Mercurial > repos > estrain > seqsero2_v1_0_1
changeset 13:66277925a124
Uploaded
| author | estrain |
|---|---|
| date | Sat, 07 Sep 2019 11:12:04 -0400 |
| parents | b43b7ef0df6a |
| children | 6d28f83c35b1 |
| files | SeqSero2_package.py |
| diffstat | 1 files changed, 7 insertions(+), 2 deletions(-) [+] |
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--- a/SeqSero2_package.py Sat Sep 07 08:19:53 2019 -0400 +++ b/SeqSero2_package.py Sat Sep 07 11:12:04 2019 -0400 @@ -12,6 +12,7 @@ import itertools from distutils.version import LooseVersion from distutils.spawn import find_executable +import math try: from .version import SeqSero2_version @@ -518,6 +519,8 @@ for z in range(len(handle[i].alignments[j].hsps)): hsp=handle[i].alignments[j].hsps[z] temp=set(range(hsp.query_start,hsp.query_end)) + # Bit score is not parsed correctly, calculate it from raw score + est_bit=(handle[i].ka_params[0]*hsp.score-math.log(handle[i].ka_params[1]))/(math.log(2)) if len(cover_region)==0: cover_region=cover_region|temp fraction=1 @@ -525,10 +528,12 @@ fraction=1-len(cover_region&temp)/float(len(temp)) cover_region=cover_region|temp if "last" in handle[i].query or "first" in handle[i].query: - score+=hsp.bits*fraction + #score+=hsp.bits*fraction + score+=est_bit*fraction ids+=float(hsp.identities)/handle[i].query_length*fraction else: - score+=hsp.bits*fraction + #score+=hsp.bits*fraction + score+=est_bit*fraction ids+=float(hsp.identities)/handle[i].query_length*fraction List_score.append(score) List_ids.append(ids)