diff --git a/ViralMSA.py b/ViralMSA.py index d770eda..d6bac21 100755 --- a/ViralMSA.py +++ b/ViralMSA.py @@ -20,7 +20,7 @@ import sys # useful constants -VERSION = '1.1.37' +VERSION = '1.1.38' RELEASES_URL = 'https://api.github.com/repos/niemasd/ViralMSA/tags' CIGAR_LETTERS = {'M','D','I','S','H','=','X'} DEFAULT_BUFSIZE = 1048576 # 1 MB #8192 # 8 KB @@ -57,31 +57,34 @@ # reference genomes for common viruses REFS = { - 'bombalivirus': 'NC_039345', # Bombali Virus (Bombali ebolavirus) - 'bundibugyovirus': 'NC_014373', # Bundibugyo Virus (Bundibugyo ebolavirus) - 'chikungunyavirus': 'NC_004162', # Chikungunya virus - 'denv1': 'NC_001477', # Dengue Virus 1 - 'denv2': 'NC_001474', # Dengue Virus 2 - 'denv3': 'NC_001475', # Dengue Virus 3 - 'denv4': 'NC_002640', # Dengue Virus 4 - 'ebolavirus': 'NC_002549', # Ebola Virus (Zaire ebolavirus) - 'hcv1': 'NC_004102', # HCV genotype 1 - 'hcv1h77': 'NC_038882', # HCV genotpye 1 (isolate H77) - 'hcv2': 'NC_009823', # HCV genotype 2 - 'hcv3': 'NC_009824', # HCV genotype 3 - 'hcv4': 'NC_009825', # HCV genotype 4 - 'hcv5': 'NC_009826', # HCV genotype 5 - 'hcv6': 'NC_009827', # HCV genotype 6 - 'hcv7': 'NC_030791', # HCV genotype 7 - 'hiv1': 'NC_001802', # HIV-1 - 'hiv2': 'NC_001722', # HIV-2 - 'monkeypox': 'NC_063383', # Monkeypox Virus - 'restonvirus': 'NC_004161', # Reston Virus (Reston ebolavirus) - 'sarscov2': 'NC_045512', # SARS-CoV-2 (COVID-19) - 'sudanvirus': 'NC_006432', # Sudan Virus (Sudan ebolavirus) - 'taiforestvirus': 'NC_014372', # Tai Forest Virus (Tai Forest ebolavirus, Cote d'Ivoire ebolavirus) + 'bombalivirus': 'NC_039345', # Bombali Virus (Bombali ebolavirus) + 'bundibugyovirus': 'NC_014373', # Bundibugyo Virus (Bundibugyo ebolavirus) + 'chikv': 'NC_004162', # Chikungunya virus + 'denv1': 'NC_001477', # Dengue Virus 1 + 'denv2': 'NC_001474', # Dengue Virus 2 + 'denv3': 'NC_001475', # Dengue Virus 3 + 'denv4': 'NC_002640', # Dengue Virus 4 + 'ebolavirus': 'NC_002549', # Ebola Virus (Zaire ebolavirus) + 'hcv1': 'NC_004102', # HCV genotype 1 + 'hcv1h77': 'NC_038882', # HCV genotpye 1 (isolate H77) + 'hcv2': 'NC_009823', # HCV genotype 2 + 'hcv3': 'NC_009824', # HCV genotype 3 + 'hcv4': 'NC_009825', # HCV genotype 4 + 'hcv5': 'NC_009826', # HCV genotype 5 + 'hcv6': 'NC_009827', # HCV genotype 6 + 'hcv7': 'NC_030791', # HCV genotype 7 + 'hiv1': 'NC_001802', # HIV-1 + 'hiv2': 'NC_001722', # HIV-2 + 'monkeypox': 'NC_063383', # Monkeypox Virus + 'restonvirus': 'NC_004161', # Reston Virus (Reston ebolavirus) + 'sarscov2': 'NC_045512', # SARS-CoV-2 (COVID-19) + 'sudanvirus': 'NC_006432', # Sudan Virus (Sudan ebolavirus) + 'taiforestvirus': 'NC_014372', # Tai Forest Virus (Tai Forest ebolavirus, Cote d'Ivoire ebolavirus) } REF_NAMES = { + 'CHIKV': { + 'chikv': 'Chikungunya virus', + }, 'DENV': { 'denv1': 'Dengue Virus 1', 'denv2': 'Dengue Virus 2',