20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,157 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+from __future__ import (absolute_import, division,
+                        print_function, unicode_literals)
+import os, sys, re
+import logging
+import argparse
+import collections
+
+logging.basicConfig(stream=sys.stderr, level=logging.INFO)
+logger = logging.getLogger(__file__)
+ 
+def main():
+
+    parser = argparse.ArgumentParser(description="estimates gene length as isoform lengths weighted by TPM expression values")
+    
+    parser.add_argument("--gene_trans_map", dest="gene_trans_map_file", type=str, default="",
+                        required=True, help="gene-to-transcript mapping file, format: gene_id(tab)transcript_id")
+
+    parser.add_argument("--trans_lengths", dest="trans_lengths_file", type=str, required=True,
+                        help="transcript length file, format: trans_id(tab)length")
+
+    parser.add_argument("--TPM_matrix", dest="TPM_matrix_file", type=str, default="",
+                        required=True, help="isoform TPM expression matrix")
+
+    parser.add_argument("--debug", required=False, action="store_true", default=False, help="debug mode")
+
+
+    args = parser.parse_args()
+
+    if args.debug:
+        logger.setLevel(logging.DEBUG)
+    
+
+    trans_to_gene_id_dict = parse_gene_trans_map(args.gene_trans_map_file)
+
+    trans_lengths_dict = parse_trans_lengths_file(args.trans_lengths_file)
+
+    trans_to_TPM_vals_dict = parse_TPM_matrix(args.TPM_matrix_file)
+
+    weighted_gene_lengths = compute_weighted_gene_lengths(trans_to_gene_id_dict,
+                                                          trans_lengths_dict,
+                                                          trans_to_TPM_vals_dict)
+
+    print("#gene_id\tlength")
+    for gene_id,length in weighted_gene_lengths.items():
+        print("\t".join([gene_id,str(length)]))
+
+
+    sys.exit(0)
+    
+
+
+def compute_weighted_gene_lengths(trans_to_gene_id_dict, trans_lengths_dict, trans_to_TPM_vals_dict):
+
+    gene_id_to_trans_list = collections.defaultdict(list)
+
+    gene_id_to_length = {}
+
+    pseudocount = 1
+
+    for trans_id,gene_id in trans_to_gene_id_dict.items():
+        gene_id_to_trans_list[gene_id].append(trans_id)
+
+    for gene_id,trans_list in gene_id_to_trans_list.items():
+
+        if len(trans_list) == 1:
+
+            gene_id_to_length[gene_id] = trans_lengths_dict[ trans_list[0] ]
+        else:
+            
+            sum_length_x_expr = 0
+            sum_expr = 0
+
+            trans_expr_lengths = []
+
+            for trans_id in trans_list:
+                trans_len = trans_lengths_dict[trans_id]
+                expr_vals = trans_to_TPM_vals_dict[trans_id]
+                trans_sum_expr = sum(expr_vals) + pseudocount
+
+                trans_expr_lengths.append((trans_len, trans_sum_expr))
+
+                sum_length_x_expr += trans_sum_expr * trans_len
+                sum_expr += trans_sum_expr
+
+
+            weighted_gene_length = sum_length_x_expr / sum_expr
+            gene_id_to_length[gene_id] = int(round(weighted_gene_length))
+
+            logger.debug("Computing weighted length of {0}: {1} => {2}".format(gene_id,
+                                                                            trans_expr_lengths,
+                                                                            weighted_gene_length))
+            
+    return gene_id_to_length
+            
+
+
+def parse_TPM_matrix(TPM_matrix_file):
+
+    trans_to_TPM_vals_dict = {}
+    
+    with open(TPM_matrix_file) as f:
+        header = next(f)
+        for line in f:
+            line = line.rstrip()
+            vals = line.split("\t")
+            trans_id = vals[0]
+            expr_vals_list = vals[1:]
+            expr_vals_list = [float(x) for x in expr_vals_list]
+            trans_to_TPM_vals_dict[trans_id] = expr_vals_list
+
+    return trans_to_TPM_vals_dict
+
+
+def parse_trans_lengths_file(trans_lengths_file):
+
+    trans_id_to_length = {}
+
+    with open(trans_lengths_file) as f:
+        for line in f:
+            line = line.rstrip()
+            if line[0] == '#':
+                continue
+            
+            (trans_id, length) = line.split("\t")
+
+            if re.match("^\d+$", length):
+                trans_id_to_length[trans_id] = int(length)
+            else:
+                print("Warning - ignoring line: [{0}] since not parsing length value as number".format(line), file=sys.stderr)
+
+    return trans_id_to_length
+
+
+
+def parse_gene_trans_map(gene_trans_map_file):
+
+    trans_to_gene_id = {}
+
+    with open(gene_trans_map_file) as f:
+        for line in f:
+            line = line.rstrip()
+            (gene_id, trans_id) = line.split("\t")
+
+            trans_to_gene_id[trans_id] = gene_id;
+        
+
+    return trans_to_gene_id
+
+
+ 
+####################
+ 
+if __name__ == "__main__":
+    main()