comparison scripts/S01b_study_seq_composition_aa.py @ 1:8de21b6eb110 draft

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

0:78dd6454f6f0

#!/usr/bin/env python
# -*- coding: ascii -*-
## 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 two "cold" species: Pg, Pp)
import sys, os
script_path = os.path.dirname(sys.argv[0])

#############
### 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)

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

##Create specific folders
Path_IN_loci_NUC = "./IN_AA"
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_AA/input.fasta')
else:
    cmd="unzip %s -d ./IN_AA"%(sys.argv[1])
    os.system(cmd)



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

        LT.append(sp)
print LT


## 2 ## PathIN
fileIN_properties = open("%s/01_AminoAcid_Properties2.csv"%(script_path), "r")
Path_IN_loci_AA = "./IN_AA"
#Path_IN_loci_AA = "02_CDS_No_Missing_Data_aa_CDS_withM"
Lloci_AA = os.listdir(Path_IN_loci_AA)

## 3 ## PathOUT

## 3.1 ## PROT composition
fileOUT_PROT_ALL=open("./OUT/13_prot_compositions_All_AA.csv","w")
fileOUT_PROT_ALL.write("LOCUS,")
for taxa in LT:
    fileOUT_PROT_ALL.write("%s_prop_K,%s_prop_R,%s_prop_A,%s_prop_F,%s_prop_I,%s_prop_L,%s_prop_M,%s_prop_V,%s_prop_W,%s_prop_N,%s_prop_Q,%s_prop_S,%s_prop_T,%s_prop_H,%s_prop_Y,%s_prop_C,%s_prop_D,%s_prop_E,%s_prop_P,%s_prop_G," %(taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa))
fileOUT_PROT_ALL.write("\n")

## 3.2 ## PROT IVYWREL
fileOUT_IVYWREL=open("./OUT/14_IVYWREL.csv","w")
fileOUT_IVYWREL.write("LOCUS,")
for taxa in LT:
    fileOUT_IVYWREL.write("%s_count_IVYWREL,%s_prop_IVYWREL," %(taxa,taxa))
fileOUT_IVYWREL.write("\n")


## 3.3 ## PROT ERK_DNQTSHA
fileOUT_ERK_DNQTSH=open("./OUT/15_ERK_DNQTSH.csv","w")
fileOUT_ERK_DNQTSH.write("LOCUS,")
for taxa in LT:
    fileOUT_ERK_DNQTSH.write("%s_count_ERK,%s_prop_ERK,%s_count_DNQTSH,%s_prop_DNQTSH,%s_ratio_ERK_vs_DNQTSH," %(taxa,taxa,taxa,taxa,taxa))
fileOUT_ERK_DNQTSH.write("\n")

## 3.4 ## PROT EK_QH
fileOUT_EK_QH=open("./OUT/16_EK_QH.csv","w")
fileOUT_EK_QH.write("LOCUS,")
for taxa in LT:
    fileOUT_EK_QH.write("%s_count_EK,%s_prop_EK,%s_count_QH,%s_prop_QH,%s_ratio_EK_vs_QH," %(taxa,taxa,taxa,taxa,taxa))
fileOUT_EK_QH.write("\n")


## 3.5 ## PROT FYMINK_GARP
fileOUT_FYMINK_GARP=open("./OUT/17_FYMINK_GARP.csv","w")
fileOUT_FYMINK_GARP.write("LOCUS,")
for taxa in LT:
    fileOUT_FYMINK_GARP.write("%s_count_FYMINK,%s_prop_FYMINK,%s_count_GARP,%s_prop_GARP," %(taxa,taxa,taxa,taxa))
fileOUT_FYMINK_GARP.write("\n")


## 3.6 ## PROT AVLIMFYW
fileOUT_AVLIMFYW=open("./OUT/18_AVLIMFYW.csv","w")
fileOUT_AVLIMFYW.write("LOCUS,")
for taxa in LT:
    fileOUT_AVLIMFYW.write("%s_count_AVLIMFYW,%s_prop_AVLIMFYW,%s_count_AVLIM,%s_prop_AVLIM,%s_count_FYW,%s_prop_FYW," %(taxa,taxa,taxa,taxa,taxa,taxa))
fileOUT_AVLIMFYW.write("\n")

## 3.7 ## PROT STNQ
fileOUT_STNQ=open("./OUT/19_STNQ.csv","w")
fileOUT_STNQ.write("LOCUS,")
for taxa in LT:
    fileOUT_STNQ.write("%s_count_STNQ,%s_prop_STNQ," %(taxa,taxa))
fileOUT_STNQ.write("\n")

