comparison scripts/S02b_study_seq_composition_nuc.py @ 2:988467f963f0 draft

planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f

1:8de21b6eb110

#!/usr/bin/env python
## Author: Eric FONTANILLAS
## Date: 21.12.10
## 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

#############
### DEF 0 ###

def simplify_fasta_name(fasta_name,LT):
    for abbreviation in LT:
        if abbreviation in fasta_name:
            new_fasta_name = abbreviation

    return(new_fasta_name)
##########################################

###########
## DEF1 ##
###########
## Generates bash, with key = fasta name; value = sequence (WITH GAP, IF ANY, REMOVED IN THIS FUNCTION)

def dico(fasta_file,LT):

    count_fastaName=0
    F1 = open(fasta_file, "r")
    
    bash1 = {}
    while 1:
        nextline = F1.readline()
        #print nextline
        if not nextline :
            break
        
        if nextline[0] == ">":
            count_fastaName = count_fastaName + 1
            fasta_name = nextline[1:-1]
            nextline = F1.readline()
            sequence = nextline[:-1]
            
            if fasta_name not in bash1.keys():
                fasta_name = simplify_fasta_name(fasta_name,LT)  ### DEF 0 ###
                bash1[fasta_name] = sequence
            else:
                print fasta_name

    # Find alignment length
    kk = bash1.keys()
    key0 = kk[0]
    seq0 = bash1[key0]
    ln_seq = len(seq0)

    F1.close()
    
    return(bash1)
#####################################



##################
###### DEF2 ######
##################
def base_composition(seq):

## 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)
    
    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))
    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()

2:988467f963f0

#!/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
from functions import simplify_fasta_name, dico

##################
###### DEF2 ######
##################
def base_composition(seq):

## 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:    
      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," %("n.a","n.a","n.a","n.a"))
        fileOUT_percent_GC.write("%s," %"n.a")
        fileOUT_percent_purine.write("%s," %"n.a")
        fileOUT_Purine_Load.write("%s,%s,%s,%s,%s," %("n.a","n.a","n.a","n.a","n.a"))
        
    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()