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blosum

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blosum - npm Package Compare versions

Comparing version
1.1.2
 to
1.1.3
+3
-2
PKG-INFO
Metadata-Version: 2.1
Name: blosum
Version: 1.1.2
Version: 1.1.3
Summary: A simple BLOSUM toolbox without dependencies.

@@ -30,2 +30,3 @@ Home-page: https://github.com/not-a-feature/blosum

![Download Badge](https://img.shields.io/pypi/dm/blosum.svg)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)

@@ -105,3 +106,3 @@ The BLOcks SUbstitution Matrices (BLOSUM) are used to score alignments between protein sequences and are therefore mainly used in bioinformatics.

```
Copyright (C) 2021 by Jules Kreuer - @not_a_feature
Copyright (C) 2022 by Jules Kreuer - @not_a_feature
This piece of software is published unter the GNU General Public License v3.0

@@ -108,0 +109,0 @@ TLDR:

+2
-1
README.md

@@ -8,2 +8,3 @@ ![blosum](https://github.com/not-a-feature/blosum/raw/main/blosum.png)

![Download Badge](https://img.shields.io/pypi/dm/blosum.svg)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)

@@ -83,3 +84,3 @@ The BLOcks SUbstitution Matrices (BLOSUM) are used to score alignments between protein sequences and are therefore mainly used in bioinformatics.

```
Copyright (C) 2021 by Jules Kreuer - @not_a_feature
Copyright (C) 2022 by Jules Kreuer - @not_a_feature
This piece of software is published unter the GNU General Public License v3.0

@@ -86,0 +87,0 @@ TLDR:

+1
-5
setup.cfg
[metadata]
name = blosum
version = 1.1.2
version = 1.1.3
description = A simple BLOSUM toolbox without dependencies.

@@ -31,3 +31,2 @@ long_description = file: README.md

pytest-cov>=2.0
flake8>=3.9
tox>=3.20

@@ -38,5 +37,2 @@

[flake8]
max-line-length = 120
[pytest]

@@ -43,0 +39,0 @@ xfail_strict = true

+3
-2
src/blosum.egg-info/PKG-INFO
Metadata-Version: 2.1
Name: blosum
Version: 1.1.2
Version: 1.1.3
Summary: A simple BLOSUM toolbox without dependencies.

@@ -30,2 +30,3 @@ Home-page: https://github.com/not-a-feature/blosum

![Download Badge](https://img.shields.io/pypi/dm/blosum.svg)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)

