.edu

{telometer-0.74 → telometer-0.76}/setup.py

@@ -2,7 +2,7 @@ import setuptools
 
 setuptools.setup(
     name="telometer",
-    version="0.74",
+    version="0.76",
     author="Santiago E Sanchez",
     author_email="ses94@stanford.edu",
     description="a simple regular expression based method for measuring individual, chromosome-specific telomere lengths from long-read sequencing data",

telometer-0.76/telometer/telometer.py

@@ -0,0 +1,163 @@
+#!/usr/bin/env python3
+# Telometer v0.76
+# Created by: Santiago E Sanchez
+# Artandi Lab, Stanford University, 2023
+# Measures telomeres from ONT or PacBio long reads aligned to a T2T genome assembly
+# Simple Usage: telometer -b sorted_t2t.bam -o output.tsv
+
+import pysam
+import re
+import regex
+import csv
+import argparse
+from multiprocessing import Pool, cpu_count
+
+def reverse_complement(seq):
+    """Returns the reverse complement of a DNA sequence."""
+    complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'N': 'N'}
+    return "".join(complement[base] for base in reversed(seq))
+
+def get_adapters(chemistry):
+    """Returns the adapter sequences based on the sequencing chemistry."""
+    if chemistry == 'r10':
+        adapters = ['TTTTTTTTCCTGTACTTCGTTCAGTTACGTATTGCT', 'GCAATACGTAACTGAACGAAGTACAGG']
+    else:
+        adapters = ['TTTTTTTTTTTAATGTACTTCGTTCAGTTACGTATTGCT', 'GCAATACGTAACTGAACGAAGT']
+
+    adapters_rc = [reverse_complement(adapter) for adapter in adapters]
+    return adapters + adapters_rc
+
+def get_telomere_repeats():
+    """Returns the telomere repeat sequences."""
+    telomere_repeats = ['GGCCA', 'CCCTAA', 'TTAGGG', 'CCCTGG', 'CTTCTT', 'TTAAAA', 'CCTGG']
+    telomere_repeats_rc = [reverse_complement(repeat) for repeat in telomere_repeats]
+    return telomere_repeats + telomere_repeats_rc
+
+def find_initial_boundary_region(sequence, patterns, max_mismatches):
+    """Finds the initial boundary region with allowed mismatches."""
+    boundary_length = 0
+    combined_pattern = '|'.join(f'({pattern})' for pattern in patterns)
+    regex_pattern = f'({combined_pattern}){{2,}}'
+
+    for match in regex.finditer(f'({regex_pattern}){{e<={max_mismatches}}}', sequence, regex.BESTMATCH):
+        boundary_length = max(boundary_length, len(match.group(0)))
+    return boundary_length
+
+def process_read(args):
+    read_data, telomere_repeats_re, adapters, minreadlen = args
+
+    if read_data['is_unmapped'] or read_data['query_sequence'] is None or len(read_data['query_sequence']) < minreadlen:
+        return None
+
+    alignment_start = read_data['reference_start']
+    alignment_end = read_data['reference_end']
+    seq = read_data['query_sequence']
+
+    if read_data['is_reverse']:
+        direction = "rev"
+        seq = reverse_complement(seq)
+    else:
+        direction = "fwd"
+
+    reference_genome_length = read_data['reference_length']
+
+    if alignment_start >= 15000 and alignment_start <= reference_genome_length - 30000:
+        return None
+
+    if alignment_start < 15000 and "q" not in read_data['reference_name']:
+        arm = "p"
+    else:
+        arm = "q"
+
+    telomere_start = [m.start() for m in re.finditer(telomere_repeats_re, seq)]
+    if telomere_start:
+        telomere_start = telomere_start[0]
+        if telomere_start > 100 and (len(seq) - telomere_start > 200):
+            return None
+
+        telomere_end = min((seq.find(adapter) for adapter in adapters), default=-1)
+        if telomere_end == -1:
+            telomere_end = len(seq)
+
+        telomere_region = seq[telomere_start:telomere_end]
+        telomere_repeat = [m.group() for m in re.finditer('|'.join(telomere_repeats_re.split('|')), telomere_region)]
+        telomere_length = len(''.join(telomere_repeat))
+
