New feature/fwd and rev reads v2

Indexed_bt2/code_for_reference/create_annoted_ref.py

@@ -0,0 +1,65 @@
+#!/usr/bin/python
+
+# This programm takes the variable region reference position
+# from variable_region_calc.py and searches for them in the
+# aligned gg otus
+
+from os import path as p
+
+
+def write(region, seq_chrom, annoted_ref):
+    with open(annoted_ref, 'a') as t:
+        if region['V1_start'] != '':
+            for counter, key in enumerate(region):
+                if (counter % 2) == 0:
+                    wordstart = f'{seq_chrom}\t{str(region[key])}'
+                else:
+                    var_reg = key[0:2]
+                    wordend = f'\t{str(region[key])}\t{var_reg}\n'
+                    words = wordstart + wordend
+                    t.write(words)
+
+
+def index(line, region):
+    boundary = {'V1_start': 189, 'V1_end': 471,
+                'V2_start': 485, 'V2_end': 1867,
+                'V3_start': 1915, 'V3_end': 2231,
+                'V4_start': 2262, 'V4_end': 4050,
+                'V5_start': 4089, 'V5_end': 4521,
+                'V6_start': 4652, 'V6_end': 4931,
+                'V7_start': 5043, 'V7_end': 5806,
+                'V8_start': 5909, 'V8_end': 6426,
+                'V9_start': 6449, 'V9_end': 6790}
+    for key in boundary:
+        list1 = list(line)
+        list1[boundary[key]] = '1'
+        list1 = ''.join(str(e) for e in list1)
+        list1 = list1.replace('-', '')
+        region[key] = int(list1.index('1')) + 1
+    return region
+
+
+def main():
+    file_ = f'{p.dirname(p.dirname(__file__))}/85_otus_aligned.fasta'
+    annoted_ref = f'{p.dirname(p.dirname(__file__))}/annoted_ref.bed'
+    with open(file_, 'r') as f:
+        for line in f:
+            region = {'V1_start': '', 'V1_end': '',
+                      'V2_start': '', 'V2_end': '',
+                      'V3_start': '', 'V3_end': '',
+                      'V4_start': '', 'V4_end': '',
+                      'V5_start': '', 'V5_end': '',
+                      'V6_start': '', 'V6_end': '',
+                      'V7_start': '', 'V7_end': '',
+                      'V8_start': '', 'V8_end': '',
+                      'V9_start': '', 'V9_end': ''}
+            if line.startswith('>'):
+                seq_chrom = line[1:]
+                seq_chrom = seq_chrom.strip('\n')
+            else:
+                index(line, region)
+                write(region, seq_chrom, annoted_ref)
+
+
+if __name__ == '__main__':
+    main()