Re: biopython
On 06/14/2010 02:59 PM, madhuri vio wrote: i cudnt run this!! Take a deep breath, and read the error message. It's very informative, and tells you exactly what the problem is, and how to fix it, if you'd just try to understand it. It would be much appreciated if you had a look at http://www.catb.org/~esr/faqs/smart-questions.html specifically the section Before you ask, ideally the whole article. and this was the error occured for seq_record in SeqIO.parse(ls_MTbH37Rv.fasta,fasta): ... print seq_record.id http://seq_record.id ... print repr(seq_record.seq) ... print len(seq_record) ... Traceback (most recent call last): File stdin, line 1, in module File /var/lib/python-support/python2.6/Bio/SeqIO/__init__.py, line 342, in parse raise TypeError(Need a file handle, not a string (i.e. not a filename)) TypeError: Need a file handle, not a string (i.e. not a filename) I think this is a fabulous error message. The programmer of this module actually anticipated the mistake you were going to make. Good for you. -- madhuri :) -- http://mail.python.org/mailman/listinfo/python-list
Re: biopython
On 14/06/2010 15:02, madhuri vio wrote: i have tried this still unable to get an output from Bio import Seq from Bio import SeqIO from Bio import SeqRecord for seq_record in SeqIO.read(ls_MTbH37Rv.fasta, fasta): print seq_record.id print repr(seq_record.seq) print len(seq_record) python bio.py Traceback (most recent call last): File bio.py, line 10, inmodule for seq_record in SeqIO.read(ls_MTbH37Rv.fasta, fasta): File /var/lib/python-support/python2.6/Bio/SeqIO/__init__.py, line 433, in read iterator = parse(handle, format, alphabet) File /var/lib/python-support/python2.6/Bio/SeqIO/__init__.py, line 342, in parse raise TypeError(Need a file handle, not a string (i.e. not a filename)) TypeError: Need a file handle, not a string (i.e. not a filename) Please read this, it'll show you your mistake. http://www.biopython.org/wiki/SeqIO#Sequence_Input Regards. Mark Lawrence. -- http://mail.python.org/mailman/listinfo/python-list
Re: biopython
On Mon, Jun 14, 2010 at 8:45 AM, madhuri vio madhuri@gmail.com wrote: i am still waiting for some help. -- madhuri :) You already have your help- the traceback tells you everything you need to know. If you don't understand what the traceback is saying, come back here and specifically ask about the part you have trouble with. But we do expect that you will at least attempt to solve this on your own before coming here. Traceback (most recent call last): File bio.py, line 10, in module for seq_record in SeqIO.read(ls_MTbH37Rv.fasta, fasta): File /var/lib/python-support/python2.6/Bio/SeqIO/__init__.py, line 433, in read iterator = parse(handle, format, alphabet) File /var/lib/python-support/python2.6/Bio/SeqIO/__init__.py, line 342, in parse raise TypeError(Need a file handle, not a string (i.e. not a filename)) TypeError: Need a file handle, not a string (i.e. not a filename) Now, what does the traceback say you are doing wrong? What are you handing the function and what should you be handing the function? -- http://mail.python.org/mailman/listinfo/python-list
Re: biopython
On 06/14/2010 05:45 PM, madhuri vio wrote: i am still waiting for some help. WHAT?! Your behaviour on this list is making me really, really angry. We are not a tech support company. You are not paying for the privilege of sending your mail here. However, Sir, you are acting as if you were entitled to an instantaneous response to all your silly little problems without even thinking about the problem yourself! If you showed us that you're an intelligent human being and that you think before you post, that you're trying to understand what you're working on, in short that you're worthy of an answer, I and no doubt many other knowledgeable folk on this list would be happy to help you along, but so far you have been but a nuisance, a spammer. Besides: your original TWO (why two??) posts got a couple of replies. One annoyed but in principle I think helpful one from myself, and one rather forthcoming one from Mark Lawrence. Are you even subscribed to the mailing list, or are you blind posting and hoping for people to CC you in their replies? -- http://mail.python.org/mailman/listinfo/python-list
Re: biopython
