comparison scripts/S02b_study_seq_composition_nuc.py @ 9:04a9ada73cc4 draft

planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty

8:705a7bf4c311

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)
result=result.split('\n')
for i in result:   
    sp=i[1:]
    if sp !='':
        LT.append(sp)
print LT

#LT = ["Ap", "Ac", "Pg"]
#os.system("grep '>' %s" %(sys.argv[1]))

## 2 ## PathIN
# fileIN_properties = open("01_AminoAcid_Properties2.csv", "r")
Lloci_NUC = os.listdir(Path_IN_loci_NUC)


## 3 ## PathOUT
## 3.1 ## NUC composition

9:04a9ada73cc4

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