fixed output error when extra_copy_number >= 10

liftoff/align_features.py

@@ -1,12 +1,14 @@
-from multiprocessing import Pool
-import math
 from functools import partial
-import numpy as np
-from pyfaidx import Fasta, Faidx
+import math
+from multiprocessing import Pool
+from os import path
 import subprocess
+
+import numpy as np
+from pyfaidx import Faidx, Fasta
 import pysam
+
 from liftoff import aligned_seg, liftoff_utils
-from os import path
 
 
 def align_features_to_target(ref_chroms, target_chroms, args, feature_hierarchy, liftover_type, unmapped_features):
@@ -54,14 +56,33 @@ def align_single_chroms(ref_chroms, target_chroms, threads, args, genome_size, l
         command = [minimap2_path, '-o', output_file, target_file, features_file] + args.mm2_options.split(" ") + [
             "--split-prefix", split_prefix, '-t', threads_arg]
         subprocess.run(command)
+        modified_sam_header(output_file)
     else:
         minimap2_index = build_minimap2_index(target_file, args, threads_arg, minimap2_path)
         command = [minimap2_path, '-o', output_file, minimap2_index, features_file] + args.mm2_options.split(" ") + [
             '-t', threads_arg]
         subprocess.run(command)
+        modified_sam_header(output_file)
     return output_file
 
 
+def modified_sam_header(sam_file):
+    header_lines, alignment_lines = [], []
+    with open(sam_file, 'r') as open_sam:
+        for eachline in open_sam.readlines():
+            if eachline[0] == '@':
+                header_lines.append(eachline)
+            else:
+                alignment_lines.append(eachline)
+    modified_header_lines = []
+    for header_line in header_lines:
+        if header_line not in modified_header_lines:
+            modified_header_lines.append(header_line)
+    with open(sam_file, 'w') as open_sam:
+        open_sam.writelines(modified_header_lines)
+        open_sam.writelines(alignment_lines)
+
+
 def get_features_file(ref_chroms, args, liftover_type, index):
     if ref_chroms[index] == args.reference and (liftover_type == "chrm_by_chrm" or liftover_type == "copies"):
         features_name = 'reference_all'

liftoff/write_new_gff.py

@@ -37,7 +37,7 @@ def add_to_copy_num_dict(parent, copy_num_dict):
 
 def add_attributes(parent, copy_num, args):
     parent.score = "."
-    parent.attributes["extra_copy_number"] = str(copy_num)
+    parent.attributes["extra_copy_number"] = [copy_num]
     parent.attributes["copy_num_ID"] = [parent.id + "_" + str(copy_num)]
     if float(parent.attributes["coverage"][0]) < args.a:
         parent.attributes["partial_mapping"] = ["True"]
@@ -49,7 +49,7 @@ def build_parent_dict(child_features, parent_dict, final_parent):
     parent_child_dict = {}
     for child in child_features:
         if child.id not in parent_dict:
-            child.attributes["extra_copy_number"] = final_parent.attributes["extra_copy_number"][0]
+            child.attributes["extra_copy_number"] = final_parent.attributes["extra_copy_number"]
             if child.attributes["Parent"][0] in parent_child_dict:
                 parent_child_dict[child.attributes["Parent"][0]].append(child)
             else:
@@ -84,7 +84,7 @@ def make_gff_line(feature):
         if attr != "copy_id":
             value_str = ""
             for value in feature.attributes[attr]:
-                value_str += value + ","
+                value_str += str(value) + ","
             attributes_str += (attr + "=" + value_str[:-1] + ";")
     return feature.seqid + "\t" + feature.source + "\t" + feature.featuretype + "\t" + str(feature.start) + \
            "\t" + str(feature.end) + "\t" + "." + "\t" + feature.strand + "\t" + "." + "\t" + attributes_str[:-1]
@@ -97,7 +97,7 @@ def make_gtf_line(feature):
             if len(feature.attributes[attr]) >0:
                 value_str = ""
                 for value in feature.attributes[attr]:
-                     value_str += value + ","
+                     value_str += str(value) + ","
                 attributes_str += (attr + " " + '"' + value_str[:-1] + '"' + "; ")
     return feature.seqid + "\t" + feature.source + "\t" + feature.featuretype + "\t" + str(feature.start) + \
-           "\t" + str(feature.end) + "\t" + "." + "\t" + feature.strand + "\t" + "." + "\t" + attributes_str
+           "\t" + str(feature.end) + "\t" + "." + "\t" + feature.strand + "\t" + "." + "\t" + attributes_str