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 = raw_input("Entrez le répertoire où sont les fichiers à analyser: ") or
None
if ab1seq == None :
print "Erreur: Pas de répertoire! \n"
"\nAu revoir \n"
sys.exit()
listrep = os.listdir(ab1seq)
#print listrep
extseq=[]
for f in listrep:
if f[-4:]==".Seq":
extseq.append(f)
# print extseq
for x in extseq:
f = open(x, "r")
seq=f.read()
f.close()
s=seq
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
seq=checkDNA(seq)
print seq
#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)
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCCCGAAGTGTCCCAGAGCAAATAAATGGACCAAAACGTTTTTAGAATACTTGAACGTGTAATCTCATTTTAA
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