refactor bam references to reads

CenterForMedicalGeneticsGhent · Mar 24, 2021 · 2d65a51 · 2d65a51
1 parent e8009fe
commit 2d65a51
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Showing 2 changed files with 15 additions and 15 deletions.
diff --git a/wisecondorX/convert_tools.py b/wisecondorX/convert_tools.py
@@ -7,24 +7,24 @@
 import sys
 
 '''
-Converts bam file to numpy array by transforming
+Converts reads file to numpy array by transforming
 individual reads to counts per bin.
 '''
 
 
-def convert_bam(args):
+def convert_reads(args):
     bins_per_chr = dict()
     for chr in range(1, 25):
         bins_per_chr[str(chr)] = None
 
     logging.info('Importing data ...')
 
     if args.infile.endswith(".sam"):
-        bam_file = pysam.AlignmentFile(args.infile, 'r')
+        reads_file = pysam.AlignmentFile(args.infile, 'r')
     elif args.infile.endswith(".bam"):
-        bam_file = pysam.AlignmentFile(args.infile, 'rb')
+        reads_file = pysam.AlignmentFile(args.infile, 'rb')
     elif args.infile.endswith(".cram"):
-        bam_file = pysam.AlignmentFile(args.infile, 'rc')
+        reads_file = pysam.AlignmentFile(args.infile, 'rc')
     else:
         logging.error(
             "Unsupported input file type. Make sure your input filename has a correct extension (sam/bam/cram)")
@@ -38,9 +38,9 @@ def convert_bam(args):
     larp = -1
     larp2 = -1
 
-    logging.info('Converting bam ... This might take a while ...')
+    logging.info('Converting reads ... This might take a while ...')
 
-    for index, chr in enumerate(bam_file.references):
+    for index, chr in enumerate(reads_file.references):
 
         chr_name = chr
         if chr_name[:3].lower() == 'chr':
@@ -49,9 +49,9 @@ def convert_bam(args):
             continue
 
         logging.info('Working at {}; processing {} bins'
-                     .format(chr, int(bam_file.lengths[index] / float(args.binsize) + 1)))
-        counts = np.zeros(int(bam_file.lengths[index] / float(args.binsize) + 1), dtype=np.int32)
-        bam_chr = bam_file.fetch(chr)
+                     .format(chr, int(reads_file.lengths[index] / float(args.binsize) + 1)))
+        counts = np.zeros(int(reads_file.lengths[index] / float(args.binsize) + 1), dtype=np.int32)
+        bam_chr = reads_file.fetch(chr)
 
         if chr_name == 'X':
             chr_name = '23'
@@ -91,9 +91,9 @@ def convert_bam(args):
         bins_per_chr[chr_name] = counts
         reads_kept += sum(counts)
 
-    qual_info = {'mapped': bam_file.mapped,
-                 'unmapped': bam_file.unmapped,
-                 'no_coordinate': bam_file.nocoordinate,
+    qual_info = {'mapped': reads_file.mapped,
+                 'unmapped': reads_file.unmapped,
+                 'no_coordinate': reads_file.nocoordinate,
                  'filter_rmdup': reads_rmdup,
                  'filter_mapq': reads_mapq,
                  'pre_retro': reads_seen,

diff --git a/wisecondorX/main.py b/wisecondorX/main.py
@@ -8,7 +8,7 @@
 
 import numpy as np
 
-from wisecondorX.convert_tools import convert_bam
+from wisecondorX.convert_tools import convert_reads
 from wisecondorX.newref_control import tool_newref_prep, tool_newref_main, tool_newref_merge
 from wisecondorX.newref_tools import train_gender_model, get_mask
 from wisecondorX.overall_tools import gender_correct, scale_sample
@@ -20,7 +20,7 @@
 def tool_convert(args):
     logging.info('Starting conversion')
 
-    sample, qual_info = convert_bam(args)
+    sample, qual_info = convert_reads(args)
     np.savez_compressed(args.outfile,
                         binsize=args.binsize,
                         sample=sample,