From p.j.a.cock at googlemail.com  Thu Dec  1 03:52:43 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 1 Dec 2011 08:52:43 +0000
Subject: [Biopython] Generator expression for SeqIO
In-Reply-To: <CAOP6n=iFrLbs5OSRBc=gRfOkD1WavuA=ywXA6ueiZhqJsPGs_Q@mail.gmail.com>
References: <CAOP6n=jQSUDxy6SDM8KyMDX_Rz9SYCRO6fz4vdEpD_WCD9=CxA@mail.gmail.com>
	<CAKVJ-_5gxqJpWPD4m_q6_SQ4xSvzGXGXvHCfk40=--6RfT3fjg@mail.gmail.com>
	<CAOP6n=iFrLbs5OSRBc=gRfOkD1WavuA=ywXA6ueiZhqJsPGs_Q@mail.gmail.com>
Message-ID: <CAKVJ-_4SsJ1ekH1sdgDekgJB6SUPQyNj1geytkHmuerPCGJmsg@mail.gmail.com>

On Wednesday, November 30, 2011, Mic <mictadlo at gmail.com> wrote:
> Thank you it is working.
>

Excellent - sorry I couldn't think of a nice way to explain the syntax.

Peter

From jmtc21 at bath.ac.uk  Thu Dec  1 09:09:33 2011
From: jmtc21 at bath.ac.uk (Jaime Tovar)
Date: Thu, 01 Dec 2011 14:09:33 +0000
Subject: [Biopython] GTF to GFF using BCBio
In-Reply-To: <CAKVJ-_5gxqJpWPD4m_q6_SQ4xSvzGXGXvHCfk40=--6RfT3fjg@mail.gmail.com>
References: <CAOP6n=jQSUDxy6SDM8KyMDX_Rz9SYCRO6fz4vdEpD_WCD9=CxA@mail.gmail.com>
	<CAKVJ-_5gxqJpWPD4m_q6_SQ4xSvzGXGXvHCfk40=--6RfT3fjg@mail.gmail.com>
Message-ID: <4ED78A9D.4080306@bath.ac.uk>

Hello all,

I was trying to find an example on how to get a gff3 formated file from 
a gtf file using the BCBio library extensions for biopython. I the doc 
it only covers non-gff-family formats to gff3. I guess is just a 
parameter thing in the GFF writer but have been looking unsuccessfully 
for the answer. Any hint will be greatly appreciated.

Best regards,

J.

From jmtc21 at bath.ac.uk  Thu Dec  1 11:45:40 2011
From: jmtc21 at bath.ac.uk (Jaime Tovar)
Date: Thu, 01 Dec 2011 16:45:40 +0000
Subject: [Biopython] GTF to GFF using BCBio
In-Reply-To: <4ED78A9D.4080306@bath.ac.uk>
References: <CAOP6n=jQSUDxy6SDM8KyMDX_Rz9SYCRO6fz4vdEpD_WCD9=CxA@mail.gmail.com>
	<CAKVJ-_5gxqJpWPD4m_q6_SQ4xSvzGXGXvHCfk40=--6RfT3fjg@mail.gmail.com>
	<4ED78A9D.4080306@bath.ac.uk>
Message-ID: <4ED7AF34.8050707@bath.ac.uk>

Reply from BCBio library's author:

https://github.com/chapmanb/bcbb/blob/master/gff/Scripts/gff/gff2_to_gff3.py

and will cover GFF2/GTF files into GFF3.

J.

On 01/12/11 14:09, Jaime Tovar wrote:
> Hello all,
>
> I was trying to find an example on how to get a gff3 formated file 
> from a gtf file using the BCBio library extensions for biopython. I 
> the doc it only covers non-gff-family formats to gff3. I guess is just 
> a parameter thing in the GFF writer but have been looking 
> unsuccessfully for the answer. Any hint will be greatly appreciated.
>
> Best regards,
>
> J.
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>


From daniel.svozil at vscht.cz  Tue Dec  6 06:39:35 2011
From: daniel.svozil at vscht.cz (Daniel Svozil)
Date: Tue, 6 Dec 2011 12:39:35 +0100
Subject: [Biopython] mmView - a tool for mmCIF exploration
In-Reply-To: <CAA6GQESfwp5oAD4KRR5x7FLmtoSa-F1KJ3fueDMNmrzg78vTqQ@mail.gmail.com>
References: <CAA6GQETVbUpUQr9TGZ_gL4GPZq0CKKn7q5jVuGXWjaDsuhOT0Q@mail.gmail.com>
	<CAA6GQERKcsa60JKmfrE-1bPGCUk8NBV9hd30n+Vxo-Yn-z3UuQ@mail.gmail.com>
	<CAA6GQETz8mCjh5QvdEpDLYP=r9TUdCiW68hD+KuvQzgaSGKBPw@mail.gmail.com>
	<CAA6GQEQ-qH3STt1=tz57Piz_TfdA1Xn58rR52sEwxKGFRYwnVQ@mail.gmail.com>
	<CAA6GQEQoGnL8S_yA8YVX0PPU1hOQjvf8_HKE8t8w6uKaopsOJg@mail.gmail.com>
	<CAA6GQEQmnuqRu1EHaUQ+o3+SR6NLguN9uXJbC-puVXak388wxg@mail.gmail.com>
	<CAA6GQESFwiV5_NYHjN+wX2v27bQCJvawk5bzVAOjF+9G5_A2bg@mail.gmail.com>
	<CAA6GQESfwp5oAD4KRR5x7FLmtoSa-F1KJ3fueDMNmrzg78vTqQ@mail.gmail.com>
Message-ID: <CAA6GQEQ46d+hEWbo3+U6H24aqf0OjFp=ZZzWvwxfLKra=s7X0w@mail.gmail.com>

Dear colleagues,

We would like to announce the availability of mmView - the web-based
application which allows to comfortably explore the structural data of
biomacromolecules stored in the mmCIF (macromolecular Crystallographic
Information File) format. The mmView software system is primarily
intended for educational purposes but it can also serve as an
auxiliary tool for working with biomolecular structures.

The mmView application is offered in two flavors: as a publicly
available web server http://ich.vscht.cz/projects/mmview/, and as an
open-source stand-alone application (available from
http://sourceforge.net/projects/mmview) that can be installed on the
user?s computer.

Petr Cech and Daniel Svozil

--
Daniel Svozil, PhD
Head of Laboratory of Informatics and Chemistry
Institute of Chemical Technology
Czech Republic

phone: +420 220 444 391
http://ich.vscht.cz/~svozil


From mictadlo at gmail.com  Tue Dec  6 23:41:25 2011
From: mictadlo at gmail.com (Mic)
Date: Wed, 7 Dec 2011 14:41:25 +1000
Subject: [Biopython] Generator expression for SeqIO
In-Reply-To: <CAKVJ-_4SsJ1ekH1sdgDekgJB6SUPQyNj1geytkHmuerPCGJmsg@mail.gmail.com>
References: <CAOP6n=jQSUDxy6SDM8KyMDX_Rz9SYCRO6fz4vdEpD_WCD9=CxA@mail.gmail.com>
	<CAKVJ-_5gxqJpWPD4m_q6_SQ4xSvzGXGXvHCfk40=--6RfT3fjg@mail.gmail.com>
	<CAOP6n=iFrLbs5OSRBc=gRfOkD1WavuA=ywXA6ueiZhqJsPGs_Q@mail.gmail.com>
	<CAKVJ-_4SsJ1ekH1sdgDekgJB6SUPQyNj1geytkHmuerPCGJmsg@mail.gmail.com>
Message-ID: <CAOP6n=ipFqLbb1VUj4PuOUBcO+ZTk6VuLBpPEFBQtRO7hdccDg@mail.gmail.com>

No worries is was perfect.

I have the following code and I do not know how to combine the *header* and
*seq* variables from the '*with*' statement with generator expression?

from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
from pprint import pprint

if __name__ == '__main__':

    *with* open('input.txt') as f:
        for line in f:
            try:
                splited_line = line.split('\t')

                *header* = splited_line[0] +'_'+ splited_line[2]
                *seq* = splited_line[3]
            except IndexError:
                continue

    fasta_file = open('output.fasta', 'w')
    records = (SeqRecord(???), id=????, description="") for i in ???)

    SeqIO.write(records, fasta_file, "fasta")

Thank you in advance.

On Thu, Dec 1, 2011 at 6:52 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

>
>
> On Wednesday, November 30, 2011, Mic <mictadlo at gmail.com> wrote:
> > Thank you it is working.
> >
>
> Excellent - sorry I couldn't think of a nice way to explain the syntax.
>
> Peter

From p.j.a.cock at googlemail.com  Wed Dec  7 03:26:08 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 7 Dec 2011 08:26:08 +0000
Subject: [Biopython] Generator expression for SeqIO
In-Reply-To: <CAOP6n=ipFqLbb1VUj4PuOUBcO+ZTk6VuLBpPEFBQtRO7hdccDg@mail.gmail.com>
References: <CAOP6n=jQSUDxy6SDM8KyMDX_Rz9SYCRO6fz4vdEpD_WCD9=CxA@mail.gmail.com>
	<CAKVJ-_5gxqJpWPD4m_q6_SQ4xSvzGXGXvHCfk40=--6RfT3fjg@mail.gmail.com>
	<CAOP6n=iFrLbs5OSRBc=gRfOkD1WavuA=ywXA6ueiZhqJsPGs_Q@mail.gmail.com>
	<CAKVJ-_4SsJ1ekH1sdgDekgJB6SUPQyNj1geytkHmuerPCGJmsg@mail.gmail.com>
	<CAOP6n=ipFqLbb1VUj4PuOUBcO+ZTk6VuLBpPEFBQtRO7hdccDg@mail.gmail.com>
Message-ID: <CAKVJ-_5Z=M2sC1Oz8PWbXb6L6TjJ4LZws-F1Nm_PpWa7TR9heA@mail.gmail.com>

On Wed, Dec 7, 2011 at 4:41 AM, Mic <mictadlo at gmail.com> wrote:
> No worries is was perfect.
>
> I have the following code and I do not know how to combine the *header* and
> *seq* variables from the '*with*' statement with generator expression?
>
> from Bio import SeqIO
> from Bio.SeqRecord import SeqRecord
> from Bio.Seq import Seq
> from pprint import pprint
>
> if __name__ == '__main__':
>
> ? ?*with* open('input.txt') as f:
> ? ? ? ?for line in f:
> ? ? ? ? ? ?try:
> ? ? ? ? ? ? ? ?splited_line = line.split('\t')
>
> ? ? ? ? ? ? ? ?*header* = splited_line[0] +'_'+ splited_line[2]
> ? ? ? ? ? ? ? ?*seq* = splited_line[3]
> ? ? ? ? ? ?except IndexError:
> ? ? ? ? ? ? ? ?continue
>
> ? ?fasta_file = open('output.fasta', 'w')
> ? ?records = (SeqRecord(???), id=????, description="") for i in ???)
>
> ? ?SeqIO.write(records, fasta_file, "fasta")
>
> Thank you in advance.

