[Biopython] error writing fasta file using SeqIO

[A M Torres, Hugo]

Hi. Can someone spot why I can't create a fasta file here? I tried following
the cookbook tutorial but something goes wrong when I try to write  the
sequence from a SeqRecord object to a fasta file:

 Lodge It

   - New <http://paste.pound-python.org/>
   - All <http://paste.pound-python.org/all/>
   - About <http://paste.pound-python.org/about/>
   - ? <http://paste.pound-python.org/help/>

 Paste #9205
Paste Details

reply <http://paste.pound-python.org/?reply_to=9205> |
raw<http://paste.pound-python.org/raw/9205/>

posted on Jul 8, 2011 4:12:16 AM

   - reply to this paste <http://paste.pound-python.org/?reply_to=9205>
   - download paste <http://paste.pound-python.org/raw/9205/>
   - compare with paste
   - select different colorscheme  Autumn Borland Bw Colorful Default Emacs
   Friendly Fruity Manni Monokai Murphy Native Pastie Perldoc Tango Trac Vs
   - toggle line numbers<http://paste.pound-python.org/show/9205/?linenos=no>

   1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78

import abifpy
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Emboss.Applications import NeedleCommandline
import os #uso a funcao listdir
from Bio import SeqIO

def acessa_ab1(arquivo,trim=True): #generalizar depois
    """acessa um arquivo ab1 e retorna um objeto SeqRecord"""
    dado = abifpy.Trace(arquivo)
    if trim:
        cortado = dado.trim(dado.seq(ambig=True))
        return SeqRecord(cortado, id=arquivo, description='dado cortado')
    else:
        return dado.seqrecord()

def abre_ref(arquivo):
    """acessa um arquivo contendo uma sequencia de referencia
      retorna um objeto SeqRecord"""
    with open(arquivo, 'rUb') as dado:
        referencia = SeqIO.read(dado, 'genbank')
    return referencia

def salva_fasta(obj_SeqRecord):
    """Pega um objeto SeqRecord e cria um fasta com a sua sequencia"""

    SeqIO.write([obj_SeqRecord], obj_SeqRecord + '.fasta','fasta')

def processar_lote(diretorio, ref):
    """abre os arquivos ab1 de uma pasta, apara, salva em fasta, faz o
alinhamento com
    o fasta de referencia e salva o alinhamento em um arquivo para analise
    posterior.
    diretorio --> uma string representando o caminho da pasta contendo
os arquivos
    ref --> uma string representando o caminho absoluto + genbank com a
    sequencia de referencia.
    """

    referencia = abre_ref(ref)
    referencia.id = 'sequencia de referencia'
    salva_fasta(referencia)
    ab1files = [x for x in os.listdir(diretorio) if x.endswith('.ab1')]
    for file in ab1files:
        dado = acessa_ab1(diretorio + file)
        salva_fasta(dado)
        needle_cline = NeedleCommandline(asequence='referencia.fasta',
                                        bsequence= file + '.fasta',
gapopen=10, gapextend=0.5,
                                        outfile=file + "_aligned.txt")
    stdout, stderr = needle_cline()




#pasta = '/home/mercutio22/Dropbox/My scripts/Fabi/vs/Seq_placa273 analisada/'
#referencia = '/home/mercutio22/Dropbox/My
scripts/Fabi/vs/Seq_placa273 analisada/BRCA1 (total) - Frag 3450.gb'

#processar_lote(pasta, referencia)

dado = acessa_ab1('/home/mercutio22/Dropbox/My
scripts/Fabi/vs/Seq_placa273 analisada/1174411_3450F_A01.ab1')
print type(dado)
salva_fasta(dado)


===============================error msg==============
<class 'Bio.SeqRecord.SeqRecord'>
Traceback (most recent call last):
  File "louise.py", line 59, in <module>
    salva_fasta(dado)
  File "louise.py", line 26, in salva_fasta
    SeqIO.write([obj_SeqRecord], obj_SeqRecord + '.fasta','fasta')
  File "/usr/lib/pymodules/python2.6/Bio/SeqIO/__init__.py", line 412, in write
    count = writer_class(handle).write_file(sequences)
  File "/usr/lib/pymodules/python2.6/Bio/SeqIO/Interfaces.py", line
271, in write_file
    count = self.write_records(records)
  File "/usr/lib/pymodules/python2.6/Bio/SeqIO/Interfaces.py", line
256, in write_records
    self.write_record(record)
  File "/usr/lib/pymodules/python2.6/Bio/SeqIO/FastaIO.py", line 134,
in write_record
    self.handle.write(">%s\n" % title)
AttributeError: 'SeqRecord' object has no attribute 'write'