comparison scripts/S02b_study_seq_composition_nuc.py @ 1:8de21b6eb110 draft

planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b

0:78dd6454f6f0

## 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,zipfile,shutil,subprocess

#############
### DEF 0 ###
#############import sys,os,zipfile
def simplify_fasta_name(fasta_name,LT):
    for abbreviation in LT:
        if abbreviation in fasta_name:
            new_fasta_name = abbreviation

##############################################

###################
### RUN RUN RUN ###
###################
import string, os,sys,zipfile





##Create specific folders
Path_IN_loci_NUC = "./IN_NUC"
outpath= "./OUT"
os.makedirs(Path_IN_loci_NUC)
os.makedirs(outpath)




#Check if the file is a zip or fasta file

the_zip_file = zipfile.ZipFile(sys.argv[1])
ret = the_zip_file.testzip()

if ret is not None:
    shutil.copy2(sys.argv[1], './IN_NUC/input.fasta')
else:
    cmd="unzip %s -d ./IN_NUC"%(sys.argv[1])
    os.system(cmd)


## 1 ## List taxa
LT=[]
cmd="grep '>' %s" % sys.argv[2]
result = subprocess.check_output(cmd, shell=True)

Lloci_NUC = os.listdir(Path_IN_loci_NUC)


## 3 ## PathOUT
## 3.1 ## NUC composition
fileOUT_NUC=open("./OUT/10_nuc_compositions.csv","w")
fileOUT_NUC.write("LOCUS,")
for taxa in LT:
    fileOUT_NUC.write("%s_prop_A,%s_prop_T,%s_prop_C,%s_prop_G," %(taxa,taxa,taxa,taxa))
fileOUT_NUC.write("\n")

## 3.2 ## NUC percent_GC
fileOUT_percent_GC=open("./OUT/11_percent_GC.csv","w")
fileOUT_percent_GC.write("LOCUS,")
for taxa in LT:
    fileOUT_percent_GC.write("%s_percent_GC," %(taxa))
fileOUT_percent_GC.write("\n")

## 3.3 ## NUC percent_purine
fileOUT_percent_purine=open("./OUT/12_percent_purine.csv","w")
fileOUT_percent_purine.write("LOCUS,")
for taxa in LT:
    fileOUT_percent_purine.write("%s_percent_purine," %(taxa))
fileOUT_percent_purine.write("\n")

## 3.4 ## Purine Load
fileOUT_Purine_Load=open("./OUT/12_Purine_Load_Indice.csv", "w")
fileOUT_Purine_Load.write("LOCUS,")
for taxa in LT:
    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("\n")

    fileOUT_NUC.write("%s," %locus)
    fileOUT_percent_GC.write("%s," %locus)
    fileOUT_percent_purine.write("%s," %locus)
    fileOUT_Purine_Load.write("%s," %locus)
    #print bash
    for taxa in LT:
        print taxa
	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_Purine_Load.write("\n")
fileOUT_NUC.close()
fileOUT_percent_GC.close()
fileOUT_percent_purine.close()
fileOUT_Purine_Load.close()

1:8de21b6eb110

## 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

##############################################

###################
### RUN RUN RUN ###
###################

##Create specific folders
Path_IN_loci_NUC = "./IN_NUC"
outpath= "./OUT"
os.makedirs(Path_IN_loci_NUC)
os.makedirs(outpath)

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 '>' %s" % sys.argv[2]
result = subprocess.check_output(cmd, shell=True)

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:
    fileOUT_NUC.write("%s_prop_A,%s_prop_T,%s_prop_C,%s_prop_G," %(taxa,taxa,taxa,taxa))
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:
    fileOUT_percent_GC.write("%s_percent_GC," %(taxa))
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:
    fileOUT_percent_purine.write("%s_percent_purine," %(taxa))
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:
    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("\n")

    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_Purine_Load.write("\n")
fileOUT_NUC.close()
fileOUT_percent_GC.close()
fileOUT_percent_purine.close()
fileOUT_Purine_Load.close()