Are you trying to parse a tabular file, with three columns
(ID, sequence, description)?

I suggest you learn about generator functions in Python.

Peter


From jordan.r.willis at Vanderbilt.Edu  Wed Dec  7 03:49:06 2011
From: jordan.r.willis at Vanderbilt.Edu (Willis, Jordan R)
Date: Wed, 7 Dec 2011 02:49:06 -0600
Subject: [Biopython] Generator expression for SeqIO
In-Reply-To: <CAKVJ-_5Z=M2sC1Oz8PWbXb6L6TjJ4LZws-F1Nm_PpWa7TR9heA@mail.gmail.com>
References: <CAOP6n=jQSUDxy6SDM8KyMDX_Rz9SYCRO6fz4vdEpD_WCD9=CxA@mail.gmail.com>
	<CAKVJ-_5gxqJpWPD4m_q6_SQ4xSvzGXGXvHCfk40=--6RfT3fjg@mail.gmail.com>
	<CAOP6n=iFrLbs5OSRBc=gRfOkD1WavuA=ywXA6ueiZhqJsPGs_Q@mail.gmail.com>
	<CAKVJ-_4SsJ1ekH1sdgDekgJB6SUPQyNj1geytkHmuerPCGJmsg@mail.gmail.com>
	<CAOP6n=ipFqLbb1VUj4PuOUBcO+ZTk6VuLBpPEFBQtRO7hdccDg@mail.gmail.com>
	<CAKVJ-_5Z=M2sC1Oz8PWbXb6L6TjJ4LZws-F1Nm_PpWa7TR9heA@mail.gmail.com>
Message-ID: <1923E9B1-AA7B-49FA-8F63-F05642E948D7@vanderbilt.edu>

Does the input.txt have fasta sequences in it and you want to write them to a file? This is what it looks like.

from Bio import SeqIO as sio

generator = sio.read('input.txt','fasta')


for i in generator:
print i.header
print i.seq

will give you header and sequence. You could of course write this to a file, but you seem to be inputting a fasta file just to write out another one.




Jordan Willis
Ph.D Candidate, CPB
Laboratory of Dr. James Crowe and Dr. Jens Meiler
11475 MRBIV
2213 Garland Ave.
Nashville, TN 37232
Cell: 816-674-5340
Office: 615-343-8263


On Dec 7, 2011, at 12:26 AM, Peter Cock wrote:

On Wed, Dec 7, 2011 at 4:41 AM, Mic <mictadlo at gmail.com<mailto:mictadlo at gmail.com>> wrote:
No worries is was perfect.

I have the following code and I do not know how to combine the *header* and
*seq* variables from the '*with*' statement with generator expression?

from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
from pprint import pprint

if __name__ == '__main__':

   *with* open('input.txt') as f:
       for line in f:
           try:
               splited_line = line.split('\t')

               *header* = splited_line[0] +'_'+ splited_line[2]
               *seq* = splited_line[3]
           except IndexError:
               continue

   fasta_file = open('output.fasta', 'w')
   records = (SeqRecord(???), id=????, description="") for i in ???)

   SeqIO.write(records, fasta_file, "fasta")

Thank you in advance.

Are you trying to parse a tabular file, with three columns
(ID, sequence, description)?

I suggest you learn about generator functions in Python.

Peter

_______________________________________________
Biopython mailing list  -  Biopython at lists.open-bio.org<mailto:Biopython at lists.open-bio.org>
http://lists.open-bio.org/mailman/listinfo/biopython




From mictadlo at gmail.com  Wed Dec  7 08:11:24 2011
From: mictadlo at gmail.com (Mic)
Date: Wed, 7 Dec 2011 23:11:24 +1000
Subject: [Biopython] Generator expression for SeqIO
In-Reply-To: <1923E9B1-AA7B-49FA-8F63-F05642E948D7@vanderbilt.edu>
References: <CAOP6n=jQSUDxy6SDM8KyMDX_Rz9SYCRO6fz4vdEpD_WCD9=CxA@mail.gmail.com>
	<CAKVJ-_5gxqJpWPD4m_q6_SQ4xSvzGXGXvHCfk40=--6RfT3fjg@mail.gmail.com>
	<CAOP6n=iFrLbs5OSRBc=gRfOkD1WavuA=ywXA6ueiZhqJsPGs_Q@mail.gmail.com>
	<CAKVJ-_4SsJ1ekH1sdgDekgJB6SUPQyNj1geytkHmuerPCGJmsg@mail.gmail.com>
	<CAOP6n=ipFqLbb1VUj4PuOUBcO+ZTk6VuLBpPEFBQtRO7hdccDg@mail.gmail.com>
	<CAKVJ-_5Z=M2sC1Oz8PWbXb6L6TjJ4LZws-F1Nm_PpWa7TR9heA@mail.gmail.com>
	<1923E9B1-AA7B-49FA-8F63-F05642E948D7@vanderbilt.edu>
Message-ID: <CAOP6n=hv1y80X4syQJbPFjwk+F0Y_SRPTQwEPddacKzY4k9NUw@mail.gmail.com>

Thank you for the solution.

My input files is not exactly a FASTA file, but it contains information to
build it. The file looks like this:
test1\t0001\a1\tAATTCC

Output should looks like:
>test1_a1
AATTCC


On Wed, Dec 7, 2011 at 6:49 PM, Willis, Jordan R <
jordan.r.willis at vanderbilt.edu> wrote:

> Does the input.txt have fasta sequences in it and you want to write them
> to a file? This is what it looks like.
>
> from Bio import SeqIO as sio
>
> generator = sio.read('input.txt','fasta')
>
>
> for i in generator:
> print i.header
> print i.seq
>
> will give you header and sequence. You could of course write this to a
> file, but you seem to be inputting a fasta file just to write out another
> one.
>
>
>
>
> Jordan Willis
> Ph.D Candidate, CPB
> Laboratory of Dr. James Crowe and Dr. Jens Meiler
> 11475 MRBIV
> 2213 Garland Ave.
> Nashville, TN 37232
> Cell: 816-674-5340
> Office: 615-343-8263
>
>
> On Dec 7, 2011, at 12:26 AM, Peter Cock wrote:
>
> On Wed, Dec 7, 2011 at 4:41 AM, Mic <mictadlo at gmail.com> wrote:
>
> No worries is was perfect.
>
>
> I have the following code and I do not know how to combine the *header* and
>
> *seq* variables from the '*with*' statement with generator expression?
>
>
> from Bio import SeqIO
>
> from Bio.SeqRecord import SeqRecord
>
> from Bio.Seq import Seq
>
> from pprint import pprint
>
>
> if __name__ == '__main__':
>
>
>    *with* open('input.txt') as f:
>
>        for line in f:
>
>            try:
>
>                splited_line = line.split('\t')
>
>
>                *header* = splited_line[0] +'_'+ splited_line[2]
>
>                *seq* = splited_line[3]
>
>            except IndexError:
>
>                continue
>
>
>    fasta_file = open('output.fasta', 'w')
>
>    records = (SeqRecord(???), id=????, description="") for i in ???)
>
>
>    SeqIO.write(records, fasta_file, "fasta")
>
>
> Thank you in advance.
>
>
> Are you trying to parse a tabular file, with three columns
> (ID, sequence, description)?
>
> I suggest you learn about generator functions in Python.
>
> Peter
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>
>

From eric.talevich at gmail.com  Wed Dec  7 11:07:57 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Wed, 7 Dec 2011 11:07:57 -0500
Subject: [Biopython] Generator expression for SeqIO
In-Reply-To: <CAOP6n=ipFqLbb1VUj4PuOUBcO+ZTk6VuLBpPEFBQtRO7hdccDg@mail.gmail.com>
References: <CAOP6n=jQSUDxy6SDM8KyMDX_Rz9SYCRO6fz4vdEpD_WCD9=CxA@mail.gmail.com>
	<CAKVJ-_5gxqJpWPD4m_q6_SQ4xSvzGXGXvHCfk40=--6RfT3fjg@mail.gmail.com>
	<CAOP6n=iFrLbs5OSRBc=gRfOkD1WavuA=ywXA6ueiZhqJsPGs_Q@mail.gmail.com>
	<CAKVJ-_4SsJ1ekH1sdgDekgJB6SUPQyNj1geytkHmuerPCGJmsg@mail.gmail.com>
	<CAOP6n=ipFqLbb1VUj4PuOUBcO+ZTk6VuLBpPEFBQtRO7hdccDg@mail.gmail.com>
Message-ID: <CAMC681nGT5kXDjf4AecLrUgSTREdqPM8ttTFq_pYEyQZ==kcsg@mail.gmail.com>

Mic,

You don't really need a generator expression here, but I recommend that you
read the Python Tutorial to learn how to use them anyway.

To solve your problem, here's one solution using Biopython and a list
comprehension (like a generator expression, but more your pace):

def row_to_seqrecord(row):
    """Convert a tab-delimited row to a SeqRecord.

    Row looks like:
    test1\t0001\a1\tAATTCC

    Record looks like (conceptually):
    >test1_a1
    AATTCC
    """
    cells = [cell.strip() for cell in row.split('\t')]
    return SeqRecord(Seq(cells[3]), id=cells[0] + '_' + cells[2])

with open('input.txt') as infile:
    records = [row_to_seqrecord(line) for line in infile]

SeqIO.write(records, 'output.txt', 'fasta')


But the nice thing about FASTA format is that there's almost no structure
to it. Here's a simpler way to do it that doesn't use Biopython:

with open('input.txt') as infile:
    with open('output.fasta', 'w+') as outfile:
        for line in infile:
            parts = [part.strip() for part in line.split('\t')]
            if len(parts) != 4:
                continue
            # Header
            outfile.write(">%s_%s\n" % (parts[0], parts[2])
            # Sequence
            outfile.write(parts[3] + '\n')



On Tue, Dec 6, 2011 at 11:41 PM, Mic <mictadlo at gmail.com> wrote:

> No worries is was perfect.
>
> I have the following code and I do not know how to combine the *header* and
> *seq* variables from the '*with*' statement with generator expression?
>
> from Bio import SeqIO
> from Bio.SeqRecord import SeqRecord
> from Bio.Seq import Seq
> from pprint import pprint
>
> if __name__ == '__main__':
>
>    *with* open('input.txt') as f:
>        for line in f:
>            try:
>                splited_line = line.split('\t')
>
>                *header* = splited_line[0] +'_'+ splited_line[2]
>                *seq* = splited_line[3]
>            except IndexError:
>                continue
>
>    fasta_file = open('output.fasta', 'w')
>    records = (SeqRecord(???), id=????, description="") for i in ???)
>
>    SeqIO.write(records, fasta_file, "fasta")
>
> Thank you in advance.
>
> On Thu, Dec 1, 2011 at 6:52 PM, Peter Cock <p.j.a.cock at googlemail.com
> >wrote:
>
> >
> >
> > On Wednesday, November 30, 2011, Mic <mictadlo at gmail.com> wrote:
> > > Thank you it is working.
> > >
> >
> > Excellent - sorry I couldn't think of a nice way to explain the syntax.
> >
> > Peter
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>

From jsanders at oeb.harvard.edu  Fri Dec  9 16:53:12 2011
From: jsanders at oeb.harvard.edu (Jon Sanders)
Date: Fri, 9 Dec 2011 16:53:12 -0500
Subject: [Biopython] help with confidence values on PhyloXML tree objects?
Message-ID: <CALHM1CE0Nu2AVqf2R32GhTHiW2aPfXNcPFAf2XCCY89bWhGC-g@mail.gmail.com>

So I have two problems.