@@ -105,3 +106,3 @@ The BLOcks SUbstitution Matrices (BLOSUM) are used to score alignments between protein sequences and are therefore mainly used in bioinformatics.

```
Copyright (C) 2021 by Jules Kreuer - @not_a_feature
Copyright (C) 2022 by Jules Kreuer - @not_a_feature
This piece of software is published unter the GNU General Public License v3.0

@@ -108,0 +109,0 @@ TLDR:

+0
-1
src/blosum.egg-info/requires.txt

@@ -5,3 +5,2 @@

pytest-cov>=2.0
flake8>=3.9
tox>=3.20
+1
-0
src/blosum/__init__.py
from ._blosum import BLOSUM
__all__ = [
"BLOSUM",
]
+5
-5
src/blosum/_blosum.py

@@ -14,3 +14,3 @@ """

class BLOSUM():
class BLOSUM:
def __init__(self, n, default: float = float("-inf")):

@@ -44,3 +44,3 @@ """

else:
raise(BaseException("Can't initate empty BLOSUM Object"))
raise (BaseException("Can't initate empty BLOSUM Object"))

@@ -94,3 +94,3 @@ def __loadMatrix(self, path: str) -> None:

# Check quadratic
if not len(blosumDict) == len(labelslist)**2:
if not len(blosumDict) == len(labelslist) ** 2:
raise EOFError("Blosum file is not quadratic.")

@@ -126,3 +126,3 @@ self.matrix = blosumDict

"""
return f'BLOSUM {self.n}\n{self.matrix}'
return f"BLOSUM {self.n}\n{self.matrix}"

@@ -139,2 +139,2 @@ def __repr__(self) -> str:

n = f'"{self.n}"'
return f'BLOSUM({n}, default={d})'
return f"BLOSUM({n}, default={d})"
+3136
-450
src/blosum/_data.py
default_blosum = {
45: {'AA': 5.0, 'AR': -2.0, 'AN': -1.0, 'AD': -2.0, 'AC': -1.0, 'AQ': -1.0, 'AE': -1.0,
'AG': 0.0, 'AH': -2.0, 'AI': -1.0, 'AL': -1.0, 'AK': -1.0, 'AM': -1.0, 'AF': -2.0,
'AP': -1.0, 'AS': 1.0, 'AT': 0.0, 'AW': -2.0, 'AY': -2.0, 'AV': 0.0, 'AB': -1.0,
'AJ': -1.0, 'AZ': -1.0, 'AX': -1.0, 'A*': -5.0, 'RA': -2.0, 'RR': 7.0, 'RN': 0.0,
'RD': -1.0, 'RC': -3.0, 'RQ': 1.0, 'RE': 0.0, 'RG': -2.0, 'RH': 0.0, 'RI': -3.0,
'RL': -2.0, 'RK': 3.0, 'RM': -1.0, 'RF': -2.0, 'RP': -2.0, 'RS': -1.0, 'RT': -1.0,
'RW': -2.0, 'RY': -1.0, 'RV': -2.0, 'RB': -1.0, 'RJ': -3.0, 'RZ': 1.0, 'RX': -1.0,
'R*': -5.0, 'NA': -1.0, 'NR': 0.0, 'NN': 6.0, 'ND': 2.0, 'NC': -2.0, 'NQ': 0.0,
'NE': 0.0, 'NG': 0.0, 'NH': 1.0, 'NI': -2.0, 'NL': -3.0, 'NK': 0.0, 'NM': -2.0,
