Mercurial > repos > dfornika > micall_lite
comparison amino2consensus.py @ 21:d099ef46fd42 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/micall-lite commit 822e7e1c2de31a72c2a13bcc15b9df06b699561f-dirty
author | dfornika |
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date | Wed, 25 Sep 2019 18:51:15 -0400 |
parents | b1e1f49ebe14 |
children | b5df889acab3 |
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20:b1e1f49ebe14 | 21:d099ef46fd42 |
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8 AMINO_ACIDS = ['A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y','*'] | 8 AMINO_ACIDS = ['A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y','*'] |
9 | 9 |
10 def determine_amino(amino_counts, threshold): | 10 def determine_amino(amino_counts, threshold): |
11 amino = "" | 11 amino = "" |
12 total_count = sum(amino_counts.values()) | 12 total_count = sum(amino_counts.values()) |
13 amino_with_max_counts = sorted(amino_counts, key=amino_counts.get, reverse=True)[0] | 13 amino_with_max_counts, count = sorted(amino_counts.items(), key=lambda item: item[1], reverse=True)[0] |
14 if total_count == 0: | 14 if total_count == 0: |
15 amino = "#" | 15 amino = "#" |
16 elif (amino_counts[amino_with_max_counts] / float(total_count)) > threshold: | 16 elif (amino_counts[amino_with_max_counts] / float(total_count)) > threshold: |
17 amino = amino_with_max_counts | 17 amino = amino_with_max_counts |
18 else: | 18 else: |