Problem 1: when importing my newick-formatted trees, which were generated
in PyCogent, the terminal labels and branch labels are read in as
confidence values because they're numerical. So

    ((((41:0.01494,44:0.00014)0.604:0...

is read in with blank name='' values and 41, 44, 0.605, etc. as
'confidence' values.



Problem 2: I would like to store multiple confidence values per node, but I
can't figure out how to do it.

I can get the plain old 'confidence' attribute set by:

   clade.confidence = .05

but can't figure out how to add and set new confidence types. Any
suggestions?


Much appreciated,
-jon


-- 
"If you hold a cat by the tail you learn things you cannot learn any other
way."
                         --Mark Twain

From eric.talevich at gmail.com  Fri Dec  9 18:26:46 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Fri, 9 Dec 2011 18:26:46 -0500
Subject: [Biopython] help with confidence values on PhyloXML tree
	objects?
In-Reply-To: <CALHM1CE0Nu2AVqf2R32GhTHiW2aPfXNcPFAf2XCCY89bWhGC-g@mail.gmail.com>
References: <CALHM1CE0Nu2AVqf2R32GhTHiW2aPfXNcPFAf2XCCY89bWhGC-g@mail.gmail.com>
Message-ID: <CAMC681nxCD9L9pA+_6A5GfhXpK8fzvVDPyyc9aH9QXemRDRPqw@mail.gmail.com>

Hi Jon,

On Fri, Dec 9, 2011 at 4:53 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:

> So I have two problems.
>
>
> Problem 1: when importing my newick-formatted trees, which were generated
> in PyCogent, the terminal labels and branch labels are read in as
> confidence values because they're numerical. So
>
>    ((((41:0.01494,44:0.00014)0.604:0...
>
> is read in with blank name='' values and 41, 44, 0.605, etc. as
> 'confidence' values.
>

Hmm, I'll take a look at the Newick parser. I think I've used numeric taxon
labels before without a problem, but PyCogent wasn't involved.

It might work if you can coax PyCogent into writing the Newick files with
an extra colon:
((((:41:0.01494,:44:0.00014):0.604:0...



> Problem 2: I would like to store multiple confidence values per node, but I
> can't figure out how to do it.
>
> I can get the plain old 'confidence' attribute set by:
>
>   clade.confidence = .05
>
> but can't figure out how to add and set new confidence types. Any
> suggestions?
>

The confidence types are instances of the Bio.Phylo.PhyloXML.Confidence
class.

In PhyloXML trees, the attribute "clade.confidence" is actually a Python
property pointing to the first element of "clade.confidences", a list of
Confidence objects. It's syntax sugar to keep compatibility with Newick,
which just has a numeric value there.

You can use it like this:

from Bio.Phylo import PhyloXML

# Create new Confidence instances
a_bootstrap_value = PhyloXML.Confidence(83, type="bootstrap")
# The second argument is optional
a_posterior_probability = PhyloXML.Confidence(0.99)

# Select a clade from your tree to modify
a_clade = mytree.clade[...]

# Modify the list of Confidences directly
a_clade.confidences.append(a_bootstrap_value)
a_clade.confidences.append(a_posterior_probability)


If you've assigned multiple confidence values to a clade, using the
PhyloXML class, then the "clade.confidence" shortcut won't work anymore
because it's not clear which confidence you mean. So you'll have to use
e.g. clade.confidences[0] or clade.confidences[1], and save it the tree in
PhyloXML format to preserve the extra data.

Hope that helps.

Best regards,
Eric

From jsanders at oeb.harvard.edu  Tue Dec 13 13:17:09 2011
From: jsanders at oeb.harvard.edu (Jon Sanders)
Date: Tue, 13 Dec 2011 13:17:09 -0500
Subject: [Biopython] help with confidence values on PhyloXML tree
	objects?
In-Reply-To: <CAMC681nxCD9L9pA+_6A5GfhXpK8fzvVDPyyc9aH9QXemRDRPqw@mail.gmail.com>
References: <CALHM1CE0Nu2AVqf2R32GhTHiW2aPfXNcPFAf2XCCY89bWhGC-g@mail.gmail.com>
	<CAMC681nxCD9L9pA+_6A5GfhXpK8fzvVDPyyc9aH9QXemRDRPqw@mail.gmail.com>
Message-ID: <CALHM1CGv4=UMOPjNhSXm+U9BWd_fbMQZQ=SYw3oYhH0yJLB70Q@mail.gmail.com>

Thanks Eric! I got the hang of the PhyloXML confidence objects now, so
that's straightened out.

Still having issues with the tree parsing. I tried throwing in extra colons
with a regex, both before and after the tip/edge label, but that didn't
change the behavior of the parser, and all the tip/edge labels were still
imported as confidence values. Poking around some documentation on the
newick format, it seems like the edge labels might be tricking the parser
into thinking there are confidence values present, since there's no clear
way to distinguish between them. I'll try playing around with supressing
the edge labels in PyCogent and see if I can't pass a decent tree to
BioPython side for proper PhyloXML output.

Ugh.

-j

On Fri, Dec 9, 2011 at 6:26 PM, Eric Talevich <eric.talevich at gmail.com>wrote:

> Hi Jon,
>
> On Fri, Dec 9, 2011 at 4:53 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>
>> So I have two problems.
>>
>>
>> Problem 1: when importing my newick-formatted trees, which were generated
>> in PyCogent, the terminal labels and branch labels are read in as
>> confidence values because they're numerical. So
>>
>>    ((((41:0.01494,44:0.00014)0.604:0...
>>
>> is read in with blank name='' values and 41, 44, 0.605, etc. as
>> 'confidence' values.
>>
>
> Hmm, I'll take a look at the Newick parser. I think I've used numeric
> taxon labels before without a problem, but PyCogent wasn't involved.
>
> It might work if you can coax PyCogent into writing the Newick files with
> an extra colon:
> ((((:41:0.01494,:44:0.00014):0.604:0...
>
>
>
>> Problem 2: I would like to store multiple confidence values per node, but
>> I
>> can't figure out how to do it.
>>
>> I can get the plain old 'confidence' attribute set by:
>>
>>   clade.confidence = .05
>>
>> but can't figure out how to add and set new confidence types. Any
>> suggestions?
>>
>
> The confidence types are instances of the Bio.Phylo.PhyloXML.Confidence
> class.
>
> In PhyloXML trees, the attribute "clade.confidence" is actually a Python
> property pointing to the first element of "clade.confidences", a list of
> Confidence objects. It's syntax sugar to keep compatibility with Newick,
> which just has a numeric value there.
>
> You can use it like this:
>
> from Bio.Phylo import PhyloXML
>
> # Create new Confidence instances
> a_bootstrap_value = PhyloXML.Confidence(83, type="bootstrap")
> # The second argument is optional
> a_posterior_probability = PhyloXML.Confidence(0.99)
>
> # Select a clade from your tree to modify
> a_clade = mytree.clade[...]
>
> # Modify the list of Confidences directly
> a_clade.confidences.append(a_bootstrap_value)
> a_clade.confidences.append(a_posterior_probability)
>
>
> If you've assigned multiple confidence values to a clade, using the
> PhyloXML class, then the "clade.confidence" shortcut won't work anymore
> because it's not clear which confidence you mean. So you'll have to use
> e.g. clade.confidences[0] or clade.confidences[1], and save it the tree in
> PhyloXML format to preserve the extra data.
>
> Hope that helps.
>
> Best regards,
> Eric
>



-- 
"If you hold a cat by the tail you learn things you cannot learn any other
way."
                         --Mark Twain

From jsanders at oeb.harvard.edu  Tue Dec 13 13:55:20 2011
From: jsanders at oeb.harvard.edu (Jon Sanders)
Date: Tue, 13 Dec 2011 13:55:20 -0500
Subject: [Biopython] help with confidence values on PhyloXML tree
	objects?
In-Reply-To: <CALHM1CGv4=UMOPjNhSXm+U9BWd_fbMQZQ=SYw3oYhH0yJLB70Q@mail.gmail.com>
References: <CALHM1CE0Nu2AVqf2R32GhTHiW2aPfXNcPFAf2XCCY89bWhGC-g@mail.gmail.com>
	<CAMC681nxCD9L9pA+_6A5GfhXpK8fzvVDPyyc9aH9QXemRDRPqw@mail.gmail.com>
	<CALHM1CGv4=UMOPjNhSXm+U9BWd_fbMQZQ=SYw3oYhH0yJLB70Q@mail.gmail.com>
Message-ID: <CALHM1CECo+233yRCus4CHxqRUhzAq7qZM1HYcefs0vM5AFjH_g@mail.gmail.com>

Update: yup, seems to be a problem with numeric tip names.

1) getting rid of internal edge name doesn't help
2) appending 'a' to tip names fixes it
3) this tree: (((1,2),(3,4)),5); loads the numeric tip names as branch
lengths
4) this tree: (((1:0.01,2:0.01):0.01,(3:0.01,4:0.01):0.01):0.01,5:0.03);
loads the numeric tip names as confidence values and branch lenghts
correctly

I might try poking around the parser too, although my python foo has little
bar.