'NF': -2.0, 'NP': -2.0, 'NS': 1.0, 'NT': 0.0, 'NW': -4.0, 'NY': -2.0, 'NV': -3.0,
'NB': 5.0, 'NJ': -3.0, 'NZ': 0.0, 'NX': -1.0, 'N*': -5.0, 'DA': -2.0, 'DR': -1.0,
'DN': 2.0, 'DD': 7.0, 'DC': -3.0, 'DQ': 0.0, 'DE': 2.0, 'DG': -1.0, 'DH': 0.0,
'DI': -4.0, 'DL': -3.0, 'DK': 0.0, 'DM': -3.0, 'DF': -4.0, 'DP': -1.0, 'DS': 0.0,
'DT': -1.0, 'DW': -4.0, 'DY': -2.0, 'DV': -3.0, 'DB': 6.0, 'DJ': -3.0, 'DZ': 1.0,
'DX': -1.0, 'D*': -5.0, 'CA': -1.0, 'CR': -3.0, 'CN': -2.0, 'CD': -3.0, 'CC': 12.0,
'CQ': -3.0, 'CE': -3.0, 'CG': -3.0, 'CH': -3.0, 'CI': -3.0, 'CL': -2.0, 'CK': -3.0,
'CM': -2.0, 'CF': -2.0, 'CP': -4.0, 'CS': -1.0, 'CT': -1.0, 'CW': -5.0, 'CY': -3.0,
'CV': -1.0, 'CB': -2.0, 'CJ': -2.0, 'CZ': -3.0, 'CX': -1.0, 'C*': -5.0, 'QA': -1.0,
'QR': 1.0, 'QN': 0.0, 'QD': 0.0, 'QC': -3.0, 'QQ': 6.0, 'QE': 2.0, 'QG': -2.0,
'QH': 1.0, 'QI': -2.0, 'QL': -2.0, 'QK': 1.0, 'QM': 0.0, 'QF': -4.0, 'QP': -1.0,
'QS': 0.0, 'QT': -1.0, 'QW': -2.0, 'QY': -1.0, 'QV': -3.0, 'QB': 0.0, 'QJ': -2.0,
'QZ': 4.0, 'QX': -1.0, 'Q*': -5.0, 'EA': -1.0, 'ER': 0.0, 'EN': 0.0, 'ED': 2.0,
'EC': -3.0, 'EQ': 2.0, 'EE': 6.0, 'EG': -2.0, 'EH': 0.0, 'EI': -3.0, 'EL': -2.0,
'EK': 1.0, 'EM': -2.0, 'EF': -3.0, 'EP': 0.0, 'ES': 0.0, 'ET': -1.0, 'EW': -3.0,
'EY': -2.0, 'EV': -3.0, 'EB': 1.0, 'EJ': -3.0, 'EZ': 5.0, 'EX': -1.0, 'E*': -5.0,
'GA': 0.0, 'GR': -2.0, 'GN': 0.0, 'GD': -1.0, 'GC': -3.0, 'GQ': -2.0, 'GE': -2.0,
'GG': 7.0, 'GH': -2.0, 'GI': -4.0, 'GL': -3.0, 'GK': -2.0, 'GM': -2.0, 'GF': -3.0,
'GP': -2.0, 'GS': 0.0, 'GT': -2.0, 'GW': -2.0, 'GY': -3.0, 'GV': -3.0, 'GB': -1.0,
'GJ': -4.0, 'GZ': -2.0, 'GX': -1.0, 'G*': -5.0, 'HA': -2.0, 'HR': 0.0, 'HN': 1.0,
'HD': 0.0, 'HC': -3.0, 'HQ': 1.0, 'HE': 0.0, 'HG': -2.0, 'HH': 10.0, 'HI': -3.0,
'HL': -2.0, 'HK': -1.0, 'HM': 0.0, 'HF': -2.0, 'HP': -2.0, 'HS': -1.0, 'HT': -2.0,
'HW': -3.0, 'HY': 2.0, 'HV': -3.0, 'HB': 0.0, 'HJ': -2.0, 'HZ': 0.0, 'HX': -1.0,
'H*': -5.0, 'IA': -1.0, 'IR': -3.0, 'IN': -2.0, 'ID': -4.0, 'IC': -3.0, 'IQ': -2.0,
'IE': -3.0, 'IG': -4.0, 'IH': -3.0, 'II': 5.0, 'IL': 2.0, 'IK': -3.0, 'IM': 2.0,
'IF': 0.0, 'IP': -2.0, 'IS': -2.0, 'IT': -1.0, 'IW': -2.0, 'IY': 0.0, 'IV': 3.0,
