problem with the logic of read files

[Guest]

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]
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

 

[gry]

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:

###### Minor -- this is better said as: if f.endswith(".Seq"):

if f[-4:]==".Seq":
extseq.append(f)
# print extseq

for x in extseq:
f = open(x, "r")

###### seq=... discards previous data and refers only to that just
read.
###### It would be simplest to process each file as it is read:
@@@@@@ seq=f.read()
@@@@@@ checkDNA(seq)

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]
return resultat

seq=checkDNA(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)NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCCCGAAGTGTCCCAGAGCAAATAAATGGACCAAAACGTTTTTAGAATACTTGAACGTGTAATCTCATTTTAA

 

[Scott David Daniels]

#!/cbi/prg/python/current/bin/python
# -*- coding: iso-8859-1 -*-
import sys
import os
from progadn import *
...
for x in extseq:
f = open(x, "r")
seq=f.read()
f.close()
s=seq

def checkDNA(seq):
...

seq=checkDNA(seq)
print seq

You terminated the loop to define checkDNA.

What you want is:
...
from progadn import *
def checkDNA(seq):
...

...
for x in extseq:
f = open(x, "r")
seq=f.read()
f.close()
s=seq
seq = checkDNA(seq)
print seq

Even better might be:
...
from progadn import *
def checkDNA(seq):
...

def main():
...
for x in extseq:
f = open(x, "r")
try:
print checkDNA(f.read())
finally:
f.close()


if __name__ = '__main__':
main()

--Scott David Daniels
(e-mail address removed)

 

[Tom Jenkins]

You may also be interested in the biopython project:
http://www.biopython.org/

tom