-j

On Tue, Dec 13, 2011 at 1:17 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:

> Thanks Eric! I got the hang of the PhyloXML confidence objects now, so
> that's straightened out.
>
> Still having issues with the tree parsing. I tried throwing in extra
> colons with a regex, both before and after the tip/edge label, but that
> didn't change the behavior of the parser, and all the tip/edge labels were
> still imported as confidence values. Poking around some documentation on
> the newick format, it seems like the edge labels might be tricking the
> parser into thinking there are confidence values present, since there's no
> clear way to distinguish between them. I'll try playing around with
> supressing the edge labels in PyCogent and see if I can't pass a decent
> tree to BioPython side for proper PhyloXML output.
>
> Ugh.
>
> -j
>
>
> On Fri, Dec 9, 2011 at 6:26 PM, Eric Talevich <eric.talevich at gmail.com>wrote:
>
>> Hi Jon,
>>
>> On Fri, Dec 9, 2011 at 4:53 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>>
>>> So I have two problems.
>>>
>>>
>>> Problem 1: when importing my newick-formatted trees, which were generated
>>> in PyCogent, the terminal labels and branch labels are read in as
>>> confidence values because they're numerical. So
>>>
>>>    ((((41:0.01494,44:0.00014)0.604:0...
>>>
>>> is read in with blank name='' values and 41, 44, 0.605, etc. as
>>> 'confidence' values.
>>>
>>
>> Hmm, I'll take a look at the Newick parser. I think I've used numeric
>> taxon labels before without a problem, but PyCogent wasn't involved.
>>
>> It might work if you can coax PyCogent into writing the Newick files with
>> an extra colon:
>> ((((:41:0.01494,:44:0.00014):0.604:0...
>>
>>
>>
>>> Problem 2: I would like to store multiple confidence values per node,
>>> but I
>>> can't figure out how to do it.
>>>
>>> I can get the plain old 'confidence' attribute set by:
>>>
>>>   clade.confidence = .05
>>>
>>> but can't figure out how to add and set new confidence types. Any
>>> suggestions?
>>>
>>
>> The confidence types are instances of the Bio.Phylo.PhyloXML.Confidence
>> class.
>>
>> In PhyloXML trees, the attribute "clade.confidence" is actually a Python
>> property pointing to the first element of "clade.confidences", a list of
>> Confidence objects. It's syntax sugar to keep compatibility with Newick,
>> which just has a numeric value there.
>>
>> You can use it like this:
>>
>> from Bio.Phylo import PhyloXML
>>
>> # Create new Confidence instances
>> a_bootstrap_value = PhyloXML.Confidence(83, type="bootstrap")
>> # The second argument is optional
>> a_posterior_probability = PhyloXML.Confidence(0.99)
>>
>> # Select a clade from your tree to modify
>> a_clade = mytree.clade[...]
>>
>> # Modify the list of Confidences directly
>> a_clade.confidences.append(a_bootstrap_value)
>> a_clade.confidences.append(a_posterior_probability)
>>
>>
>> If you've assigned multiple confidence values to a clade, using the
>> PhyloXML class, then the "clade.confidence" shortcut won't work anymore
>> because it's not clear which confidence you mean. So you'll have to use
>> e.g. clade.confidences[0] or clade.confidences[1], and save it the tree in
>> PhyloXML format to preserve the extra data.
>>
>> Hope that helps.
>>
>> Best regards,
>> Eric
>>
>
>
>
> --
> "If you hold a cat by the tail you learn things you cannot learn any other
> way."
>                          --Mark Twain
>
>


-- 
"If you hold a cat by the tail you learn things you cannot learn any other
way."
                         --Mark Twain

From eric.talevich at gmail.com  Tue Dec 13 17:28:11 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Tue, 13 Dec 2011 17:28:11 -0500
Subject: [Biopython] help with confidence values on PhyloXML tree
	objects?
In-Reply-To: <CALHM1CECo+233yRCus4CHxqRUhzAq7qZM1HYcefs0vM5AFjH_g@mail.gmail.com>
References: <CALHM1CE0Nu2AVqf2R32GhTHiW2aPfXNcPFAf2XCCY89bWhGC-g@mail.gmail.com>
	<CAMC681nxCD9L9pA+_6A5GfhXpK8fzvVDPyyc9aH9QXemRDRPqw@mail.gmail.com>
	<CALHM1CGv4=UMOPjNhSXm+U9BWd_fbMQZQ=SYw3oYhH0yJLB70Q@mail.gmail.com>
	<CALHM1CECo+233yRCus4CHxqRUhzAq7qZM1HYcefs0vM5AFjH_g@mail.gmail.com>
Message-ID: <CAMC681nG8ThRvAXCzRSAwn0TnzpH47AG99+8TvHTYjrBCug1NQ@mail.gmail.com>

On Tue, Dec 13, 2011 at 1:55 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:

> Update: yup, seems to be a problem with numeric tip names.
>
> 1) getting rid of internal edge name doesn't help
> 2) appending 'a' to tip names fixes it
> 3) this tree: (((1,2),(3,4)),5); loads the numeric tip names as branch
> lengths
> 4) this tree: (((1:0.01,2:0.01):0.01,(3:0.01,4:0.01):0.01):0.01,5:0.03);
> loads the numeric tip names as confidence values and branch lenghts
> correctly
>
> I might try poking around the parser too, although my python foo has
> little bar.
>
> -j
>

All right, sounds like you've got it working then -- thanks for sharing
your investigations. Looking back at my own work, I see that when I used
numbered taxon labels earlier, I prefixed them with the letter "t"; I never
actually used plain integers, so I didn't hit this issue. For now, I
suppose your best bet is to temporarily add a letter prefix or suffix to
the names when transferring between PyCogent and Biopython.

According to the spec for the Nexus format (
http://www.ncbi.nlm.nih.gov/pubmed/11975335), which includes Newick,
all-numeric taxon names are illegal. So, I suppose the Biopython parser's
behavior is technically correct -- at least for parsing the tree section of
Nexus files.

In any case, this behavior is surprising and at least deserves a mention in
a docstring or an error message. I'll try to take a look at PyCogent's
parser to see how they handle ambiguous cases like the ones you listed.

-E


On Fri, Dec 9, 2011 at 6:26 PM, Eric Talevich <eric.talevich at gmail.com>wrote:
>
>> Hi Jon,
>>
>> On Fri, Dec 9, 2011 at 4:53 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>>
>>> So I have two problems.
>>>
>>>
>>> Problem 1: when importing my newick-formatted trees, which were generated
>>> in PyCogent, the terminal labels and branch labels are read in as
>>> confidence values because they're numerical. So
>>>
>>>    ((((41:0.01494,44:0.00014)0.604:0...
>>>
>>> is read in with blank name='' values and 41, 44, 0.605, etc. as
>>> 'confidence' values.
>>>
>>
>> Hmm, I'll take a look at the Newick parser. I think I've used numeric
>> taxon labels before without a problem, but PyCogent wasn't involved.
>>
>> It might work if you can coax PyCogent into writing the Newick files with
>> an extra colon:
>> ((((:41:0.01494,:44:0.00014):0.604:0...
>>
>>
>>
>>> Problem 2: I would like to store multiple confidence values per node,
>>> but I
>>> can't figure out how to do it.
>>>
>>> I can get the plain old 'confidence' attribute set by:
>>>
>>>   clade.confidence = .05
>>>
>>> but can't figure out how to add and set new confidence types. Any
>>> suggestions?
>>>
>>
>> The confidence types are instances of the Bio.Phylo.PhyloXML.Confidence
>> class.
>>
>> In PhyloXML trees, the attribute "clade.confidence" is actually a Python
>> property pointing to the first element of "clade.confidences", a list of
>> Confidence objects. It's syntax sugar to keep compatibility with Newick,
>> which just has a numeric value there.
>>
>> You can use it like this:
>>
>> from Bio.Phylo import PhyloXML
>>
>> # Create new Confidence instances
>> a_bootstrap_value = PhyloXML.Confidence(83, type="bootstrap")
>> # The second argument is optional
>> a_posterior_probability = PhyloXML.Confidence(0.99)
>>
>> # Select a clade from your tree to modify
>> a_clade = mytree.clade[...]
>>
>> # Modify the list of Confidences directly
>> a_clade.confidences.append(a_bootstrap_value)
>> a_clade.confidences.append(a_posterior_probability)
>>
>>
>> If you've assigned multiple confidence values to a clade, using the
>> PhyloXML class, then the "clade.confidence" shortcut won't work anymore
>> because it's not clear which confidence you mean. So you'll have to use
>> e.g. clade.confidences[0] or clade.confidences[1], and save it the tree in
>> PhyloXML format to preserve the extra data.
>>
>> Hope that helps.
>>
>> Best regards,
>> Eric
>>
>
>

From jsanders at oeb.harvard.edu  Fri Dec 16 13:44:07 2011
From: jsanders at oeb.harvard.edu (Jon Sanders)
Date: Fri, 16 Dec 2011 13:44:07 -0500
Subject: [Biopython] Bug in Phylo.write('phyloxml')?
Message-ID: <CALHM1CEjeYomEiidxjS0UC0JLjGfqmx_GNbfHvtdYjGn1sk-OQ@mail.gmail.com>

My XML trees exported in biopython (with confidence values, thanks Eric!)
don't open in most XML tree viewing programs.

The problem seems to be a spurious <name /> tag at the beginning of the
tree.

<phy:phyloxml xmlns:phy="http://www.phyloxml.org">
  <phy:phylogeny rooted="false">
    <phy:name />
    <phy:clade>

If I delete this tag they open fine.


-- 
"If you hold a cat by the tail you learn things you cannot learn any other
way."
                         --Mark Twain

From eric.talevich at gmail.com  Sun Dec 18 00:03:51 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Sun, 18 Dec 2011 00:03:51 -0500
Subject: [Biopython] Bug in Phylo.write('phyloxml')?
In-Reply-To: <CALHM1CEjeYomEiidxjS0UC0JLjGfqmx_GNbfHvtdYjGn1sk-OQ@mail.gmail.com>
References: <CALHM1CEjeYomEiidxjS0UC0JLjGfqmx_GNbfHvtdYjGn1sk-OQ@mail.gmail.com>
Message-ID: <CAMC681kgx14Bd+gfQwHZew9KYhn3+qJXzUvRrx9C8ddN7CzNHQ@mail.gmail.com>

On Fri, Dec 16, 2011 at 1:44 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:

> My XML trees exported in biopython (with confidence values, thanks Eric!)
> don't open in most XML tree viewing programs.
>
> The problem seems to be a spurious <name /> tag at the beginning of the
> tree.
>
> <phy:phyloxml xmlns:phy="http://www.phyloxml.org">
>  <phy:phylogeny rooted="false">
>    <phy:name />
>    <phy:clade>
>
> If I delete this tag they open fine.
>
>
Hi Jon,

Thanks for reporting this. I'll check the spec to see if an empty 'name'
tag is even valid. Can you give me the name of one or two programs that are
supposed to handle phyloXML, but don't like this input? Is Archaeopteryx
one of them?

-Eric

From jsanders at oeb.harvard.edu  Sun Dec 18 00:08:14 2011
From: jsanders at oeb.harvard.edu (Jon Sanders)
Date: Sun, 18 Dec 2011 00:08:14 -0500
Subject: [Biopython] Bug in Phylo.write('phyloxml')?
In-Reply-To: <CAMC681kgx14Bd+gfQwHZew9KYhn3+qJXzUvRrx9C8ddN7CzNHQ@mail.gmail.com>
References: <CALHM1CEjeYomEiidxjS0UC0JLjGfqmx_GNbfHvtdYjGn1sk-OQ@mail.gmail.com>
	<CAMC681kgx14Bd+gfQwHZew9KYhn3+qJXzUvRrx9C8ddN7CzNHQ@mail.gmail.com>
Message-ID: <CALHM1CFPurXY5U=qsu5=b0uHNVJoBs7eUus-aMsJ0YUdy6Hwog@mail.gmail.com>

Archaeopteryx is the one program that read the trees fine. I also tried
HyperTree, TreeGraph2, and Treevolution, which failed.

