comparison scripts/S01b_study_seq_composition_aa.py @ 2:988467f963f0 draft

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

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

###########
## 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):

            fileOUT_PAYRE.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f," %(count_PAYRE,prop_PAYRE,count_AC,prop_AC,count_MVGDS,prop_MVGDS,ratio_PAYRE_vs_MVGDS,ratio_AC_vs_MVGDS))
            fileOUT_TotalResidueWeight.write("%.5f," %Total_Residue_Weight)
            fileOUT_TotalResidueVolume.write("%.5f," %Total_Residue_Volume)
            fileOUT_TotalPartialSpecificVolume.write("%.5f," %(Total_Partial_Specific_Volume))
            fileOUT_TotalHydratation.write("%.5f," % Total_Hydration)
        
    ## END LINE
    fileOUT_PROT_ALL.write("\n")
    fileOUT_IVYWREL.write("\n")
    fileOUT_ERK_DNQTSH.write("\n")

    fileOUT_TotalResidueWeight.write("\n")
    fileOUT_TotalResidueVolume.write("\n")
    fileOUT_TotalPartialSpecificVolume.write("\n")
    fileOUT_TotalHydratation.write("\n")

    
    

2:988467f963f0

#!/usr/bin/env python
# -*- coding: ascii -*-
## 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 two "cold" species: Pg, Pp)

import sys,os,shutil,subprocess,string
from functions import simplify_fasta_name, dico

script_path = os.path.dirname(sys.argv[0])

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

            fileOUT_PAYRE.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f," %(count_PAYRE,prop_PAYRE,count_AC,prop_AC,count_MVGDS,prop_MVGDS,ratio_PAYRE_vs_MVGDS,ratio_AC_vs_MVGDS))
            fileOUT_TotalResidueWeight.write("%.5f," %Total_Residue_Weight)
            fileOUT_TotalResidueVolume.write("%.5f," %Total_Residue_Volume)
            fileOUT_TotalPartialSpecificVolume.write("%.5f," %(Total_Partial_Specific_Volume))
            fileOUT_TotalHydratation.write("%.5f," % Total_Hydration)
        else:
            fileOUT_PROT_ALL.write("%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s," %("n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a"))
            fileOUT_IVYWREL.write("%s,%s," %("n.a", "n.a"))
            fileOUT_ERK_DNQTSH.write("%s,%s,%s,%s,%s," %("n.a","n.a","n.a","n.a","n.a"))
            fileOUT_EK_QH.write("%s,%s,%s,%s,%s," %("n.a","n.a","n.a","n.a","n.a"))
            fileOUT_FYMINK_GARP.write("%s,%s,%s,%s," %("n.a","n.a","n.a","n.a"))
            fileOUT_AVLIMFYW.write("%s,%s,%s,%s,%s,%s," %("n.a","n.a","n.a","n.a","n.a","n.a"))
            fileOUT_STNQ.write("%s,%s," %("n.a","n.a"))
            fileOUT_RHKDE.write("%s,%s,%s,%s,%s,%s,"%("n.a","n.a","n.a","n.a","n.a","n.a"))
            fileOUT_PAYRE.write("%s,%s,%s,%s,%s,%s,%s,%s," %("n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a"))
            fileOUT_TotalResidueWeight.write("%s," %"n.a")
            fileOUT_TotalResidueVolume.write("%s," %"n.a")
            fileOUT_TotalPartialSpecificVolume.write("%s," %"n.a")
            fileOUT_TotalHydratation.write("%s," %"n.a")
        
    ## END LINE
    fileOUT_PROT_ALL.write("\n")
    fileOUT_IVYWREL.write("\n")
    fileOUT_ERK_DNQTSH.write("\n")

    fileOUT_TotalResidueWeight.write("\n")
    fileOUT_TotalResidueVolume.write("\n")
    fileOUT_TotalPartialSpecificVolume.write("\n")
    fileOUT_TotalHydratation.write("\n")