+        boundary_mm1_length = find_initial_boundary_region(telomere_region, telomere_repeats_re.split('|'), max_mismatches=1)
+
+        return {
+            'chromosome': read_data['reference_name'],
+            'reference_start': alignment_start,
+            'reference_end': alignment_end,
+            'telomere_length': telomere_length,
+            'subtel_boundary_length': boundary_mm1_length,
+            'read_id': read_data['query_name'],
+            'mapping_quality': read_data['mapping_quality'],
+            'read_length': len(seq),
+            'arm': arm,
+            'direction': direction
+        }
+    return None
+
+def calculate_telomere_length():
+    parser = argparse.ArgumentParser(description='Calculate telomere length from a BAM file.')
+    parser.add_argument('-b', '--bam', help='The path to the sorted BAM file.', required=True)
+    parser.add_argument('-o', '--output', help='The path to the output file.', required=True)
+    parser.add_argument('-c', '--chemistry', default="r10", help="Sequencing chemistry (r9 or r10, default=r10). Optional", required=False)
+    parser.add_argument('-m', '--minreadlen', default=1000, type=int, help='Minimum read length to consider (Default: 1000 for telomere capture, use 4000 for WGS). Optional', required=False)
+    args = parser.parse_args()
+    bam_file = pysam.AlignmentFile(args.bam, "rb")
+
+    adapters = get_adapters(args.chemistry)
+    telomere_repeats = get_telomere_repeats()
+    telomere_repeats_re = "|".join(f'({repeat}){{2,}}' for repeat in telomere_repeats)
+
+    read_data_list = [{
+        'query_name': read.query_name,
+        'is_unmapped': read.is_unmapped,
+        'is_reverse': read.is_reverse,
+        'reference_start': read.reference_start,
+        'reference_end': read.reference_end,
+        'reference_name': read.reference_name,
+        'mapping_quality': read.mapping_quality,
+        'query_sequence': read.query_sequence,
+        'reference_length': bam_file.get_reference_length(read.reference_name) if read.reference_name is not None else None
+    } for read in bam_file if read.reference_name is not None and read.reference_name != 'chrM']
+
+    with Pool(processes=cpu_count()) as pool:
+        results = pool.map(
+            process_read,
+            [(read_data, telomere_repeats_re, adapters, args.minreadlen) for read_data in read_data_list]
+        )
+
+    results = [result for result in results if result]
+
+    # Ensure only the best result per read_id is saved
+    best_results = {}
+    for result in results:
+        read_id = result['read_id']
+        if read_id not in best_results:
+            best_results[read_id] = result
+        else:
+            existing_result = best_results[read_id]
+            if result['mapping_quality'] > existing_result['mapping_quality']:
+                best_results[read_id] = result
+            elif result['mapping_quality'] == existing_result['mapping_quality']:
+                if result['telomere_length'] > existing_result['telomere_length']:
+                    best_results[read_id] = result
+                elif result['telomere_length'] == existing_result['telomere_length']:
+                    # Arbitrarily keep the existing one if both telomere_length and mapping_quality are the same
+                    pass
+
+    final_results = list(best_results.values())
+
+    if final_results:
+        with open(args.output, 'w', newline='') as output_file:
+            writer = csv.DictWriter(output_file, fieldnames=final_results[0].keys(), delimiter='\t')
+            writer.writeheader()
+            writer.writerows(final_results)
+
+    print(f"Telometer completed successfully. Total telomeres measured: {len(final_results)}")
+
+if __name__ == "__main__":
+    calculate_telomere_length()

