ATTN : Georges ( gry@ll.mit.edu)

**Pierre-Frédéric Caillaud** · Jul 18 '05, 11:54 PM

Re: ATTN : Georges ( gry@ll.mit.edu)

[color=blue]
> My code so far:
> # -*- coding: iso-8859-1 -*-
> import sys
> import os
> from progadn import *
>
> ab1seq = raw_input("Entr ez le répertoire où sont les fichiers à
> analyser: ") or None[/color]

Ce serait mieux d'utiliser sys.argv pour spécifier le répertoire dans la
ligne de commande du programme :
import sys
help(sys.argv)
[color=blue]
> if ab1seq == None :
> print "Erreur: Pas de répertoire! \n" \
> "\nAu revoir \n"
> sys.exit()[/color]

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() )
[color=blue]
> 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(le n(seq))
> indinv.reverse( )
> resultat=""
> for i in indinv:
> resultat +=comp[seq[i]]
> return resultat[/color]

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.revers e()
return ''.join( resultat )

[color=blue]
>
> seq=checkDNA(se q)
>
> -------------------------------------------------------------------------------------------------------------------------
>
> Path:
> news3!feeder.ne ws-service.com!new s.glorb.com!pos tnews.google.co m!o13g2000cwo.g ooglegroups.com !not-for-mail
> From: gry@ll.mit.edu
> Newsgroups: comp.lang.pytho n
> Subject: Re: problem with the logic of read files
> Date: 12 Apr 2005 10:47:17 -0700
> Organization: http://groups.google.com
> Lines: 104[/color]
2> Message-ID: <1113328037.070 319.136110@o13g 2000cwo.googleg roups.com>[color=blue]
> References: <68da8$425bf954 $43461874$29054 @nf1.news-service.com>
> NNTP-Posting-Host: 129.55.200.20
> Mime-Version: 1.0
> Content-Type: text/plain; charset="iso-8859-1"
> Content-Transfer-Encoding: quoted-printable
> X-Trace: posting.google. com 1113328069 32347 127.0.0.1 (12 Apr 2005
> 17:47:49 GMT)
> X-Complaints-To: groups-abuse@google.co m
> NNTP-Posting-Date: Tue, 12 Apr 2005 17:47:49 +0000 (UTC)
> In-Reply-To: <68da8$425bf954 $43461874$29054 @nf1.news-service.com>
> User-Agent: G2/0.2
> Complaints-To: groups-abuse@google.co m
> Injection-Info: o13g2000cwo.goo glegroups.com; posting-host=129.55.200 .20;
> posting-account=tzIXbQw AAACT3z3X4eITVL tksgiDRxhx
> Xref: news-x2.support.nl comp.lang.pytho n:438583
>
>
> <m_t...@yahoo.c om> wrote:[color=green]
>> I am new to python and I am not in computer science. In fact I am a[/color]
> biologist and I ma trying to learn python. So if someone can help me, I
> will appreciate it.[color=green]
>> Thanks
>>
>>
>> #!/cbi/prg/python/current/bin/python
>> # -*- coding: iso-8859-1 -*-
>> import sys
>> import os
>> from progadn import *
>>
>> ab1seq =3D raw_input("Entr ez le r=E9pertoire o=F9 sont les fichiers =E0[/color]
> analyser: ") or None[color=green]
>> if ab1seq =3D=3D None :
>> print "Erreur: Pas de r=E9pertoire! \n"
>> "\nAu revoir \n"
>> sys.exit()
>>
>> listrep =3D os.listdir(ab1s eq)
>> #print listrep
>>
>> extseq=3D[]
>>
>> for f in listrep:[/color]
> ###### Minor -- this is better said as: if f.endswith(".Se q"):[color=green]
>> if f[-4:]=3D=3D".Seq":
>> extseq.append(f )
>> # print extseq
>>
>> for x in extseq:
>> f =3D open(x, "r")[/color]
> ###### 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)[color=green]
>> seq=3Df.read()
>> f.close()
>> s=3Dseq
>>
>> def checkDNA(seq):
>> """Retourne une liste des caract=E8res non conformes =E0[/color]
> l'IUPAC."""[color=green]
>>
>> 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 " %[/color]
> (seq[c],c)[color=green]
>> 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[/color]
>
> ##### 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[color=green]
>>
>> #I got the following ( as you see only one file is proceed by the[/color]
> function even if more files is in extseq[color=green]
>>
>> ['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',[/color]
> 'B1-18_win3F_D04_08 .ab1.Seq'][color=green]
>> ['B1-11_win3F_B04_04 .ab1.Seq', 'B1-11_win3R_C04_06 .ab1.Seq',[/color]
> 'B1-18_win3F_D04_08 .ab1.Seq', 'B1-18_win3R_E04_10 .ab1.Seq'][color=green]
>> ['B1-11_win3F_B04_04 .ab1.Seq', 'B1-11_win3R_C04_06 .ab1.Seq',[/color]
> 'B1-18_win3F_D04_08 .ab1.Seq', 'B1-18_win3R_E04_10 .ab1.Seq',
> 'B1-19_win3F_F04_12 .ab1.Seq'][color=green]
>> ..
>> ['B1-11_win3F_B04_04 .ab1.Seq', 'B1-11_win3R_C04_06 .ab1.Seq',[/color]
> '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_B0 5_03.ab1.Seq', 'M7757_win3R_C0 5_05.ab1.Seq',
> 'M7759_win3F_D0 5_07.ab1.Seq', 'M7759_win3R_E0 5_09.ab1.Seq',
> 'TCR700-114_win3F_H05_1 5.ab1.Seq', 'TCR700-114_win3R_A06_0 2.ab1.Seq',
> 'TRC666-100_win3F_F05_1 1.ab1.Seq', 'TRC666-100_win3R_G05_1 3.ab1.Seq'][color=green]
>>
>> after this listing my programs proceed only the last element of this[/color]
> listing (TRC666-100_win3R_G05_1 3.ab1.Seq)[color=green]
>>
>>[/color]
> NNNNNNNNNNNNNNN NNNNNNNNNNNNNNN TCCCGAAGTGTCCCA GAGCAAATAAATGGA CCAAAACGTTTTTAG =
> NNNNNNNNNNNNNNN NNNNNNNNNNNNNNN TCCCGAAGTGTCCCA GAGCAAATAAATGGA CCAAAACGTTTTTAG =
> AATACTTGAACGTGT AATCTCATTTTAA
>
>
>
> **********End Of Post*********** **
>
>
>
>[/color]

ATTN : Georges ( gry@ll.mit.edu)

ATTN : Georges ( gry@ll.mit.edu)

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