Nucleone 1.0.0__py3-none-any.whl

Nucleone/__init__.py

@@ -0,0 +1,199 @@
+
+def Kernel(u,h):
+    return pow(1-pow(u/h,2),3)
+
+def Tri(M,h):
+    S=[]
+    for i in range(h):
+        S.append(0)
+    for D in M:
+        S.append(D)
+    for i in range(h):
+        S.append(0)
+    for i in range(h,len(S)-h):
+        s=0
+        for j in range(i-h,i+h):
+            s=s+Kernel(i-j,h)*S[j]
+        M[i-h]=s/h
+
+def ComSeq(seq):
+    s=''
+    seq=seq[::-1]
+    for i in range(0,len(seq)):
+        if seq[i]=='A':
+            s=s+'T'
+        if seq[i]=='T':
+            s=s+'A'
+        if seq[i]=='C':
+            s=s+'G'
+        if seq[i]=='G':
+            s=s+'C'
+    return s
+
+def DisSC(Seq,Dyad):
+    sc=0
+    PTR=['AG','AG','AGT','TTA','CAT','CTT','CCA','CCG','GAC','GC','GGA','GGG','AT','AAA','TTC','CAT','GAC','GTA','GC']
+    Dis=[61,-45,18,12,19,60,35,-20,70,-34,47,3,-98,-96,-90,-98,-82,881,-79]
+    cSeq=ComSeq(Seq)
+    for i in range(len(PTR)):
+        cp=ComSeq(PTR[i])
+        if cp not in PTR:
+            PTR.append(cp)
+            Dis.append(Dis[i])
+    for i in range(len(PTR)):
+        P=PTR[i]
+        D=Dis[i]
+        s=1
+        if D<0:
+            s=-1
+        l=len(P)
+        if (Seq[Dyad-D:Dyad-D+l]==P)|(cSeq[Dyad-D:Dyad-D+l]==P):
+            sc+=s
+        if (Seq[Dyad+D:Dyad+D+l]==P)|(cSeq[Dyad+D:Dyad+D+l]==P):
+            sc+=s
+    return sc
+
+def CS(Seq,Dyad):
+    sc=0
+    MO=['ACT','AG','CAT','CA','GCA','CC','GG','CG','GC']
+    MI=['AT','AAAA','AAA']
+    MIL=[]
+    for i in range(Dyad-5,Dyad-70,-10):
+        MIL.append(i)
+    for i in range(Dyad+5,Dyad+70,10):
+        MIL.append(i)
+    MOL=[]
+    for i in range(Dyad-10,Dyad-70,-10):
+        MOL.append(i)
+    for i in range(Dyad+10,Dyad+70,10):
+        MOL.append(i)
+    ComSq=ComSeq(Seq)
+    for i in MIL:
+        for M in MI:
+            l=int(len(M)/2)
+            r=int(len(M)/2)+1
+            SS=Seq[i-l:i+r]
+            SSC=ComSq[i-l:i+r]
+            if (M in SS)|(M in SSC):
+                sc+=1
+        for M in MO:
+            l=int(len(M)/2)
+            r=int(len(M)/2)+1
+            SS=Seq[i-l:i+r]
+            SSC=ComSq[i-l:i+r]
+            if (M in SS)|(M in SSC):
+                sc-=1
+    for i in MOL:
+        for M in MO:
+            l=int(len(M)/2)
+            r=int(len(M)/2)+1
+            SS=Seq[i-l:i+r]
+            SSC=ComSq[i-l:i+r]
+            if (M in SS)|(M in SSC):
+                sc+=1
+        for M in MI:
+            l=int(len(M)/2)
+            r=int(len(M)/2)+1
+            SS=Seq[i-l:i+r]
+            SSC=ComSq[i-l:i+r]
+            if (M in SS)|(M in SSC):
+                sc-=1
+    return sc
+
+def GetFre(Seq,W,S):
+    WW=['AA','TT','AT','TA']
+    SS=['CC','GG','CG','GC']
+    for i in range(0,141):
+        if Seq[i:i+2] in WW:
+            W[i]=W[i]+1
+        if Seq[i:i+2] in SS:
+            S[i]=S[i]+1
+
+
+def DetDyad(Seq,SC,l,h,Po):
+    if h-l>200:
+        S=SC[l:h]
+        ma=max(S)
+        D=S.index(ma)+l 
+        sl=[]
+        for d in range(D-5,D+6):
+            DNA=Seq[d-100:d+101]
+            sc=CS(DNA,101)
+            sc=sc+DisSC(DNA,101)
+            sl.append(sc)
+        ma=max(sl)
+        inx=sl.index(ma)
+        inx=inx-5
+        dyad=D+inx
+        Po[dyad]=1
+        DetDyad(Seq,SC,l,dyad-150,Po)
+        DetDyad(Seq,SC,dyad+150,h,Po)
+
+def GetDyad(Seq,Sc):
+    Po=[]
+    Tri(Sc,15)
+    for i in range(len(Sc)):
+        Po.append(0)
+    DetDyad(Seq,Sc,100,len(Seq)-100,Po)
+    Dy=[]
+    for i in range(len(Po)):
+        if Po[i]==1:
+            Dy.append(i)
+    return Dy
+
+
+
+def Nucleone(SEFP,SCFP,OF):
+    F=open(SEFP,'r')
+    seq=F.readlines()
+    F.close()
+    Seq=''
+    for S in seq:
+        if '>' in S:
+            continue
+        Seq=Seq+S.replace("\n",'').replace("\r","")
+    F=open(SCFP,'r')
+    DY=F.readlines()
+    F.close()
+    dc=[]
+    for d in DY:
+        if '>' in d:
+            continue
+        DC=d.replace("\n",'').replace("\t",'').replace("\r","").split(',')
+        for D in DC:
+            dc.append(D)
+    print('The algorithm is processing your input data. Please wait while the results are being generated.')
+    Sc=[]
+    for D in dc:
+        if len(D)>0:
+            Sc.append(int(D))
+    import matplotlib.pyplot as plt
+    plt.figure(figsize=(12, 6))
+    plt.subplot(2,1,1)
+    for i in range(len(Sc)):
+        plt.bar(i,Sc[i],color='blue')
+    plt.xlabel('Coordinate',fontsize=14)
+    plt.ylabel('Dyad Count',fontsize=14)
+    plt.title('The Given Nucleosome Occupancy Profile',fontsize=16)
+    Dy=GetDyad(Seq,Sc)
+    plt.subplot(2,1,2)
+    for i in range(len(Sc)):
+        plt.bar(i,Sc[i],color='green')
+    for i in range(len(Dy)):
+        plt.scatter(Dy[i],Sc[Dy[i]],color='brown', s=120, marker='o', zorder=5)
+    plt.xlabel('Coordinate',fontsize=14)
+    plt.ylabel('Smoothed Dyad Count',fontsize=14)
+    plt.title('The Smoothed Nucleosome Occupancy Profile',fontsize=16)
+    plt.tight_layout()
+    plt.savefig(OF+'.jpg',dpi=300,bbox_inches='tight')
+    plt.close()
+    FI=open(OF+'.txt','w')
+    FI.write('> Smoothed Dyad Counts\n')
+    for i in range(len(Sc)-1):
+        FI.write(str(Sc[i])+',')
+    FI.write(str(Sc[-1])+'\n\n')
+    FI.write('> Identified dyads\n')
+    for i in range(len(Dy)):
+        FI.write(str(Dy[i])+'\n')
+    FI.close()
+    print('The analysis has been completed, and the output files have been generated.')

