remove old code and bump version

differr/output.py

@@ -68,32 +68,4 @@ def write_stats_to_bed(bed_fn, results):
                 G_stat_A_p_val=G_A_p,
                 G_stat_B=G_B,
                 G_stat_B_p_val=G_B_p
-            ))
-
-
-PHASING_BED_RECORD = (
-    '{chrom}\t{start:d}\t{end:d}\t'
-    'DER_site\t{score:.0f}\t{strand}\t'
-    '{n_polya_sites:d}\t{G_stat:.2f}\t{p_val:.2f}\t'
-    '{q_val:.2f}\t{homo_G_stat:.2f}\n'
-)
-
-
-def write_phasing_stats_to_bed(bed_fn, results):
-    '''
-    Write the results to a bed file (with a bunch of extra columns for G-test results)
-    '''
-    with open(bed_fn, 'w') as bed:
-        for _, chrom, pos, strand, n_polya_sites, homo_G, hetero_G, p_val, fdr in results.itertuples():
-            bed.write(PHASING_BED_RECORD.format(
-                chrom=chrom,
-                start=pos,
-                end=pos + 1,
-                score=nlog10(fdr),
-                strand=strand,
-                n_polya_sites=n_polya_sites,
-                G_stat=hetero_G,
-                p_val=nlog10(p_val),
-                q_val=nlog10(fdr),
-                homo_G_stat=homo_G
-            ))
+            ))

setup.py

@@ -3,16 +3,14 @@
 
 setup(
     name='differr',
-    version='0.1',
+    version='0.2',
     description=(
         'identify sites with differential mismatches caused by m6A in ONT DRS data'
     ),
     author='Matthew Parker',
     entry_points={
         'console_scripts': [
             'differr = differr.main:differr',
-            'phaserr = differr.phasing:identify_three_prime_phasing',
-            'polya_test = differr.cluster:find_polya_clusters',
         ]
     },
     packages=[