'IB': -3.0, 'IJ': 4.0, 'IZ': -3.0, 'IX': -1.0, 'I*': -5.0, 'LA': -1.0, 'LR': -2.0,
'LN': -3.0, 'LD': -3.0, 'LC': -2.0, 'LQ': -2.0, 'LE': -2.0, 'LG': -3.0, 'LH': -2.0,
'LI': 2.0, 'LL': 5.0, 'LK': -3.0, 'LM': 2.0, 'LF': 1.0, 'LP': -3.0, 'LS': -3.0,
'LT': -1.0, 'LW': -2.0, 'LY': 0.0, 'LV': 1.0, 'LB': -3.0, 'LJ': 4.0, 'LZ': -2.0,
'LX': -1.0, 'L*': -5.0, 'KA': -1.0, 'KR': 3.0, 'KN': 0.0, 'KD': 0.0, 'KC': -3.0,
'KQ': 1.0, 'KE': 1.0, 'KG': -2.0, 'KH': -1.0, 'KI': -3.0, 'KL': -3.0, 'KK': 5.0,
'KM': -1.0, 'KF': -3.0, 'KP': -1.0, 'KS': -1.0, 'KT': -1.0, 'KW': -2.0, 'KY': -1.0,
'KV': -2.0, 'KB': 0.0, 'KJ': -3.0, 'KZ': 1.0, 'KX': -1.0, 'K*': -5.0, 'MA': -1.0,
'MR': -1.0, 'MN': -2.0, 'MD': -3.0, 'MC': -2.0, 'MQ': 0.0, 'ME': -2.0, 'MG': -2.0,
'MH': 0.0, 'MI': 2.0, 'ML': 2.0, 'MK': -1.0,
'MM': 6.0, 'MF': 0.0, 'MP': -2.0, 'MS': -2.0, 'MT': -1.0, 'MW': -2.0, 'MY': 0.0,
'MV': 1.0, 'MB': -2.0, 'MJ': 2.0, 'MZ': -1.0, 'MX': -1.0, 'M*': -5.0, 'FA': -2.0,
'FR': -2.0, 'FN': -2.0, 'FD': -4.0, 'FC': -2.0, 'FQ': -4.0, 'FE': -3.0, 'FG': -3.0,
'FH': -2.0, 'FI': 0.0, 'FL': 1.0, 'FK': -3.0, 'FM': 0.0, 'FF': 8.0, 'FP': -3.0,
'FS': -2.0, 'FT': -1.0, 'FW': 1.0, 'FY': 3.0, 'FV': 0.0, 'FB': -3.0, 'FJ': 1.0,
'FZ': -3.0, 'FX': -1.0, 'F*': -5.0, 'PA': -1.0, 'PR': -2.0, 'PN': -2.0, 'PD': -1.0,
'PC': -4.0, 'PQ': -1.0, 'PE': 0.0, 'PG': -2.0, 'PH': -2.0, 'PI': -2.0, 'PL': -3.0,
'PK': -1.0, 'PM': -2.0, 'PF': -3.0, 'PP': 9.0, 'PS': -1.0, 'PT': -1.0, 'PW': -3.0,
'PY': -3.0, 'PV': -3.0, 'PB': -2.0, 'PJ': -3.0, 'PZ': -1.0, 'PX': -1.0, 'P*': -5.0,
'SA': 1.0, 'SR': -1.0, 'SN': 1.0, 'SD': 0.0, 'SC': -1.0, 'SQ': 0.0, 'SE': 0.0,
'SG': 0.0, 'SH': -1.0, 'SI': -2.0, 'SL': -3.0, 'SK': -1.0, 'SM': -2.0, 'SF': -2.0,
'SP': -1.0, 'SS': 4.0, 'ST': 2.0, 'SW': -4.0, 'SY': -2.0, 'SV': -1.0, 'SB': 0.0,
'SJ': -2.0, 'SZ': 0.0, 'SX': -1.0, 'S*': -5.0, 'TA': 0.0, 'TR': -1.0, 'TN': 0.0,
'TD': -1.0, 'TC': -1.0, 'TQ': -1.0, 'TE': -1.0, 'TG': -2.0, 'TH': -2.0, 'TI': -1.0,
'TL': -1.0, 'TK': -1.0, 'TM': -1.0, 'TF': -1.0, 'TP': -1.0, 'TS': 2.0, 'TT': 5.0,
'TW': -3.0, 'TY': -1.0, 'TV': 0.0, 'TB': 0.0, 'TJ': -1.0, 'TZ': -1.0, 'TX': -1.0,