On 14/06/2010 16:45, madhuri vio wrote: i am still waiting for some help. You cheeky git, this is simply *NOT* cricket! Your 1st post was timed at 13:59 BST, the response from Thomas Jollans at 14:12. Your 2nd post was at 15:02 and I replied at 15:12. Now you're back again at 16:45, to which Thomas and Benjamin Kaplan have already responded. Here is is the reference that I previously gave you. http://www.biopython.org/wiki/SeqIO#Sequence_Input If you don't understand something then please ask, but I suggest you (re)read this first. http://www.catb.org/~esr/faqs/smart-questions.html HTH. Mark Lawrence -- http://mail.python.org/mailman/listinfo/python-list
Re: biopython
On Mon, Jun 14, 2010 at 9:38 AM, Thomas Jollans tho...@jollans.com wrote: On 06/14/2010 05:45 PM, madhuri vio wrote: i am still waiting for some help. Besides: your original TWO (why two??) posts got a couple of replies. One annoyed but in principle I think helpful one from myself, and one rather forthcoming one from Mark Lawrence. Are you even subscribed to the mailing list, or are you blind posting and hoping for people to CC you in their replies? From the incessant posts and lack of mention of the previous helps she has received, it seems that the OP isn't even subscribed to this list! A reply by Mark points the exact solution: http://www.biopython.org/wiki/SeqIO#Sequence_Input -- http://mail.python.org/mailman/listinfo/python-list
Re: biopython
On Mon, Jun 14, 2010 at 9:38 AM, Thomas Jollans tho...@jollans.com wrote: On 06/14/2010 05:45 PM, madhuri vio wrote: i am still waiting for some help. WHAT?! Your behaviour on this list is making me really, really angry. We are not a tech support company. You are not paying for the privilege of sending your mail here. However, Sir, you are acting as if you were entitled to an instantaneous response to all your silly little problems without even thinking about the problem yourself! If you showed us that you're an intelligent human being and that you think before you post, that you're trying to understand what you're working on, in short that you're worthy of an answer, I and no doubt many other knowledgeable folk on this list would be happy to help you along, but so far you have been but a nuisance, a spammer. Besides: your original TWO (why two??) posts got a couple of replies. One annoyed but in principle I think helpful one from myself, and one rather forthcoming one from Mark Lawrence. Are you even subscribed to the mailing list, or are you blind posting and hoping for people to CC you in their replies? That was beautiful. I think I've got something in my eye. Geremy Condra -- http://mail.python.org/mailman/listinfo/python-list
Re: biopython
On Mon, Jun 14, 2010 at 11:02 AM, madhuri vio madhuri@gmail.com wrote: TypeError: Need a file handle, not a string (i.e. not a filename) This says that the error is that you are using a filename where you should be using a filehandle. So this line: for seq_record in SeqIO.read(ls_MTbH37Rv.fasta, fasta): Should be changed to: fh = open(ls_MTbH37Rv.fasta) for seq_record in SeqIO.read(fh, fasta): I think that in some version of Biopython you would be able to use just the name. Best, SB. Python for Bioinformatics book: http://www.tinyurl.com/biopython Python for Bioinformatics blog: http://www.py4bio.com -- http://mail.python.org/mailman/listinfo/python-list
Re: biopython
from Bio import Entrez Traceback (most recent call last): File stdin, line 1, in ? ImportError: cannot import name Entrez Can you import Bio, e.g.: import Bio ? If not, check to see where it's installed and make sure the directory containing Bio (or Bio.py) is in sys.path, either by setting the PYTHONPATH environment variable before running Python or adding a Bio.pth file to a directory which is in sys.path so it can be found. http://docs.python.org/lib/module-site.html http://docs.python.org/tut/node8.html Skip -- http://mail.python.org/mailman/listinfo/python-list
Re: biopython
En Tue, 09 Sep 2008 05:53:19 -0300, Beema Shafreen [EMAIL PROTECTED] escribió: Hi all, I am using Biopython to fetch pumed Id's ,The module i use is (from Bio import Entrez) But i am getting this error from Bio import Entrez Traceback (most recent call last): File stdin, line 1, in ? ImportError: cannot import name Entrez what should i do know can anybody suggest me an alternative for this Ensure that you don't have *another* Bio module that is being imported instead of the true one. -- Gabriel Genellina -- http://mail.python.org/mailman/listinfo/python-list