-j

On Sun, Dec 18, 2011 at 12:03 AM, Eric Talevich <eric.talevich at gmail.com>wrote:

> On Fri, Dec 16, 2011 at 1:44 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>
>> My XML trees exported in biopython (with confidence values, thanks Eric!)
>> don't open in most XML tree viewing programs.
>>
>> The problem seems to be a spurious <name /> tag at the beginning of the
>> tree.
>>
>> <phy:phyloxml xmlns:phy="http://www.phyloxml.org">
>>  <phy:phylogeny rooted="false">
>>    <phy:name />
>>    <phy:clade>
>>
>> If I delete this tag they open fine.
>>
>>
> Hi Jon,
>
> Thanks for reporting this. I'll check the spec to see if an empty 'name'
> tag is even valid. Can you give me the name of one or two programs that are
> supposed to handle phyloXML, but don't like this input? Is Archaeopteryx
> one of them?
>
> -Eric
>



-- 
"If you hold a cat by the tail you learn things you cannot learn any other
way."
                         --Mark Twain

From eric.talevich at gmail.com  Mon Dec 19 00:31:48 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Sun, 18 Dec 2011 21:31:48 -0800
Subject: [Biopython] Bug in Phylo.write('phyloxml')?
In-Reply-To: <CALHM1CFPurXY5U=qsu5=b0uHNVJoBs7eUus-aMsJ0YUdy6Hwog@mail.gmail.com>
References: <CALHM1CEjeYomEiidxjS0UC0JLjGfqmx_GNbfHvtdYjGn1sk-OQ@mail.gmail.com>
	<CAMC681kgx14Bd+gfQwHZew9KYhn3+qJXzUvRrx9C8ddN7CzNHQ@mail.gmail.com>
	<CALHM1CFPurXY5U=qsu5=b0uHNVJoBs7eUus-aMsJ0YUdy6Hwog@mail.gmail.com>
Message-ID: <CAMC681mSsQcMooQzGq_zmbxiH0b17wrRmdpNCq5yqcXa3H3avw@mail.gmail.com>

Alrighty,

I think the main problem in your case is that the Newick parser creates
trees with the 'name' attribute set to the empty string "" instead of None.
When converting to PhyloXML, that value stays in place and gets serialized
as an empty element. The author of the phyloXML spec is the author of
Archaeopteryx, so all of that makes sense.

For your case, Jon, and others having this problem: before writing a tree
as phyloXML, set the tree name to None if it's not already named.

if tree.name == "":
    tree.name = None
Phylo.write(tree, 'example.xml', 'newick')


For the future, I guess the best approach is to change the Newick parser to
set the tree name to None instead of "" by default. Any issues with that
solution?

-Eric


On Sat, Dec 17, 2011 at 9:08 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:

> Archaeopteryx is the one program that read the trees fine. I also tried
> HyperTree, TreeGraph2, and Treevolution, which failed.
>
> -j
>
>
> On Sun, Dec 18, 2011 at 12:03 AM, Eric Talevich <eric.talevich at gmail.com>wrote:
>
>> On Fri, Dec 16, 2011 at 1:44 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>>
>>> My XML trees exported in biopython (with confidence values, thanks Eric!)
>>> don't open in most XML tree viewing programs.
>>>
>>> The problem seems to be a spurious <name /> tag at the beginning of the
>>> tree.
>>>
>>> <phy:phyloxml xmlns:phy="http://www.phyloxml.org">
>>>  <phy:phylogeny rooted="false">
>>>    <phy:name />
>>>    <phy:clade>
>>>
>>> If I delete this tag they open fine.
>>>
>>>
>> Hi Jon,
>>
>> Thanks for reporting this. I'll check the spec to see if an empty 'name'
>> tag is even valid. Can you give me the name of one or two programs that are
>> supposed to handle phyloXML, but don't like this input? Is Archaeopteryx
>> one of them?
>>
>> -Eric
>>
>
>
>
> --
> "If you hold a cat by the tail you learn things you cannot learn any other
> way."
>                          --Mark Twain
>
>

From jsanders at oeb.harvard.edu  Mon Dec 19 10:44:51 2011
From: jsanders at oeb.harvard.edu (Jon Sanders)
Date: Mon, 19 Dec 2011 10:44:51 -0500
Subject: [Biopython] Bug in Phylo.write('phyloxml')?
In-Reply-To: <CAMC681mSsQcMooQzGq_zmbxiH0b17wrRmdpNCq5yqcXa3H3avw@mail.gmail.com>
References: <CALHM1CEjeYomEiidxjS0UC0JLjGfqmx_GNbfHvtdYjGn1sk-OQ@mail.gmail.com>
	<CAMC681kgx14Bd+gfQwHZew9KYhn3+qJXzUvRrx9C8ddN7CzNHQ@mail.gmail.com>
	<CALHM1CFPurXY5U=qsu5=b0uHNVJoBs7eUus-aMsJ0YUdy6Hwog@mail.gmail.com>
	<CAMC681mSsQcMooQzGq_zmbxiH0b17wrRmdpNCq5yqcXa3H3avw@mail.gmail.com>
Message-ID: <CALHM1CEYOEzc-MTJX9rDnjvN5fy7imYUVGH15C-=J3=z+_XeTQ@mail.gmail.com>

Yup, that seems to work just fine, and it's way easier and safer than
writing a script to open the tree file and kill the tag, which is what I
was going to do. Thanks again!

-j

On Mon, Dec 19, 2011 at 12:31 AM, Eric Talevich <eric.talevich at gmail.com>wrote:

> Alrighty,
>
> I think the main problem in your case is that the Newick parser creates
> trees with the 'name' attribute set to the empty string "" instead of None.
> When converting to PhyloXML, that value stays in place and gets serialized
> as an empty element. The author of the phyloXML spec is the author of
> Archaeopteryx, so all of that makes sense.
>
> For your case, Jon, and others having this problem: before writing a tree
> as phyloXML, set the tree name to None if it's not already named.
>
> if tree.name == "":
>     tree.name = None
> Phylo.write(tree, 'example.xml', 'newick')
>
>
> For the future, I guess the best approach is to change the Newick parser
> to set the tree name to None instead of "" by default. Any issues with that
> solution?
>
> -Eric
>
>
>
> On Sat, Dec 17, 2011 at 9:08 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>
>> Archaeopteryx is the one program that read the trees fine. I also tried
>> HyperTree, TreeGraph2, and Treevolution, which failed.
>>
>> -j
>>
>>
>> On Sun, Dec 18, 2011 at 12:03 AM, Eric Talevich <eric.talevich at gmail.com>wrote:
>>
>>> On Fri, Dec 16, 2011 at 1:44 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>>>
>>>> My XML trees exported in biopython (with confidence values, thanks
>>>> Eric!)
>>>> don't open in most XML tree viewing programs.
>>>>
>>>> The problem seems to be a spurious <name /> tag at the beginning of the
>>>> tree.
>>>>
>>>> <phy:phyloxml xmlns:phy="http://www.phyloxml.org">
>>>>  <phy:phylogeny rooted="false">
>>>>    <phy:name />
>>>>    <phy:clade>
>>>>
>>>> If I delete this tag they open fine.
>>>>
>>>>
>>> Hi Jon,
>>>
>>> Thanks for reporting this. I'll check the spec to see if an empty 'name'
>>> tag is even valid. Can you give me the name of one or two programs that are
>>> supposed to handle phyloXML, but don't like this input? Is Archaeopteryx
>>> one of them?
>>>
>>> -Eric
>>>
>>
>>
>>
>> --
>> "If you hold a cat by the tail you learn things you cannot learn any
>> other way."
>>                          --Mark Twain
>>
>>
>


-- 
"If you hold a cat by the tail you learn things you cannot learn any other
way."
                         --Mark Twain

From benjamin.ys.li at gmail.com  Tue Dec 20 03:25:00 2011
From: benjamin.ys.li at gmail.com (Benjamin Li)
Date: Tue, 20 Dec 2011 16:25:00 +0800
Subject: [Biopython] To do Blast alignment of two proteins by biopython
Message-ID: <CAAgdehyjEOVj6JA8rjYf1Xocc+9Q4w8TyFkCNMnudMGGF_T=zw@mail.gmail.com>

Hi all,

I have posted the same question on BioStar, but I think some of the
Biopython users may not check Biostar so I also post it to the mail list.

I am new to biopython and I am not sure if it is a stupid question.

I would like to perform the same task as the one can be done on the web
based blast.

I am trying to align two protein by providing their GIs and receive the
e-value. But I can only find examples to blast one protein in the biopython
tutorial.

How can I align two protein using the qblast function?

I have tried the command

result_handle = NCBIWWW.qblast("blastp", "pat", "330186","118881")

But it returns me a lot of alignments and a lot of e-values.

I also found that it takes a few minutes for my computer to complete the
query, where if I use the web based blast only takes a few seconds.

Is my query anything wrong?


Merry Christmas!

Benjamin Li

From p.j.a.cock at googlemail.com  Tue Dec 20 05:10:06 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 20 Dec 2011 10:10:06 +0000
Subject: [Biopython] To do Blast alignment of two proteins by biopython
In-Reply-To: <CAAgdehyjEOVj6JA8rjYf1Xocc+9Q4w8TyFkCNMnudMGGF_T=zw@mail.gmail.com>
References: <CAAgdehyjEOVj6JA8rjYf1Xocc+9Q4w8TyFkCNMnudMGGF_T=zw@mail.gmail.com>
Message-ID: <CAKVJ-_7jvNHsh2fnmkRJjeCBKw_jXGHxgx=xs-pSA8KRS67Jcw@mail.gmail.com>

On Tue, Dec 20, 2011 at 8:25 AM, Benjamin Li <benjamin.ys.li at gmail.com> wrote:
> Hi all,
>
> I have posted the same question on BioStar, but I think some of the
> Biopython users may not check Biostar so I also post it to the mail list.
>
> I am new to biopython and I am not sure if it is a stupid question.
>
> I would like to perform the same task as the one can be done on the web
> based blast.
>
> I am trying to align two protein by providing their GIs and receive the
> e-value. But I can only find examples to blast one protein in the biopython
> tutorial.
>
> How can I align two protein using the qblast function?

I don't think you can. The main BLAST webpage is actually very
advanced, doing things like trying to guide you with parameter
choices and so on. The QBLAST URL API is much simpler.
http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html

> I have tried the command
>
> result_handle = NCBIWWW.qblast("blastp", "pat", "330186","118881")
>
> But it returns me a lot of alignments and a lot of e-values.
>
> I also found that it takes a few minutes for my computer to complete the
> query, where if I use the web based blast only takes a few seconds.
>
> Is my query anything wrong?

