Serious Error!!!!

[Hiiragizawa]

Found a very serious error in this code, when you use gap_open = -5, gap_extend = -1, the alignment is meaningless( works fine if you don't put any). I tried to do the same in the old version (0.3.0 that works in python2), attached the results:

• Your nwaling version:

import nwaling3
nwalign3.global_align("SHMYAPKLQGPVAVYTWEGNQVNITCEVFAYPSATISWFRDGQLLPSSNYSNIKIYNTPSASYLEVTPDSENDFGNYNCTAVNRIGQESLEFILVQADTPSSPSIDQVEPYSSTAQVQFDEPEATGGVPILKYKAEWRAVGEEVWHSKWYDAKEASMEGIVTIVGLKPETTYAVRLAALNGKGLGEISAASEFKTQP", "SVAPTMMNVLYAGIDNPINIAVPGVAQQNVSATINNGTLTRRGNLWIARPTKVGSEAIISVTAQSGGRTIQMAKTTLRVRALPDPLPYIEYKDVQGNTKRFKGGRLGKREILAAGGIKAALDDDLLEVNYTVVKFQLVFYDSMGNSIPEVSDGASFSERQKRQIQNLGKGKRFYVTEVIARGPDGIERKIPAIEVIVN",gap_open=-5,gap_extend=-1, matrix='BLOSUM62')

OUTPUT:('---------------------------SHMYAPKLQ-GPVAVYTWEGNQ-V-NITCEVFAYPSATIS-WFRDG-QLLPSSNYSNIKIYNTPSA-SYLEVTPDSENDFGNYN-CTAVNRIGQESLEFILVQADTPSSPSIDQ-V-EP-YSSTAQVQFDEPEATGGVPILKYKAEWRAVGEEVWHSKWYDAKEASMEGIVTIVGLKPETTYAVRLAALNGK-GLGE--ISAASEFKTQP', 'SVAPTMMNVLYAGIDNPINIAVPGVAQQNVSAT-INNG-T-L-TRRGNLWIARPT-KV-G-SEAIISVTAQSGGRTIQMAK-TTLRVRALPDPLPYIEYK-DVQ---GNTKRFKG-GRLGKR--E-ILA-AGGIKA-ALDDDLLEVNY--TV-VKF-Q------L-VF-YDSMGNSI-PEVSDGASFSERQ-KRQ-IQNL-G-KGKRFYVTEVIA-RGPDGI-ERKIPAI-EVIVN-')

• The older one:

nwalign.global_align("SHMYAPKLQGPVAVYTWEGNQVNITCEVFAYPSATISWFRDGQLLPSSNYSNIKIYNTPSASYLEVTPDSENDFGNYNCTAVNRIGQESLEFILVQADTPSSPSIDQVEPYSSTAQVQFDEPEATGGVPILKYKAEWRAVGEEVWHSKWYDAKEASMEGIVTIVGLKPETTYAVRLAALNGKGLGEISAASEFKTQP", "SVAPTMMNVLYAGIDNPINIAVPGVAQQNVSATINNGTLTRRGNLWIARPTKVGSEAIISVTAQSGGRTIQMAKTTLRVRALPDPLPYIEYKDVQGNTKRFKGGRLGKREILAAGGIKAALDDDLLEVNYTVVKFQLVFYDSMGNSIPEVSDGASFSERQKRQIQNLGKGKRFYVTEVIARGPDGIERKIPAIEVIVN",gap_open=-5,gap_extend=-1, matrix='/BLOSUM62')

OUTPUT: ('SHMYAPKLQGPVAVYTWEGNQVNITCEVFAYP--SATISWFRDGQLLPSSNYSNIKIYNTPSASYLEVTPDSENDFGNYNCTAVN-RIGQESLEFI-L--VQADTPS-SPS-IDQVEPYSSTA-QVQFDEPEATGGVPILKYKAE-WRAVGEEVWH-SKWYDAKEASMEGIVTIVGLKPETTYAVRLAALNGK-GLG-EISAASEFKTQP', 'S--VAPTMMN-V-LYAGIDNPINIAVPGVAQQNVSATIN---NGTLTRRGNLWIARPTKVGSEAIISVTAQSGGRTIQMAKTTLRVRALPDPLPYIEYKDVQGNTKRFKGGRLGKREILAAGGIKAALDDDLLEVNYTVVKFQLVFYDSMGNSIPEVSDGASFSERQKRQIQNL-G-KGKRFYVTEVIA-RGPDGIERKIPAI-EVIVN-')