## 3.8 ## PROT RHKDE
fileOUT_RHKDE=open("./OUT/20_RHKDE.csv","w")
fileOUT_RHKDE.write("LOCUS,")
for taxa in LT:
    fileOUT_RHKDE.write("%s_count_RHKDE,%s_prop_RHKDE,%s_count_RHK,%s_prop_RHK,%s_count_DE,%s_prop_DE," %(taxa,taxa,taxa,taxa,taxa,taxa))
fileOUT_RHKDE.write("\n")

## 3.9 ## PROT DIDER CRITERIA
fileOUT_PAYRE=open("./OUT/21_PAYRE-MVGDS.csv","w")
fileOUT_PAYRE.write("LOCUS,")
for taxa in LT:
    fileOUT_PAYRE.write("%s_count_PAYRE,%s_prop_PAYRE,%s_count_AC,%s_prop_AC,%s_count_MVGDS,%s_prop_MVGDS,%s_ratio_PAYRE_vs_MVGDS,%s_ratio_AC_vs_MVGDS," %(taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa))
fileOUT_PAYRE.write("\n")

## 3.10 ## PROT Total residue weight
fileOUT_TotalResidueWeight=open("./OUT/22_TotalResidueWeight.csv","w")
fileOUT_TotalResidueWeight.write("LOCUS,")
for taxa in LT:
    fileOUT_TotalResidueWeight.write("%s_Total_Residue_Weight," %taxa)
fileOUT_TotalResidueWeight.write("\n")

## 3.11 ## PROT Total residue volume
fileOUT_TotalResidueVolume=open("./OUT/23_TotalResidueVolume.csv","w")
fileOUT_TotalResidueVolume.write("LOCUS,")
for taxa in LT:
    fileOUT_TotalResidueVolume.write("%s_Total_Residue_Volume," %taxa)
fileOUT_TotalResidueVolume.write("\n")

## 3.12 ## PROT Total partial specific volume
fileOUT_TotalPartialSpecificVolume=open("./OUT/24_TotalPartialSpecificVolume.csv","w")
fileOUT_TotalPartialSpecificVolume.write("LOCUS,")
for taxa in LT:
    fileOUT_TotalPartialSpecificVolume.write("%s_Total_Partial_Specific_Volume," %taxa)
fileOUT_TotalPartialSpecificVolume.write("\n")

## 3.13 ## PROT Total hydratation
fileOUT_TotalHydratation=open("./OUT/25_TotalHydratation.csv","w")
fileOUT_TotalHydratation.write("LOCUS,")
for taxa in LT:
    fileOUT_TotalHydratation.write("%s_Total_Hydratation," %taxa)
fileOUT_TotalHydratation.write("\n")

    fileOUT_TotalHydratation.write("\n")

    
    

1:8de21b6eb110

#!/usr/bin/env python
# -*- coding: ascii -*-
## 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 two "cold" species: Pg, Pp)
import sys,os,shutil,subprocess,string
script_path = os.path.dirname(sys.argv[0])

#############
### 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)

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


##Create specific folders
Path_IN_loci_NUC = "./IN_AA"
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)

        LT.append(sp)
print LT


## 2 ## PathIN
fileIN_properties = open("amino_acid_properties.csv", "r")
Path_IN_loci_AA = "./IN_AA"
#Path_IN_loci_AA = "02_CDS_No_Missing_Data_aa_CDS_withM"
Lloci_AA = os.listdir(Path_IN_loci_AA)

## 3 ## PathOUT

## 3.1 ## PROT composition
fileOUT_PROT_ALL=open("./OUT/prot_compositions_All_AA.csv","w")
fileOUT_PROT_ALL.write("LOCUS,")
for taxa in LT:
    fileOUT_PROT_ALL.write("%s_prop_K,%s_prop_R,%s_prop_A,%s_prop_F,%s_prop_I,%s_prop_L,%s_prop_M,%s_prop_V,%s_prop_W,%s_prop_N,%s_prop_Q,%s_prop_S,%s_prop_T,%s_prop_H,%s_prop_Y,%s_prop_C,%s_prop_D,%s_prop_E,%s_prop_P,%s_prop_G," %(taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa))
fileOUT_PROT_ALL.write("\n")

## 3.2 ## PROT IVYWREL
fileOUT_IVYWREL=open("./OUT/IVYWREL.csv","w")
fileOUT_IVYWREL.write("LOCUS,")
for taxa in LT:
    fileOUT_IVYWREL.write("%s_count_IVYWREL,%s_prop_IVYWREL," %(taxa,taxa))
fileOUT_IVYWREL.write("\n")


## 3.3 ## PROT ERK_DNQTSHA
fileOUT_ERK_DNQTSH=open("./OUT/ERK_DNQTSH.csv","w")
fileOUT_ERK_DNQTSH.write("LOCUS,")
for taxa in LT:
    fileOUT_ERK_DNQTSH.write("%s_count_ERK,%s_prop_ERK,%s_count_DNQTSH,%s_prop_DNQTSH,%s_ratio_ERK_vs_DNQTSH," %(taxa,taxa,taxa,taxa,taxa))
fileOUT_ERK_DNQTSH.write("\n")