Probably not. The Biopython qblast function uses a 3 second
delay between checking for results, which may partly explain
this. Also the NCBI may give priority to the website.

Have you considered downloading the sequences and running
standalone BLAST on your computer?

Peter

From member at linkedin.com  Sun Dec 25 16:36:34 2011
From: member at linkedin.com (Justinas Daugmaudis via LinkedIn)
Date: Sun, 25 Dec 2011 21:36:34 +0000 (UTC)
Subject: [Biopython] Invitation to connect on LinkedIn
Message-ID: <2000945239.20014961.1324848994821.JavaMail.app@ela4-app0130.prod>

LinkedIn
------------




    Justinas Daugmaudis requested to add you as a connection on LinkedIn:
  

------------------------------------------

Michele,

I'd like to add you to my professional network on LinkedIn.

- Justinas

Accept invitation from Justinas Daugmaudis
http://www.linkedin.com/e/l8bh8w-gwmkvuv5-4/qqAvDr0lR7bVZ5oUF-GdFl1c_dfVGAwasCwqz9Wv-gP/blk/I66984156_16/pmpxnSRJrSdvj4R5fnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_dz5vdzkNd3wVdzp9bQZKiCFvdCRDbPgTcPATc3cOcPkLrCBxbOYWrSlI/EML_comm_afe/?hs=false&tok=3Hoj7CCzUMXl01

View invitation from Justinas Daugmaudis
http://www.linkedin.com/e/l8bh8w-gwmkvuv5-4/qqAvDr0lR7bVZ5oUF-GdFl1c_dfVGAwasCwqz9Wv-gP/blk/I66984156_16/0SclYSdj4Qe3ASdAALqnpPbOYWrSlI/svi/?hs=false&tok=3kaJ0Zs-UMXl01 

------------------------------------------
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-- 
(c) 2011, LinkedIn Corporation

From mmokrejs at fold.natur.cuni.cz  Mon Dec 26 12:55:09 2011
From: mmokrejs at fold.natur.cuni.cz (Martin Mokrejs)
Date: Mon, 26 Dec 2011 18:55:09 +0100
Subject: [Biopython] GO parsers in biopython
Message-ID: <4EF8B4FD.6050601@fold.natur.cuni.cz>

Hi,
  I would like to parse some OBO/OWL files in python. I searched
for some existing code and found http://biopython.org/wiki/Gene_Ontology
pointing to some OWL parser from Ed Cannon (follow a link on the page
listed above). Unfortunately, the code is gone? :((

  I also discovered an OBO parser at http://hal.elte.hu/~nepusz/development,
the sources can be fetched from

http://bazaar.launchpad.net/~ntamas/+junk/go-parser/tarball/7?start_revid=7

  It can open the .obo files for me although I do not see much methods available.

  Finally, I found https://github.com/gotgenes/biopython/tree/a4824ceb71f3a687b3eb5e1fefd0ad3c278bf185/Bio/GO so my question is when will this be available in released biopython
and what are your opinions/suggestions now. Does it offer more than the
go-parser from ~ntamas?

  I want to cluster some sequences based on anatomical terms, so
I think what I want is to be able to lookup easily all parents
(probably except the very root node or so) and compare whether
they overlap with any parent of another sequence.

Thank you for your comments,
Martin
P.S.: I want to parse OBO from http://www.evocontology.org/

From eric.talevich at gmail.com  Mon Dec 26 15:34:28 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Mon, 26 Dec 2011 12:34:28 -0800
Subject: [Biopython] Bug in Phylo.write('phyloxml')?
In-Reply-To: <CALHM1CEYOEzc-MTJX9rDnjvN5fy7imYUVGH15C-=J3=z+_XeTQ@mail.gmail.com>
References: <CALHM1CEjeYomEiidxjS0UC0JLjGfqmx_GNbfHvtdYjGn1sk-OQ@mail.gmail.com>
	<CAMC681kgx14Bd+gfQwHZew9KYhn3+qJXzUvRrx9C8ddN7CzNHQ@mail.gmail.com>
	<CALHM1CFPurXY5U=qsu5=b0uHNVJoBs7eUus-aMsJ0YUdy6Hwog@mail.gmail.com>
	<CAMC681mSsQcMooQzGq_zmbxiH0b17wrRmdpNCq5yqcXa3H3avw@mail.gmail.com>
	<CALHM1CEYOEzc-MTJX9rDnjvN5fy7imYUVGH15C-=J3=z+_XeTQ@mail.gmail.com>
Message-ID: <CAMC681krw1cxjjNXfckOuA=4SbxD0GyaQOCP6i=BtyM82PmVqg@mail.gmail.com>

Here's the fix:
https://github.com/biopython/biopython/commit/85c3f5d35a0ae349cc35ea94754037f5c329b9b3

The 'name' attribute for clades already defaulted to None instead of the
empty string (""), so I think it was just an oversight that the Tree 'name'
attribute defaulted to "" before this patch.

That should fix your problem, Jon. I'm not so concerned about the empty
<name /> tag crashing other tree viewers because it's valid XML, it fits
the phyloXML spec, and Archaeopteryx accepts it. This patch should keep
that troublesome attribute value from arising inadvertently, though.


Cheers & best wishes,
Eric


On Mon, Dec 19, 2011 at 7:44 AM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:

> Yup, that seems to work just fine, and it's way easier and safer than
> writing a script to open the tree file and kill the tag, which is what I
> was going to do. Thanks again!
>
> -j
>
>
> On Mon, Dec 19, 2011 at 12:31 AM, Eric Talevich <eric.talevich at gmail.com>wrote:
>
>> Alrighty,
>>
>> I think the main problem in your case is that the Newick parser creates
>> trees with the 'name' attribute set to the empty string "" instead of None.
>> When converting to PhyloXML, that value stays in place and gets serialized
>> as an empty element. The author of the phyloXML spec is the author of
>> Archaeopteryx, so all of that makes sense.
>>
>> For your case, Jon, and others having this problem: before writing a tree
>> as phyloXML, set the tree name to None if it's not already named.
>>
>> if tree.name == "":
>>     tree.name = None
>> Phylo.write(tree, 'example.xml', 'newick')
>>
>>
>> For the future, I guess the best approach is to change the Newick parser
>> to set the tree name to None instead of "" by default. Any issues with that
>> solution?
>>
>> -Eric
>>
>>
>>
>> On Sat, Dec 17, 2011 at 9:08 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>>
>>> Archaeopteryx is the one program that read the trees fine. I also tried
>>> HyperTree, TreeGraph2, and Treevolution, which failed.
>>>
>>> -j
>>>
>>>
>>> On Sun, Dec 18, 2011 at 12:03 AM, Eric Talevich <eric.talevich at gmail.com
>>> > wrote:
>>>
>>>> On Fri, Dec 16, 2011 at 1:44 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>>>>
>>>>> My XML trees exported in biopython (with confidence values, thanks
>>>>> Eric!)
>>>>> don't open in most XML tree viewing programs.
>>>>>
>>>>> The problem seems to be a spurious <name /> tag at the beginning of the
>>>>> tree.
>>>>>
>>>>> <phy:phyloxml xmlns:phy="http://www.phyloxml.org">
>>>>>  <phy:phylogeny rooted="false">
>>>>>    <phy:name />
>>>>>    <phy:clade>
>>>>>
>>>>> If I delete this tag they open fine.
>>>>>
>>>>>
>>>> Hi Jon,
>>>>
>>>> Thanks for reporting this. I'll check the spec to see if an empty
>>>> 'name' tag is even valid. Can you give me the name of one or two programs
>>>> that are supposed to handle phyloXML, but don't like this input? Is
>>>> Archaeopteryx one of them?
>>>>
>>>> -Eric
>>>>
>>>
>>>
>>>
>>> --
>>> "If you hold a cat by the tail you learn things you cannot learn any
>>> other way."
>>>                          --Mark Twain
>>>
>>>
>>
>
>
> --
> "If you hold a cat by the tail you learn things you cannot learn any other
> way."
>                          --Mark Twain
>
>

From p.j.a.cock at googlemail.com  Thu Dec  1 08:52:43 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 1 Dec 2011 08:52:43 +0000
Subject: [Biopython] Generator expression for SeqIO
In-Reply-To: <CAOP6n=iFrLbs5OSRBc=gRfOkD1WavuA=ywXA6ueiZhqJsPGs_Q@mail.gmail.com>
References: <CAOP6n=jQSUDxy6SDM8KyMDX_Rz9SYCRO6fz4vdEpD_WCD9=CxA@mail.gmail.com>
	<CAKVJ-_5gxqJpWPD4m_q6_SQ4xSvzGXGXvHCfk40=--6RfT3fjg@mail.gmail.com>
	<CAOP6n=iFrLbs5OSRBc=gRfOkD1WavuA=ywXA6ueiZhqJsPGs_Q@mail.gmail.com>
Message-ID: <CAKVJ-_4SsJ1ekH1sdgDekgJB6SUPQyNj1geytkHmuerPCGJmsg@mail.gmail.com>

On Wednesday, November 30, 2011, Mic <mictadlo at gmail.com> wrote:
> Thank you it is working.
>

Excellent - sorry I couldn't think of a nice way to explain the syntax.

Peter


From jmtc21 at bath.ac.uk  Thu Dec  1 14:09:33 2011
From: jmtc21 at bath.ac.uk (Jaime Tovar)
Date: Thu, 01 Dec 2011 14:09:33 +0000
Subject: [Biopython] GTF to GFF using BCBio
In-Reply-To: <CAKVJ-_5gxqJpWPD4m_q6_SQ4xSvzGXGXvHCfk40=--6RfT3fjg@mail.gmail.com>
References: <CAOP6n=jQSUDxy6SDM8KyMDX_Rz9SYCRO6fz4vdEpD_WCD9=CxA@mail.gmail.com>
	<CAKVJ-_5gxqJpWPD4m_q6_SQ4xSvzGXGXvHCfk40=--6RfT3fjg@mail.gmail.com>
Message-ID: <4ED78A9D.4080306@bath.ac.uk>

Hello all,

I was trying to find an example on how to get a gff3 formated file from 
a gtf file using the BCBio library extensions for biopython. I the doc 
it only covers non-gff-family formats to gff3. I guess is just a 
parameter thing in the GFF writer but have been looking unsuccessfully 
for the answer. Any hint will be greatly appreciated.

Best regards,

J.