'T*': -5.0, 'WA': -2.0, 'WR': -2.0, 'WN': -4.0, 'WD': -4.0, 'WC': -5.0, 'WQ': -2.0,
'WE': -3.0, 'WG': -2.0, 'WH': -3.0, 'WI': -2.0, 'WL': -2.0, 'WK': -2.0, 'WM': -2.0,
'WF': 1.0, 'WP': -3.0, 'WS': -4.0, 'WT': -3.0, 'WW': 15.0, 'WY': 3.0, 'WV': -3.0,
'WB': -4.0, 'WJ': -2.0, 'WZ': -2.0, 'WX': -1.0, 'W*': -5.0, 'YA': -2.0, 'YR': -1.0,
'YN': -2.0, 'YD': -2.0, 'YC': -3.0, 'YQ': -1.0, 'YE': -2.0, 'YG': -3.0, 'YH': 2.0,
'YI': 0.0, 'YL': 0.0, 'YK': -1.0, 'YM': 0.0, 'YF': 3.0, 'YP': -3.0, 'YS': -2.0,
'YT': -1.0, 'YW': 3.0, 'YY': 8.0, 'YV': -1.0, 'YB': -2.0, 'YJ': 0.0, 'YZ': -2.0,
'YX': -1.0, 'Y*': -5.0, 'VA': 0.0, 'VR': -2.0, 'VN': -3.0, 'VD': -3.0, 'VC': -1.0,
'VQ': -3.0, 'VE': -3.0, 'VG': -3.0, 'VH': -3.0, 'VI': 3.0, 'VL': 1.0, 'VK': -2.0,
'VM': 1.0, 'VF': 0.0, 'VP': -3.0, 'VS': -1.0, 'VT': 0.0, 'VW': -3.0, 'VY': -1.0,
'VV': 5.0, 'VB': -3.0, 'VJ': 2.0, 'VZ': -3.0, 'VX': -1.0, 'V*': -5.0, 'BA': -1.0,
'BR': -1.0, 'BN': 5.0, 'BD': 6.0, 'BC': -2.0, 'BQ': 0.0, 'BE': 1.0, 'BG': -1.0,
'BH': 0.0, 'BI': -3.0, 'BL': -3.0, 'BK': 0.0, 'BM': -2.0, 'BF': -3.0, 'BP': -2.0,
'BS': 0.0, 'BT': 0.0, 'BW': -4.0, 'BY': -2.0, 'BV': -3.0, 'BB': 5.0, 'BJ': -3.0,
'BZ': 1.0, 'BX': -1.0, 'B*': -5.0, 'JA': -1.0, 'JR': -3.0, 'JN': -3.0, 'JD': -3.0,
'JC': -2.0, 'JQ': -2.0, 'JE': -3.0, 'JG': -4.0, 'JH': -2.0, 'JI': 4.0, 'JL': 4.0,
'JK': -3.0, 'JM': 2.0, 'JF': 1.0, 'JP': -3.0, 'JS': -2.0, 'JT': -1.0, 'JW': -2.0,
'JY': 0.0, 'JV': 2.0, 'JB': -3.0, 'JJ': 4.0, 'JZ': -2.0, 'JX': -1.0, 'J*': -5.0,
'ZA': -1.0, 'ZR': 1.0, 'ZN': 0.0, 'ZD': 1.0, 'ZC': -3.0, 'ZQ': 4.0, 'ZE': 5.0,
'ZG': -2.0, 'ZH': 0.0, 'ZI': -3.0, 'ZL': -2.0, 'ZK': 1.0, 'ZM': -1.0, 'ZF': -3.0,
'ZP': -1.0, 'ZS': 0.0, 'ZT': -1.0, 'ZW': -2.0, 'ZY': -2.0, 'ZV': -3.0, 'ZB': 1.0,
'ZJ': -2.0, 'ZZ': 5.0, 'ZX': -1.0, 'Z*': -5.0, 'XA': -1.0, 'XR': -1.0, 'XN': -1.0,
'XD': -1.0, 'XC': -1.0, 'XQ': -1.0, 'XE': -1.0, 'XG': -1.0, 'XH': -1.0, 'XI': -1.0,
'XL': -1.0, 'XK': -1.0, 'XM': -1.0, 'XF': -1.0, 'XP': -1.0, 'XS': -1.0, 'XT': -1.0,
'XW': -1.0, 'XY': -1.0, 'XV': -1.0, 'XB': -1.0, 'XJ': -1.0, 'XZ': -1.0, 'XX': -1.0,
'X*': -5.0, '*A': -5.0, '*R': -5.0, '*N': -5.0, '*D': -5.0, '*C': -5.0, '*Q': -5.0,