## 3.4 ## PROT EK_QH
fileOUT_EK_QH=open("./OUT/EK_QH.csv","w")
fileOUT_EK_QH.write("LOCUS,")
for taxa in LT:
    fileOUT_EK_QH.write("%s_count_EK,%s_prop_EK,%s_count_QH,%s_prop_QH,%s_ratio_EK_vs_QH," %(taxa,taxa,taxa,taxa,taxa))
fileOUT_EK_QH.write("\n")


## 3.5 ## PROT FYMINK_GARP
fileOUT_FYMINK_GARP=open("./OUT/FYMINK_GARP.csv","w")
fileOUT_FYMINK_GARP.write("LOCUS,")
for taxa in LT:
    fileOUT_FYMINK_GARP.write("%s_count_FYMINK,%s_prop_FYMINK,%s_count_GARP,%s_prop_GARP," %(taxa,taxa,taxa,taxa))
fileOUT_FYMINK_GARP.write("\n")


## 3.6 ## PROT AVLIMFYW
fileOUT_AVLIMFYW=open("./OUT/AVLIMFYW.csv","w")
fileOUT_AVLIMFYW.write("LOCUS,")
for taxa in LT:
    fileOUT_AVLIMFYW.write("%s_count_AVLIMFYW,%s_prop_AVLIMFYW,%s_count_AVLIM,%s_prop_AVLIM,%s_count_FYW,%s_prop_FYW," %(taxa,taxa,taxa,taxa,taxa,taxa))
fileOUT_AVLIMFYW.write("\n")

## 3.7 ## PROT STNQ
fileOUT_STNQ=open("./OUT/STNQ.csv","w")
fileOUT_STNQ.write("LOCUS,")
for taxa in LT:
    fileOUT_STNQ.write("%s_count_STNQ,%s_prop_STNQ," %(taxa,taxa))
fileOUT_STNQ.write("\n")

## 3.8 ## PROT RHKDE
fileOUT_RHKDE=open("./OUT/RHKDE.csv","w")
fileOUT_RHKDE.write("LOCUS,")
for taxa in LT:
    fileOUT_RHKDE.write("%s_count_RHKDE,%s_prop_RHKDE,%s_count_RHK,%s_prop_RHK,%s_count_DE,%s_prop_DE," %(taxa,taxa,taxa,taxa,taxa,taxa))
fileOUT_RHKDE.write("\n")

## 3.9 ## PROT DIDER CRITERIA
fileOUT_PAYRE=open("./OUT/PAYRE-MVGDS.csv","w")
fileOUT_PAYRE.write("LOCUS,")
for taxa in LT:
    fileOUT_PAYRE.write("%s_count_PAYRE,%s_prop_PAYRE,%s_count_AC,%s_prop_AC,%s_count_MVGDS,%s_prop_MVGDS,%s_ratio_PAYRE_vs_MVGDS,%s_ratio_AC_vs_MVGDS," %(taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa))
fileOUT_PAYRE.write("\n")

## 3.10 ## PROT Total residue weight
fileOUT_TotalResidueWeight=open("./OUT/TotalResidueWeight.csv","w")
fileOUT_TotalResidueWeight.write("LOCUS,")
for taxa in LT:
    fileOUT_TotalResidueWeight.write("%s_Total_Residue_Weight," %taxa)
fileOUT_TotalResidueWeight.write("\n")

## 3.11 ## PROT Total residue volume
fileOUT_TotalResidueVolume=open("./OUT/TotalResidueVolume.csv","w")
fileOUT_TotalResidueVolume.write("LOCUS,")
for taxa in LT:
    fileOUT_TotalResidueVolume.write("%s_Total_Residue_Volume," %taxa)
fileOUT_TotalResidueVolume.write("\n")

## 3.12 ## PROT Total partial specific volume
fileOUT_TotalPartialSpecificVolume=open("./OUT/TotalPartialSpecificVolume.csv","w")
fileOUT_TotalPartialSpecificVolume.write("LOCUS,")
for taxa in LT:
    fileOUT_TotalPartialSpecificVolume.write("%s_Total_Partial_Specific_Volume," %taxa)
fileOUT_TotalPartialSpecificVolume.write("\n")

## 3.13 ## PROT Total hydratation
fileOUT_TotalHydratation=open("./OUT/TotalHydratation.csv","w")
fileOUT_TotalHydratation.write("LOCUS,")
for taxa in LT:
    fileOUT_TotalHydratation.write("%s_Total_Hydratation," %taxa)
fileOUT_TotalHydratation.write("\n")

    fileOUT_TotalHydratation.write("\n")