diff scripts/S02b_study_seq_composition_nuc.py @ 10:f62c76aab669 draft default tip

planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1

--- a/scripts/S02b_study_seq_composition_nuc.py	Tue Jul 03 10:55:46 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,205 +0,0 @@
-#!/usr/bin/env python
-## Author: Eric FONTANILLAS
-## Date: 21.12.10
-## Last Version : 12/2017 by Victor Mataigne
-## Object: Test for compositional bias in genome and proteome as marker of thermal adaptation (comparison between 2 "hot" species: Ap and Ps and one "cold" species: Pg)
-
-import sys,os,shutil,subprocess, string, itertools
-from functions import simplify_fasta_name, dico
-
-##################
-###### DEF2 ######
-##################
-def base_composition(seq):
-      count_A=string.count(seq, "A") + string.count(seq, "a")
-      count_T=string.count(seq, "T") + string.count(seq, "t")
-      count_C=string.count(seq, "C") + string.count(seq, "c")
-      count_G=string.count(seq, "G") + string.count(seq, "g")
-      ## 3 ## Nucleotide proportions
-      ln = count_C+count_G+count_T+count_A
-      if (ln!=0):
-
-            CG = count_C+count_G
-            AT = count_T+count_A
-      
-            AG = count_A+count_G
-            TC = count_T+count_C
-
-            ## 1 ## Search for compositional bias in genome as marker of thermal adaptation: CG vs AT
-            ratio_CG_AT = float(CG)/float(AT)
-            percent_CG = float(CG)/(float(AT) + float(CG))*100
-      
-            ## 2 ## Search for compositional bias in genome as marker of thermal adaptation: AG vs TC
-            ratio_purine_pyrimidine=float(AG)/float(TC)
-            percent_purine=float(AG)/(float(AG)+float(TC))*100      
-      
-     
-            prop_A = float(count_A)/float(ln)
-            prop_T = float(count_T)/float(ln)
-            prop_C = float(count_C)/float(ln)
-            prop_G = float(count_G)/float(ln)
-      else:
-            percent_CG=0
-            percent_purine=0
-            prop_A=0
-            prop_T=0
-            prop_C=0
-            prop_G=0
-      
-      return(percent_CG, percent_purine, prop_A, prop_T, prop_C, prop_G)
-##############################################
-
-##################
-###### DEF3 ######
-##################
-def purine_loading(seq):
-      count_A=string.count(seq, "A") + string.count(seq, "a")
-      count_T=string.count(seq, "T") + string.count(seq, "t")
-      count_C=string.count(seq, "C") + string.count(seq, "c")
-      count_G=string.count(seq, "G") + string.count(seq, "g")
-      ## 3 ## Nucleotide proportions
-      TOTAL = count_C+count_G+count_T+count_A
-      if (TOTAL!=0):
-     
-            ## PLI : Purine loading indice (Forsdyke et al.)
-            # (G-C)/N * 1000 et (A-T)/N * 1000
-      
-            DIFF_GC = count_G - count_C
-            DIFF_AT = count_A - count_T
-
-            # Per bp
-            PLI_GC = float(DIFF_GC)/float(TOTAL)
-            PLI_AT = float(DIFF_AT)/float(TOTAL)
-      
-            # Per 1000 bp
-            PLI_GC_1000 = PLI_GC*1000
-            PLI_AT_1000 = PLI_AT*1000
-      else:
-            DIFF_GC=0
-            DIFF_AT=0
-            PLI_GC=0
-            PLI_AT=0
-            PLI_GC_1000=0
-            PLI_AT_1000=0
-
-      return(TOTAL, DIFF_GC, DIFF_AT,PLI_GC,PLI_AT,PLI_GC_1000,PLI_AT_1000)
-##############################################
-
-###################
-### RUN RUN RUN ###
-###################
-
-##Create specific folders
-Path_IN_loci_NUC = "./IN_NUC"
-outpath= "./OUT"
-os.makedirs(Path_IN_loci_NUC)
-os.makedirs(outpath)
-
-infiles = []
-with open(sys.argv[2], 'r') as f:
-    for line in f.readlines():
-        infiles.append(line.strip('\n'))
-
-#infiles = str.split(sys.argv[1], ",")
-for file in infiles:
-    os.system("cp %s %s" %(file, Path_IN_loci_NUC))
-
-## 1 ## List taxa
-LT=[]
-cmd="grep '>' {}".format(sys.argv[1])
-result = subprocess.check_output(cmd, shell=True)