'*E': -5.0, '*G': -5.0, '*H': -5.0, '*I': -5.0, '*L': -5.0, '*K': -5.0, '*M': -5.0,
'*F': -5.0, '*P': -5.0, '*S': -5.0, '*T': -5.0, '*W': -5.0, '*Y': -5.0, '*V': -5.0,
'*B': -5.0, '*J': -5.0, '*Z': -5.0, '*X': -5.0, '**': 1.0},
50: {'AA': 5.0, 'AR': -2.0, 'AN': -1.0, 'AD': -2.0, 'AC': -1.0, 'AQ': -1.0, 'AE': -1.0,
'AG': 0.0, 'AH': -2.0, 'AI': -1.0, 'AL': -2.0, 'AK': -1.0, 'AM': -1.0, 'AF': -3.0,
'AP': -1.0, 'AS': 1.0, 'AT': 0.0, 'AW': -3.0, 'AY': -2.0, 'AV': 0.0, 'AB': -2.0,
'AJ': -2.0, 'AZ': -1.0, 'AX': -1.0, 'A*': -5.0, 'RA': -2.0, 'RR': 7.0, 'RN': -1.0,
'RD': -2.0, 'RC': -4.0, 'RQ': 1.0, 'RE': 0.0, 'RG': -3.0, 'RH': 0.0, 'RI': -4.0,
'RL': -3.0, 'RK': 3.0, 'RM': -2.0, 'RF': -3.0, 'RP': -3.0, 'RS': -1.0, 'RT': -1.0,
'RW': -3.0, 'RY': -1.0, 'RV': -3.0, 'RB': -1.0, 'RJ': -3.0, 'RZ': 0.0, 'RX': -1.0,
'R*': -5.0, 'NA': -1.0, 'NR': -1.0, 'NN': 7.0, 'ND': 2.0, 'NC': -2.0, 'NQ': 0.0,
'NE': 0.0, 'NG': 0.0, 'NH': 1.0, 'NI': -3.0, 'NL': -4.0, 'NK': 0.0, 'NM': -2.0,
'NF': -4.0, 'NP': -2.0, 'NS': 1.0, 'NT': 0.0, 'NW': -4.0, 'NY': -2.0, 'NV': -3.0,
'NB': 5.0, 'NJ': -4.0, 'NZ': 0.0, 'NX': -1.0, 'N*': -5.0, 'DA': -2.0, 'DR': -2.0,
'DN': 2.0, 'DD': 8.0, 'DC': -4.0, 'DQ': 0.0, 'DE': 2.0, 'DG': -1.0, 'DH': -1.0,
'DI': -4.0, 'DL': -4.0, 'DK': -1.0, 'DM': -4.0, 'DF': -5.0, 'DP': -1.0, 'DS': 0.0,
'DT': -1.0, 'DW': -5.0, 'DY': -3.0, 'DV': -4.0, 'DB': 6.0, 'DJ': -4.0, 'DZ': 1.0,
'DX': -1.0, 'D*': -5.0, 'CA': -1.0, 'CR': -4.0, 'CN': -2.0, 'CD': -4.0, 'CC': 13.0,
'CQ': -3.0, 'CE': -3.0, 'CG': -3.0, 'CH': -3.0, 'CI': -2.0, 'CL': -2.0, 'CK': -3.0,
'CM': -2.0, 'CF': -2.0, 'CP': -4.0, 'CS': -1.0, 'CT': -1.0, 'CW': -5.0, 'CY': -3.0,
'CV': -1.0, 'CB': -3.0, 'CJ': -2.0, 'CZ': -3.0, 'CX': -1.0, 'C*': -5.0, 'QA': -1.0,
'QR': 1.0, 'QN': 0.0, 'QD': 0.0, 'QC': -3.0, 'QQ': 7.0, 'QE': 2.0, 'QG': -2.0,
'QH': 1.0, 'QI': -3.0, 'QL': -2.0, 'QK': 2.0, 'QM': 0.0, 'QF': -4.0, 'QP': -1.0,
'QS': 0.0, 'QT': -1.0, 'QW': -1.0, 'QY': -1.0, 'QV': -3.0, 'QB': 0.0, 'QJ': -3.0,
'QZ': 4.0, 'QX': -1.0, 'Q*': -5.0, 'EA': -1.0, 'ER': 0.0, 'EN': 0.0, 'ED': 2.0,
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