nucleone-1.0.0.dist-info/METADATA

@@ -0,0 +1,13 @@
+Metadata-Version: 2.4
+Name: Nucleone
+Version: 1.0.0
+Summary: Dyad identification from nucleosome occupancy profile
+Author: Yosef Masoudi-Sobhanzadeh, Sushant Kumar
+License: MIT
+Project-URL: Homepage, https://nucleone.org/
+Project-URL: Repository, https://nucleone.org/
+Requires-Python: >=3.0
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: matplotlib>=3.5
+Dynamic: license-file

nucleone-1.0.0.dist-info/RECORD

@@ -0,0 +1,6 @@
+Nucleone/__init__.py,sha256=6TNH2bfmzkqAGVGRYudzoFtLwE4g5J6ErwdcbAQiG7k,5421
+nucleone-1.0.0.dist-info/licenses/LICENSE,sha256=wUNcwhy3qGifYqVaXt9qUVxmziv7KYGFzkFMK3-uaws,1101
+nucleone-1.0.0.dist-info/METADATA,sha256=1Fivq6T3lNXaJJ_pEJaKPgx_x3P1EJFFVlfJmWiJmfY,420
+nucleone-1.0.0.dist-info/WHEEL,sha256=YVMoNqKzERt-wjUZwJ33xBGAwnFl-4cqbYkTtWa4itE,91
+nucleone-1.0.0.dist-info/top_level.txt,sha256=KeeJrStf291rJ7ajmQ7w2ifk8RJkVjCD2iduX-8weRI,9
+nucleone-1.0.0.dist-info/RECORD,,

nucleone-1.0.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (84.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

nucleone-1.0.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Yosef Masoudi-Sobhanzadeh
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

nucleone-1.0.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+Nucleone