My code so far: # -*- coding: iso-8859-1 -*- import sys import os from progadn import *
ab1seq = raw_input("Entrez le répertoire où sont les fichiers à analyser: ") or None
Ce serait mieux d'utiliser sys.argv pour spécifier le répertoire dans la ligne de commande du programme :
import sys
help(sys.argv)
if ab1seq == None :
print "Erreur: Pas de répertoire! \n" \
"\nAu revoir \n"
sys.exit()
je propose :
import os, os.path, sys
def usage():
print "documentation..."
sys.exit(-1)
args = sys.argv[1:]
if not args:
usage()files = []
for path in args:
if os.path.isfile( path ):
files.append( path )
elif os.path.isdir( path ):
files.extend( [os.path.join( path, fname ) for fname in os.listdir( path )] )
else:
print "%s n'est ni un fichier ni un répertoire..." % path
usage()
files = [ fname for fname in files if fname.endswith( ".Seq" ) ]
88
if not files:
print "Aucun fichier a traiter."
usage()print "Fichier à traiter :" print ", ".join( files )
for path in files:
print path
checkDNA( open( path ).read() )def checkDNA(seq): """Retourne une liste des caractères non conformes à l'IUPAC."""
junk=[]
for c in range (len(seq)):
if seq[c] not in iupac:
junk.append([seq[c],c])
#print junk
print "ATTN: Il y a le caractère %s en position %s " % (seq[c],c)
if junk == []:
indinv=range(len(seq))
indinv.reverse()
resultat=""
for i in indinv:
resultat +=comp[seq[i]]
return resultat
Je réécris un peu votre fonction d'une manière plus "python", à placer dans le programme avant son appel bien sûr !
def checkDNA( seq ):
seq = seq.strip()
if not seq:
print "Fichier vide."
return
resultat = []
for i,c in enumerate(seq):
try:
resultat.append( comp[c] )
except KeyError:
print "Catactère <%s> en position <%d> invalide" % (c,i)
resultat.reverse()
return ''.join( resultat )
2> Message-ID: <[EMAIL PROTECTED]>
seq=checkDNA(seq)
-------------------------------------------------------------------------------------------------------------------------
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From: gry@ll.mit.edu
Newsgroups: comp.lang.python
Subject: Re: problem with the logic of read files
Date: 12 Apr 2005 10:47:17 -0700
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<[EMAIL PROTECTED]> wrote:I am new to python and I am not in computer science. In fact I am abiologist and I ma trying to learn python. So if someone can help me, I will appreciate it.analyser: ") or NoneThanks
#!/cbi/prg/python/current/bin/python # -*- coding: iso-8859-1 -*- import sys import os from progadn import *
ab1seq =3D raw_input("Entrez le r=E9pertoire o=F9 sont les fichiers =E0###### Minor -- this is better said as: if f.endswith(".Seq"):if ab1seq =3D=3D None : print "Erreur: Pas de r=E9pertoire! \n" "\nAu revoir \n" sys.exit()
listrep =3D os.listdir(ab1seq) #print listrep
extseq=3D[]
for f in listrep:if f[-4:]=3D=3D".Seq": extseq.append(f) # print extseq
for x in extseq: f =3D open(x, "r")###### seq=3D... discards previous data and refers only to that just read. ###### It would be simplest to process each file as it is read: @@@@@@ seq=3Df.read() @@@@@@ checkDNA(seq)l'IUPAC."""seq=3Df.read() f.close() s=3Dseq
def checkDNA(seq): """Retourne une liste des caract=E8res non conformes =E0(seq[c],c)
junk=3D[] for c in range (len(seq)): if seq[c] not in iupac: junk.append([seq[c],c]) #print junk print "ATTN: Il y a le caract=E8re %s en position %s " %if junk =3D=3D []: indinv=3Drange(len(seq)) indinv.reverse() resultat=3D"" for i in indinv: resultat +=3Dcomp[seq[i]] return resultat
seq=3DcheckDNA(seq) print seq
##### The program segment you posted did not define "comp" or "iupac", ##### so it's a little hard to guess how it's supposed to work. It would ##### be helpful if you gave a concise description of what you want the
##### program to do, as well as brief sample of input data. ##### I hope this helps! -- Georgefunction even if more files is in extseq
#I got the following ( as you see only one file is proceed by the'B1-18_win3F_D04_08.ab1.Seq']
['B1-11_win3F_B04_04.ab1.Seq'] ['B1-11_win3F_B04_04.ab1.Seq', 'B1-11_win3R_C04_06.ab1.Seq'] ['B1-11_win3F_B04_04.ab1.Seq', 'B1-11_win3R_C04_06.ab1.Seq',['B1-11_win3F_B04_04.ab1.Seq', 'B1-11_win3R_C04_06.ab1.Seq','B1-18_win3F_D04_08.ab1.Seq', 'B1-18_win3R_E04_10.ab1.Seq']['B1-11_win3F_B04_04.ab1.Seq', 'B1-11_win3R_C04_06.ab1.Seq','B1-18_win3F_D04_08.ab1.Seq', 'B1-18_win3R_E04_10.ab1.Seq', 'B1-19_win3F_F04_12.ab1.Seq'].. ['B1-11_win3F_B04_04.ab1.Seq', 'B1-11_win3R_C04_06.ab1.Seq','B1-18_win3F_D04_08.ab1.Seq', 'B1-18_win3R_E04_10.ab1.Seq', 'B1-19_win3F_F04_12.ab1.Seq', 'B1-19_win3R_G04_14.ab1.Seq', 'B90_win3F_H04_16.ab1.Seq', 'B90_win3R_A05_01.ab1.Seq', 'DL2-11_win3F_H03_15.ab1.Seq', 'DL2-11_win3R_A04_02.ab1.Seq', 'DL2-12_win3F_F03_11.ab1.Seq', 'DL2-12_win3R_G03_13.ab1.Seq', 'M7757_win3F_B05_03.ab1.Seq', 'M7757_win3R_C05_05.ab1.Seq', 'M7759_win3F_D05_07.ab1.Seq', 'M7759_win3R_E05_09.ab1.Seq', 'TCR700-114_win3F_H05_15.ab1.Seq', 'TCR700-114_win3R_A06_02.ab1.Seq', 'TRC666-100_win3F_F05_11.ab1.Seq', 'TRC666-100_win3R_G05_13.ab1.Seq']listing (TRC666-100_win3R_G05_13.ab1.Seq)
after this listing my programs proceed only the last element of this
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCCCGAAGTGTCCCAGAGCAAATAAATGGACCAAAACGTTTTTAG= NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCCCGAAGTGTCCCAGAGCAAATAAATGGACCAAAACGTTTTTAG= AATACTTGAACGTGTAATCTCATTTTAA
**********End Of Post*************
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