-result=result.split('\n')
-for i in result:   
-    sp=i[1:]
-    if sp !='':
-        LT.append(sp)
-print LT
-
-## 2 ## PathIN
-Lloci_NUC = os.listdir(Path_IN_loci_NUC)
-
-
-## 3 ## PathOUT
-## 3.1 ## NUC composition
-fileOUT_NUC=open("./OUT/nuc_compositions.csv","w")
-fileOUT_NUC.write("LOCUS,")
-for taxa in LT[0:-1]:
-    fileOUT_NUC.write("%s_prop_A,%s_prop_T,%s_prop_C,%s_prop_G," %(taxa,taxa,taxa,taxa))
-fileOUT_NUC.write("%s_prop_A,%s_prop_T,%s_prop_C,%s_prop_G" %(LT[-1],LT[-1],LT[-1],LT[-1]))
-fileOUT_NUC.write("\n")
-
-## 3.2 ## NUC percent_GC
-fileOUT_percent_GC=open("./OUT/percent_GC.csv","w")
-fileOUT_percent_GC.write("LOCUS,")
-for taxa in LT[0:-1]:
-    fileOUT_percent_GC.write("%s_percent_GC," %(taxa))
-fileOUT_percent_GC.write("%s_percentGC" %(LT[-1]))
-fileOUT_percent_GC.write("\n")
-
-## 3.3 ## NUC percent_purine
-fileOUT_percent_purine=open("./OUT/percent_purine.csv","w")
-fileOUT_percent_purine.write("LOCUS,")
-for taxa in LT[0:-1]:
-    fileOUT_percent_purine.write("%s_percent_purine," %(taxa))
-fileOUT_percent_purine.write("%s_percent_purine" %(LT[-1]))
-fileOUT_percent_purine.write("\n")
-
-## 3.4 ## Purine Load
-fileOUT_Purine_Load=open("./OUT/Purine_Load_Indice.csv", "w")
-fileOUT_Purine_Load.write("LOCUS,")
-for taxa in LT[0:-1]:
-    fileOUT_Purine_Load.write("%s_TOTAL,%s_DIFF_GC,%s_DIFF_AT,%s_PLI_GC1000,%s_PLI_AT1000," %(taxa,taxa,taxa,taxa,taxa))
-fileOUT_Purine_Load.write("%s_TOTAL,%s_DIFF_GC,%s_DIFF_AT,%s_PLI_GC1000,%s_PLI_AT1000" %(LT[-1],LT[-1],LT[-1],LT[-1],LT[-1]))
-fileOUT_Purine_Load.write("\n")
-
-#####################
-## 4 ## Process Loci
-#####################
-for locus in Lloci_NUC:
-    print locus
-    path_locus = "%s/%s" %(Path_IN_loci_NUC, locus)
-    bash = dico(path_locus,LT) 
-
-    fileOUT_NUC.write("%s," %locus)
-    fileOUT_percent_GC.write("%s," %locus)
-    fileOUT_percent_purine.write("%s," %locus)
-    fileOUT_Purine_Load.write("%s," %locus)
-
-    for taxa in LT[0:-1]:    
-      if taxa in bash.keys():        
-        seq = bash[taxa]            
-        percent_GC, percent_purine,prop_A, prop_T, prop_C, prop_G = base_composition(seq)   ### DEF2 ###
-        TOTAL, DIFF_GC, DIFF_AT,PLI_GC,PLI_AT,PLI_GC_1000,PLI_AT_1000 = purine_loading(seq) ### DEF3 ###
-        fileOUT_NUC.write("%.5f,%.5f,%.5f,%.5f," %(prop_A,prop_T,prop_C,prop_G))
-        fileOUT_percent_GC.write("%.5f," %percent_GC)
-        fileOUT_percent_purine.write("%.5f," %percent_purine)
-        fileOUT_Purine_Load.write("%d,%d,%d,%.5f,%.5f," %(TOTAL, DIFF_GC, DIFF_AT,PLI_GC_1000, PLI_AT_1000))
-      else:
-        fileOUT_NUC.write("%s,%s,%s,%s," %("NA","NA","NA","NA"))
-        fileOUT_percent_GC.write("%s," %"NA")
-        fileOUT_percent_purine.write("%s," %"NA")
-        fileOUT_Purine_Load.write("%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA"))
-        
-    if LT[-1] in bash.keys():
-      seq = bash[LT[-1]]            
-      percent_GC, percent_purine,prop_A, prop_T, prop_C, prop_G = base_composition(seq)   ### DEF2 ###
-      TOTAL, DIFF_GC, DIFF_AT,PLI_GC,PLI_AT,PLI_GC_1000,PLI_AT_1000 = purine_loading(seq) ### DEF3 ###
-      fileOUT_NUC.write("%.5f,%.5f,%.5f,%.5f" %(prop_A,prop_T,prop_C,prop_G))
-      fileOUT_percent_GC.write("%.5f" %percent_GC)
-      fileOUT_percent_purine.write("%.5f" %percent_purine)
-      fileOUT_Purine_Load.write("%d,%d,%d,%.5f,%.5f" %(TOTAL, DIFF_GC, DIFF_AT,PLI_GC_1000, PLI_AT_1000))
-    else:
-      fileOUT_NUC.write("%s,%s,%s,%s" %("NA","NA","NA","NA"))
-      fileOUT_percent_GC.write("%s" %"NA")
-      fileOUT_percent_purine.write("%s" %"NA")
-      fileOUT_Purine_Load.write("%s,%s,%s,%s,%s" %("NA","NA","NA","NA","NA"))
-
-
-    fileOUT_NUC.write("\n")
-    fileOUT_percent_GC.write("\n")
-    fileOUT_percent_purine.write("\n")
-    fileOUT_Purine_Load.write("\n")
-fileOUT_NUC.close()
-fileOUT_percent_GC.close()
-fileOUT_percent_purine.close()
-fileOUT_Purine_Load.close()