ATTN : Georges ( gry at ll.mit.edu)
Pierre-Frédéric Caillaud
peufeu at free.fr
Tue Apr 12 15:10:36 EDT 2005
> 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 )
>
> seq=checkDNA(seq)
>
> -------------------------------------------------------------------------------------------------------------------------
>
> Path:
> news3!feeder.news-service.com!news.glorb.com!postnews.google.com!o13g2000cwo.googlegroups.com!not-for-mail
> From: gry at ll.mit.edu
> Newsgroups: comp.lang.python
> Subject: Re: problem with the logic of read files
> Date: 12 Apr 2005 10:47:17 -0700
> Organization: http://groups.google.com
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>
>
> <m_t... at yahoo.com> wrote:
>> I am new to python and I am not in computer science. In fact I am a
> biologist and I ma trying to learn python. So if someone can help me, I
> will appreciate it.
>> Thanks
>>
>>
>> #!/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
> analyser: ") or None
>> 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:
> ###### Minor -- this is better said as: if f.endswith(".Seq"):
>> 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)
>> seq=3Df.read()
>> f.close()
>> s=3Dseq
>>
>> def checkDNA(seq):
>> """Retourne une liste des caract=E8res non conformes =E0
> l'IUPAC."""
>>
>> 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 " %
> (seq[c],c)
>> 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! -- George
>>
>> #I got the following ( as you see only one file is proceed by the
> function even if more files is in extseq
>>
>> ['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',
> 'B1-18_win3F_D04_08.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']
>>
>> after this listing my programs proceed only the last element of this
> listing (TRC666-100_win3R_G05_13.ab1.Seq)
>>
>>
> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCCCGAAGTGTCCCAGAGCAAATAAATGGACCAAAACGTTTTTAG=
> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCCCGAAGTGTCCCAGAGCAAATAAATGGACCAAAACGTTTTTAG=
> AATACTTGAACGTGTAATCTCATTTTAA
>
>
>
> **********End Of Post*************
>
>
>
>
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