Mercurial > repos > galaxyp > metagene_annotator
comparison convert_mga.py @ 1:17c7ab82bfbc draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc
author | galaxyp |
---|---|
date | Mon, 18 Mar 2024 12:34:58 +0000 |
parents | b04960a7abf5 |
children |
comparison
equal
deleted
inserted
replaced
0:b04960a7abf5 | 1:17c7ab82bfbc |
---|---|
33 'seq_id', 'seq_model', 'seq_gc', 'seq_rbs', | 33 'seq_id', 'seq_model', 'seq_gc', 'seq_rbs', |
34 'gene ID', 'start pos', 'end pos', 'strand', 'frame', | 34 'gene ID', 'start pos', 'end pos', 'strand', 'frame', |
35 'complete/partial', 'gene score', 'used model', | 35 'complete/partial', 'gene score', 'used model', |
36 'rbs start', 'rbs end', 'rbs score'])) | 36 'rbs start', 'rbs end', 'rbs score'])) |
37 | 37 |
38 gc_rbs_pat = '# gc = (-?[0-9]*[.]?[0-9]+), rbs = (-?[0-9]*[.]?[0-9]+)' | 38 gc_rbs_pat = '# gc = (-?[0-9]*[.]?[0-9]+), rbs = (-?[0-9]*[.]?[0-9]+)' |
39 seq_count = 0 | 39 seq_count = 0 |
40 gene_count = 0 | 40 gene_count = 0 |
41 for i, line in enumerate(input_rdr): | 41 for i, line in enumerate(input_rdr): |
42 # 1317/1 | 42 # 1317/1 |
43 # gc = 0.272955, rbs = -1 | 43 # gc = 0.272955, rbs = -1 |
44 # self: - | 44 # self: - |
45 if line.startswith('# gc'): | 45 if line.startswith('# gc'): |
46 try: | 46 try: |
47 m = re.match(gc_rbs_pat, line.strip()) | 47 m = re.match(gc_rbs_pat, line.strip()) |
48 seq_gc, seq_rbs = m.groups() | 48 seq_gc, seq_rbs = m.groups() |
49 except: | 49 except ValueError: |
50 seq_gc = seq_rbs = '' | 50 seq_gc = seq_rbs = '' |
51 elif line.startswith('# self:'): | 51 elif line.startswith('# self:'): |
52 seq_type = re.sub('# self:', '', line.rstrip()) | 52 seq_type = re.sub('# self:', '', line.rstrip()) |
53 elif line.startswith('# '): | 53 elif line.startswith('# '): |
54 seq_name = re.sub('# (\S+).*$', '\\1', line.rstrip()) | 54 seq_name = re.sub(r'# (\S+).*$', '\\1', line.rstrip()) |
55 seq_count += 1 | 55 seq_count += 1 |
56 else: | 56 else: |
57 fields = line.split('\t') | 57 fields = line.split('\t') |
58 if len(fields) == 11: | 58 if len(fields) == 11: |
59 gene_count += 1 | 59 gene_count += 1 |