{telometer-0.74 → telometer-0.76}/telometer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: telometer
-Version: 0.74
+Version: 0.76
 Summary: a simple regular expression based method for measuring individual, chromosome-specific telomere lengths from long-read sequencing data
 Author: Santiago E Sanchez
 Author-email: ses94@stanford.edu

telometer-0.74/telometer/telometer.py

@@ -1,159 +0,0 @@
-#!/usr/bin/env python3
-# Telometer v0.74
-# Created by: Santiago E Sanchez
-# Artandi Lab, Stanford University, 2023
-# Measures telomeres from ONT or PacBio long reads aligned to a T2T genome assembly
-# Simple Usage: telometer -b sorted_t2t.bam -o output.tsv
-
-import pysam
-import re
-import regex
-import csv
-import argparse
-import pandas as pd
-
-def reverse_complement(seq):
-    """Returns the reverse complement of a DNA sequence."""
-    complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'N': 'N'}
-    return "".join(complement[base] for base in reversed(seq))
-
-def get_adapters(chemistry):
-    """Returns the adapter sequences based on the sequencing chemistry."""
-    if chemistry == 'r10':
-        adapters = ['TTTTTTTTCCTGTACTTCGTTCAGTTACGTATTGCT', 'GCAATACGTAACTGAACGAAGTACAGG']
-    else:
-        adapters = ['TTTTTTTTTTTAATGTACTTCGTTCAGTTACGTATTGCT', 'GCAATACGTAACTGAACGAAGT']
-
-    adapters_rc = [reverse_complement(adapter) for adapter in adapters]
-    return adapters + adapters_rc
-
-def get_telomere_repeats():
-    """Returns the telomere repeat sequences."""
-    telomere_repeats = ['GGCCA', 'CCCTAA', 'TTAGGG', 'CCCTGG', 'CTTCTT', 'TTAAAA', 'CCTGG']
-    telomere_repeats_rc = [reverse_complement(repeat) for repeat in telomere_repeats]
-    return telomere_repeats + telomere_repeats_rc
-
-def find_initial_boundary_region(sequence, patterns, max_mismatches):
-    """Finds the initial boundary region with allowed mismatches."""
-    boundary_length = 0
-    combined_pattern = '|'.join(f'({pattern})' for pattern in patterns)
-    regex_pattern = f'({combined_pattern}){{2,}}'
-
-    for match in regex.finditer(f'({regex_pattern}){{e<={max_mismatches}}}', sequence, regex.BESTMATCH):
-        boundary_length = max(boundary_length, len(match.group(0)))
-    return boundary_length
-
-def extend_boundary_region(sequence, start, end, patterns, window_size, mismatch_threshold):
-    """Extends the boundary region around the initial match, allowing some mismatches."""
-    extended_start = max(0, start - window_size)
-    extended_end = min(len(sequence), end + window_size)
-    extended_seq = sequence[extended_start:extended_end]
-
-    combined_pattern = ''.join(patterns)
-    mismatches = sum(1 for base in extended_seq if base not in combined_pattern)
-
-    if mismatches / len(extended_seq) <= mismatch_threshold:
-        return len(extended_seq) - (end - start)  # Additional length
-    return 0
-
-def calculate_telomere_length():
-    # required inputs: bam_file_path, output_file_path, chemistry
-    parser = argparse.ArgumentParser(description='Calculate telomere length from a BAM file.')
-    parser.add_argument('-b', '--bam', help='The path to the sorted BAM file.', required=True)
-    parser.add_argument('-o', '--output', help='The path to the output file.', required=True)
-    parser.add_argument('-c', '--chemistry', default="r10", help="Sequencing chemistry (r9 or r10, default=r10). Optional", required=False)
-    parser.add_argument('-m', '--minreadlen', default=1000, type=int, help='Minimum read length to consider (Default: 1000 for telomere capture, use 4000 for WGS). Optional', required=False)
-    args = parser.parse_args()
-    bam_file = pysam.AlignmentFile(args.bam, "rb")
-
-    adapters = get_adapters(args.chemistry)
-    telomere_repeats = get_telomere_repeats()
-    telomere_repeats_re = "|".join(f'({repeat}){{2,}}' for repeat in telomere_repeats)
-
-    highest_mapping_quality = {}
-    results = []
-    p_count = 0
-    q_count = 0
-    rev_count = 0
-    fwd_count = 0
-    p_tel = 0
-    q_tel = 0
-
-    for read in bam_file:
-        if read.is_unmapped or read.query_sequence is None or len(read.query_sequence) < args.minreadlen:
-            continue
-
-        alignment_start = read.reference_start
-        alignment_end = read.reference_end
-        seq = read.query_sequence
-
-        if read.is_reverse:
-            rev_count += 1
-            direction = "rev"
-            seq = reverse_complement(seq)
-        else:
-            fwd_count += 1
-            direction = "fwd"
-
-        reference_genome_length = bam_file.get_reference_length(read.reference_name)
-
-        if alignment_start < 15000 or alignment_start > reference_genome_length - 30000:
-            if alignment_start < 15000 and "q" not in read.reference_name:
-                arm = "p"
-                p_count += 1
-            else:
-                arm = "q"
-                q_count += 1
-
-            telomere_start = [m.start() for m in re.finditer(telomere_repeats_re, seq)]
-            if telomere_start:
-                telomere_start = telomere_start[0]
-                if telomere_start > 100 and (len(seq) - telomere_start > 200):
-                    continue
-
-                telomere_end = min((seq.find(adapter) for adapter in adapters), default=-1)
-                if telomere_end == -1:
-                    telomere_end = len(seq)
-
-                telomere_region = seq[telomere_start:telomere_end]
-                telomere_repeat = [m.group() for m in re.finditer('|'.join(telomere_repeats), telomere_region)]
-                telomere_length = len(''.join(telomere_repeat))
-
-                boundary_mm1_length = find_initial_boundary_region(telomere_region, telomere_repeats, max_mismatches=1)
-
-                if telomere_length < boundary_mm1_length:
-                    telomere_length = boundary_mm1_length
-                if telomere_length < boundary_mm2_length:
-                    telomere_length = boundary_mm2_length
-
-                if read.query_name not in highest_mapping_quality or read.mapping_quality > highest_mapping_quality[read.query_name]:
-                    if arm == "p":
-                        p_tel += 1
-                    else:
-                        q_tel += 1
-                    highest_mapping_quality[read.query_name] = read.mapping_quality
-                    results.append({
-                        'chromosome': read.reference_name,
-                        'reference_start': alignment_start,
-                        'reference_end': alignment_end,
-                        'telomere_length': telomere_length,
-                        'subtel_boundary_length': boundary_mm1_length,
-                        'read_id': read.query_name,
-                        'mapping_quality': read.mapping_quality,
-                        'read_length': len(seq),
-                        'arm': arm,
-                        'direction': direction
-                    })
-
-    bam_file.close()
-
-    with open(args.output, 'w', newline='') as output_file:
-        writer = csv.DictWriter(output_file, fieldnames=results[0].keys(), delimiter='\t')
-        writer.writeheader()
-        writer.writerows(results)
-
-    # Print the total number of telomeres measured
-    print(f"Telometer completed successfully. Total telomeres measured: {len(results)}")
-
-if __name__ == "__main__":
-    calculate_telomere_length()