From jmtc21 at bath.ac.uk  Thu Dec  1 16:45:40 2011
From: jmtc21 at bath.ac.uk (Jaime Tovar)
Date: Thu, 01 Dec 2011 16:45:40 +0000
Subject: [Biopython] GTF to GFF using BCBio
In-Reply-To: <4ED78A9D.4080306@bath.ac.uk>
References: <CAOP6n=jQSUDxy6SDM8KyMDX_Rz9SYCRO6fz4vdEpD_WCD9=CxA@mail.gmail.com>
	<CAKVJ-_5gxqJpWPD4m_q6_SQ4xSvzGXGXvHCfk40=--6RfT3fjg@mail.gmail.com>
	<4ED78A9D.4080306@bath.ac.uk>
Message-ID: <4ED7AF34.8050707@bath.ac.uk>

Reply from BCBio library's author:

https://github.com/chapmanb/bcbb/blob/master/gff/Scripts/gff/gff2_to_gff3.py

and will cover GFF2/GTF files into GFF3.

J.

On 01/12/11 14:09, Jaime Tovar wrote:
> Hello all,
>
> I was trying to find an example on how to get a gff3 formated file 
> from a gtf file using the BCBio library extensions for biopython. I 
> the doc it only covers non-gff-family formats to gff3. I guess is just 
> a parameter thing in the GFF writer but have been looking 
> unsuccessfully for the answer. Any hint will be greatly appreciated.
>
> Best regards,
>
> J.
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



From daniel.svozil at vscht.cz  Tue Dec  6 11:39:35 2011
From: daniel.svozil at vscht.cz (Daniel Svozil)
Date: Tue, 6 Dec 2011 12:39:35 +0100
Subject: [Biopython] mmView - a tool for mmCIF exploration
In-Reply-To: <CAA6GQESfwp5oAD4KRR5x7FLmtoSa-F1KJ3fueDMNmrzg78vTqQ@mail.gmail.com>
References: <CAA6GQETVbUpUQr9TGZ_gL4GPZq0CKKn7q5jVuGXWjaDsuhOT0Q@mail.gmail.com>
	<CAA6GQERKcsa60JKmfrE-1bPGCUk8NBV9hd30n+Vxo-Yn-z3UuQ@mail.gmail.com>
	<CAA6GQETz8mCjh5QvdEpDLYP=r9TUdCiW68hD+KuvQzgaSGKBPw@mail.gmail.com>
	<CAA6GQEQ-qH3STt1=tz57Piz_TfdA1Xn58rR52sEwxKGFRYwnVQ@mail.gmail.com>
	<CAA6GQEQoGnL8S_yA8YVX0PPU1hOQjvf8_HKE8t8w6uKaopsOJg@mail.gmail.com>
	<CAA6GQEQmnuqRu1EHaUQ+o3+SR6NLguN9uXJbC-puVXak388wxg@mail.gmail.com>
	<CAA6GQESFwiV5_NYHjN+wX2v27bQCJvawk5bzVAOjF+9G5_A2bg@mail.gmail.com>
	<CAA6GQESfwp5oAD4KRR5x7FLmtoSa-F1KJ3fueDMNmrzg78vTqQ@mail.gmail.com>
Message-ID: <CAA6GQEQ46d+hEWbo3+U6H24aqf0OjFp=ZZzWvwxfLKra=s7X0w@mail.gmail.com>

Dear colleagues,

We would like to announce the availability of mmView - the web-based
application which allows to comfortably explore the structural data of
biomacromolecules stored in the mmCIF (macromolecular Crystallographic
Information File) format. The mmView software system is primarily
intended for educational purposes but it can also serve as an
auxiliary tool for working with biomolecular structures.

The mmView application is offered in two flavors: as a publicly
available web server http://ich.vscht.cz/projects/mmview/, and as an
open-source stand-alone application (available from
http://sourceforge.net/projects/mmview) that can be installed on the
user?s computer.

Petr Cech and Daniel Svozil

--
Daniel Svozil, PhD
Head of Laboratory of Informatics and Chemistry
Institute of Chemical Technology
Czech Republic

phone: +420 220 444 391
http://ich.vscht.cz/~svozil



From mictadlo at gmail.com  Wed Dec  7 04:41:25 2011
From: mictadlo at gmail.com (Mic)
Date: Wed, 7 Dec 2011 14:41:25 +1000
Subject: [Biopython] Generator expression for SeqIO
In-Reply-To: <CAKVJ-_4SsJ1ekH1sdgDekgJB6SUPQyNj1geytkHmuerPCGJmsg@mail.gmail.com>
References: <CAOP6n=jQSUDxy6SDM8KyMDX_Rz9SYCRO6fz4vdEpD_WCD9=CxA@mail.gmail.com>
	<CAKVJ-_5gxqJpWPD4m_q6_SQ4xSvzGXGXvHCfk40=--6RfT3fjg@mail.gmail.com>
	<CAOP6n=iFrLbs5OSRBc=gRfOkD1WavuA=ywXA6ueiZhqJsPGs_Q@mail.gmail.com>
	<CAKVJ-_4SsJ1ekH1sdgDekgJB6SUPQyNj1geytkHmuerPCGJmsg@mail.gmail.com>
Message-ID: <CAOP6n=ipFqLbb1VUj4PuOUBcO+ZTk6VuLBpPEFBQtRO7hdccDg@mail.gmail.com>

No worries is was perfect.

I have the following code and I do not know how to combine the *header* and
*seq* variables from the '*with*' statement with generator expression?

from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
from pprint import pprint

if __name__ == '__main__':

    *with* open('input.txt') as f:
        for line in f:
            try:
                splited_line = line.split('\t')

                *header* = splited_line[0] +'_'+ splited_line[2]
                *seq* = splited_line[3]
            except IndexError:
                continue

    fasta_file = open('output.fasta', 'w')
    records = (SeqRecord(???), id=????, description="") for i in ???)

    SeqIO.write(records, fasta_file, "fasta")

Thank you in advance.

On Thu, Dec 1, 2011 at 6:52 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

>
>
> On Wednesday, November 30, 2011, Mic <mictadlo at gmail.com> wrote:
> > Thank you it is working.
> >
>
> Excellent - sorry I couldn't think of a nice way to explain the syntax.
>
> Peter


From p.j.a.cock at googlemail.com  Wed Dec  7 08:26:08 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 7 Dec 2011 08:26:08 +0000
Subject: [Biopython] Generator expression for SeqIO
In-Reply-To: <CAOP6n=ipFqLbb1VUj4PuOUBcO+ZTk6VuLBpPEFBQtRO7hdccDg@mail.gmail.com>
References: <CAOP6n=jQSUDxy6SDM8KyMDX_Rz9SYCRO6fz4vdEpD_WCD9=CxA@mail.gmail.com>
	<CAKVJ-_5gxqJpWPD4m_q6_SQ4xSvzGXGXvHCfk40=--6RfT3fjg@mail.gmail.com>
	<CAOP6n=iFrLbs5OSRBc=gRfOkD1WavuA=ywXA6ueiZhqJsPGs_Q@mail.gmail.com>
	<CAKVJ-_4SsJ1ekH1sdgDekgJB6SUPQyNj1geytkHmuerPCGJmsg@mail.gmail.com>
	<CAOP6n=ipFqLbb1VUj4PuOUBcO+ZTk6VuLBpPEFBQtRO7hdccDg@mail.gmail.com>
Message-ID: <CAKVJ-_5Z=M2sC1Oz8PWbXb6L6TjJ4LZws-F1Nm_PpWa7TR9heA@mail.gmail.com>

On Wed, Dec 7, 2011 at 4:41 AM, Mic <mictadlo at gmail.com> wrote:
> No worries is was perfect.
>
> I have the following code and I do not know how to combine the *header* and
> *seq* variables from the '*with*' statement with generator expression?
>
> from Bio import SeqIO
> from Bio.SeqRecord import SeqRecord
> from Bio.Seq import Seq
> from pprint import pprint
>
> if __name__ == '__main__':
>
> ? ?*with* open('input.txt') as f:
> ? ? ? ?for line in f:
> ? ? ? ? ? ?try:
> ? ? ? ? ? ? ? ?splited_line = line.split('\t')
>
> ? ? ? ? ? ? ? ?*header* = splited_line[0] +'_'+ splited_line[2]
> ? ? ? ? ? ? ? ?*seq* = splited_line[3]
> ? ? ? ? ? ?except IndexError:
> ? ? ? ? ? ? ? ?continue
>
> ? ?fasta_file = open('output.fasta', 'w')
> ? ?records = (SeqRecord(???), id=????, description="") for i in ???)
>
> ? ?SeqIO.write(records, fasta_file, "fasta")
>
> Thank you in advance.

Are you trying to parse a tabular file, with three columns
(ID, sequence, description)?

I suggest you learn about generator functions in Python.

Peter



From jordan.r.willis at Vanderbilt.Edu  Wed Dec  7 08:49:06 2011
From: jordan.r.willis at Vanderbilt.Edu (Willis, Jordan R)
Date: Wed, 7 Dec 2011 02:49:06 -0600
Subject: [Biopython] Generator expression for SeqIO
In-Reply-To: <CAKVJ-_5Z=M2sC1Oz8PWbXb6L6TjJ4LZws-F1Nm_PpWa7TR9heA@mail.gmail.com>
References: <CAOP6n=jQSUDxy6SDM8KyMDX_Rz9SYCRO6fz4vdEpD_WCD9=CxA@mail.gmail.com>
	<CAKVJ-_5gxqJpWPD4m_q6_SQ4xSvzGXGXvHCfk40=--6RfT3fjg@mail.gmail.com>
	<CAOP6n=iFrLbs5OSRBc=gRfOkD1WavuA=ywXA6ueiZhqJsPGs_Q@mail.gmail.com>
	<CAKVJ-_4SsJ1ekH1sdgDekgJB6SUPQyNj1geytkHmuerPCGJmsg@mail.gmail.com>
	<CAOP6n=ipFqLbb1VUj4PuOUBcO+ZTk6VuLBpPEFBQtRO7hdccDg@mail.gmail.com>
	<CAKVJ-_5Z=M2sC1Oz8PWbXb6L6TjJ4LZws-F1Nm_PpWa7TR9heA@mail.gmail.com>
Message-ID: <1923E9B1-AA7B-49FA-8F63-F05642E948D7@vanderbilt.edu>

Does the input.txt have fasta sequences in it and you want to write them to a file? This is what it looks like.

from Bio import SeqIO as sio

generator = sio.read('input.txt','fasta')


for i in generator:
print i.header
print i.seq

will give you header and sequence. You could of course write this to a file, but you seem to be inputting a fasta file just to write out another one.




Jordan Willis
Ph.D Candidate, CPB
Laboratory of Dr. James Crowe and Dr. Jens Meiler
11475 MRBIV
2213 Garland Ave.
Nashville, TN 37232
Cell: 816-674-5340
Office: 615-343-8263


On Dec 7, 2011, at 12:26 AM, Peter Cock wrote:

On Wed, Dec 7, 2011 at 4:41 AM, Mic <mictadlo at gmail.com<mailto:mictadlo at gmail.com>> wrote:
No worries is was perfect.

I have the following code and I do not know how to combine the *header* and
*seq* variables from the '*with*' statement with generator expression?

from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
from pprint import pprint

if __name__ == '__main__':

   *with* open('input.txt') as f:
       for line in f:
           try:
               splited_line = line.split('\t')

               *header* = splited_line[0] +'_'+ splited_line[2]
               *seq* = splited_line[3]
           except IndexError:
               continue

   fasta_file = open('output.fasta', 'w')
   records = (SeqRecord(???), id=????, description="") for i in ???)

   SeqIO.write(records, fasta_file, "fasta")

Thank you in advance.

Are you trying to parse a tabular file, with three columns
(ID, sequence, description)?

I suggest you learn about generator functions in Python.

Peter

_______________________________________________
Biopython mailing list  -  Biopython at lists.open-bio.org<mailto:Biopython at lists.open-bio.org>
http://lists.open-bio.org/mailman/listinfo/biopython





From mictadlo at gmail.com  Wed Dec  7 13:11:24 2011
From: mictadlo at gmail.com (Mic)
Date: Wed, 7 Dec 2011 23:11:24 +1000
Subject: [Biopython] Generator expression for SeqIO
In-Reply-To: <1923E9B1-AA7B-49FA-8F63-F05642E948D7@vanderbilt.edu>
References: <CAOP6n=jQSUDxy6SDM8KyMDX_Rz9SYCRO6fz4vdEpD_WCD9=CxA@mail.gmail.com>
	<CAKVJ-_5gxqJpWPD4m_q6_SQ4xSvzGXGXvHCfk40=--6RfT3fjg@mail.gmail.com>
	<CAOP6n=iFrLbs5OSRBc=gRfOkD1WavuA=ywXA6ueiZhqJsPGs_Q@mail.gmail.com>
	<CAKVJ-_4SsJ1ekH1sdgDekgJB6SUPQyNj1geytkHmuerPCGJmsg@mail.gmail.com>
	<CAOP6n=ipFqLbb1VUj4PuOUBcO+ZTk6VuLBpPEFBQtRO7hdccDg@mail.gmail.com>
	<CAKVJ-_5Z=M2sC1Oz8PWbXb6L6TjJ4LZws-F1Nm_PpWa7TR9heA@mail.gmail.com>
	<1923E9B1-AA7B-49FA-8F63-F05642E948D7@vanderbilt.edu>
Message-ID: <CAOP6n=hv1y80X4syQJbPFjwk+F0Y_SRPTQwEPddacKzY4k9NUw@mail.gmail.com>

Thank you for the solution.

My input files is not exactly a FASTA file, but it contains information to
build it. The file looks like this:
test1\t0001\a1\tAATTCC

Output should looks like:
>test1_a1
AATTCC


On Wed, Dec 7, 2011 at 6:49 PM, Willis, Jordan R <
jordan.r.willis at vanderbilt.edu> wrote:

> Does the input.txt have fasta sequences in it and you want to write them
> to a file? This is what it looks like.
>
> from Bio import SeqIO as sio
>
> generator = sio.read('input.txt','fasta')
>
>
> for i in generator:
> print i.header
> print i.seq
>
> will give you header and sequence. You could of course write this to a
> file, but you seem to be inputting a fasta file just to write out another
> one.
>
>
>
>
> Jordan Willis
> Ph.D Candidate, CPB
> Laboratory of Dr. James Crowe and Dr. Jens Meiler
> 11475 MRBIV
> 2213 Garland Ave.
> Nashville, TN 37232
> Cell: 816-674-5340
> Office: 615-343-8263
>
>
> On Dec 7, 2011, at 12:26 AM, Peter Cock wrote:
>
> On Wed, Dec 7, 2011 at 4:41 AM, Mic <mictadlo at gmail.com> wrote:
>
> No worries is was perfect.
>
>
> I have the following code and I do not know how to combine the *header* and
>
> *seq* variables from the '*with*' statement with generator expression?
>
>
> from Bio import SeqIO
>
> from Bio.SeqRecord import SeqRecord
>
> from Bio.Seq import Seq
>
> from pprint import pprint
>
>
> if __name__ == '__main__':
>
>
>    *with* open('input.txt') as f:
>
>        for line in f:
>
>            try:
>
>                splited_line = line.split('\t')
>
>
>                *header* = splited_line[0] +'_'+ splited_line[2]
>
>                *seq* = splited_line[3]
>
>            except IndexError:
>
>                continue
>
>
>    fasta_file = open('output.fasta', 'w')
>
>    records = (SeqRecord(???), id=????, description="") for i in ???)
>
>
>    SeqIO.write(records, fasta_file, "fasta")
>
>
> Thank you in advance.
>
>
> Are you trying to parse a tabular file, with three columns
> (ID, sequence, description)?
>
> I suggest you learn about generator functions in Python.
>
> Peter
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>
>


From eric.talevich at gmail.com  Wed Dec  7 16:07:57 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Wed, 7 Dec 2011 11:07:57 -0500
Subject: [Biopython] Generator expression for SeqIO
In-Reply-To: <CAOP6n=ipFqLbb1VUj4PuOUBcO+ZTk6VuLBpPEFBQtRO7hdccDg@mail.gmail.com>
References: <CAOP6n=jQSUDxy6SDM8KyMDX_Rz9SYCRO6fz4vdEpD_WCD9=CxA@mail.gmail.com>
	<CAKVJ-_5gxqJpWPD4m_q6_SQ4xSvzGXGXvHCfk40=--6RfT3fjg@mail.gmail.com>
	<CAOP6n=iFrLbs5OSRBc=gRfOkD1WavuA=ywXA6ueiZhqJsPGs_Q@mail.gmail.com>
	<CAKVJ-_4SsJ1ekH1sdgDekgJB6SUPQyNj1geytkHmuerPCGJmsg@mail.gmail.com>
	<CAOP6n=ipFqLbb1VUj4PuOUBcO+ZTk6VuLBpPEFBQtRO7hdccDg@mail.gmail.com>
Message-ID: <CAMC681nGT5kXDjf4AecLrUgSTREdqPM8ttTFq_pYEyQZ==kcsg@mail.gmail.com>

Mic,

You don't really need a generator expression here, but I recommend that you
read the Python Tutorial to learn how to use them anyway.

To solve your problem, here's one solution using Biopython and a list
comprehension (like a generator expression, but more your pace):

def row_to_seqrecord(row):
    """Convert a tab-delimited row to a SeqRecord.

    Row looks like:
    test1\t0001\a1\tAATTCC

    Record looks like (conceptually):
    >test1_a1
    AATTCC
    """
    cells = [cell.strip() for cell in row.split('\t')]
    return SeqRecord(Seq(cells[3]), id=cells[0] + '_' + cells[2])

with open('input.txt') as infile:
    records = [row_to_seqrecord(line) for line in infile]

SeqIO.write(records, 'output.txt', 'fasta')


But the nice thing about FASTA format is that there's almost no structure
to it. Here's a simpler way to do it that doesn't use Biopython:

with open('input.txt') as infile:
    with open('output.fasta', 'w+') as outfile:
        for line in infile:
            parts = [part.strip() for part in line.split('\t')]
            if len(parts) != 4:
                continue
            # Header
            outfile.write(">%s_%s\n" % (parts[0], parts[2])
            # Sequence
            outfile.write(parts[3] + '\n')



On Tue, Dec 6, 2011 at 11:41 PM, Mic <mictadlo at gmail.com> wrote:

> No worries is was perfect.
>
> I have the following code and I do not know how to combine the *header* and
> *seq* variables from the '*with*' statement with generator expression?
>
> from Bio import SeqIO
> from Bio.SeqRecord import SeqRecord
> from Bio.Seq import Seq
> from pprint import pprint
>
> if __name__ == '__main__':
>
>    *with* open('input.txt') as f:
>        for line in f:
>            try:
>                splited_line = line.split('\t')
>
>                *header* = splited_line[0] +'_'+ splited_line[2]
>                *seq* = splited_line[3]
>            except IndexError:
>                continue
>
>    fasta_file = open('output.fasta', 'w')
>    records = (SeqRecord(???), id=????, description="") for i in ???)
>
>    SeqIO.write(records, fasta_file, "fasta")
>
> Thank you in advance.
>
> On Thu, Dec 1, 2011 at 6:52 PM, Peter Cock <p.j.a.cock at googlemail.com
> >wrote:
>
> >
> >
> > On Wednesday, November 30, 2011, Mic <mictadlo at gmail.com> wrote:
> > > Thank you it is working.
> > >
> >
> > Excellent - sorry I couldn't think of a nice way to explain the syntax.
> >
> > Peter
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>


From jsanders at oeb.harvard.edu  Fri Dec  9 21:53:12 2011
From: jsanders at oeb.harvard.edu (Jon Sanders)
Date: Fri, 9 Dec 2011 16:53:12 -0500
Subject: [Biopython] help with confidence values on PhyloXML tree objects?
Message-ID: <CALHM1CE0Nu2AVqf2R32GhTHiW2aPfXNcPFAf2XCCY89bWhGC-g@mail.gmail.com>

So I have two problems.


Problem 1: when importing my newick-formatted trees, which were generated
in PyCogent, the terminal labels and branch labels are read in as
confidence values because they're numerical. So

    ((((41:0.01494,44:0.00014)0.604:0...

is read in with blank name='' values and 41, 44, 0.605, etc. as
'confidence' values.



Problem 2: I would like to store multiple confidence values per node, but I
can't figure out how to do it.

I can get the plain old 'confidence' attribute set by:

   clade.confidence = .05

but can't figure out how to add and set new confidence types. Any
suggestions?


Much appreciated,
-jon


-- 
"If you hold a cat by the tail you learn things you cannot learn any other
way."
                         --Mark Twain


From eric.talevich at gmail.com  Fri Dec  9 23:26:46 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Fri, 9 Dec 2011 18:26:46 -0500
Subject: [Biopython] help with confidence values on PhyloXML tree
	objects?
In-Reply-To: <CALHM1CE0Nu2AVqf2R32GhTHiW2aPfXNcPFAf2XCCY89bWhGC-g@mail.gmail.com>
References: <CALHM1CE0Nu2AVqf2R32GhTHiW2aPfXNcPFAf2XCCY89bWhGC-g@mail.gmail.com>
Message-ID: <CAMC681nxCD9L9pA+_6A5GfhXpK8fzvVDPyyc9aH9QXemRDRPqw@mail.gmail.com>

Hi Jon,

On Fri, Dec 9, 2011 at 4:53 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:

> So I have two problems.
>
>
> Problem 1: when importing my newick-formatted trees, which were generated
> in PyCogent, the terminal labels and branch labels are read in as
> confidence values because they're numerical. So
>
>    ((((41:0.01494,44:0.00014)0.604:0...
>
> is read in with blank name='' values and 41, 44, 0.605, etc. as
> 'confidence' values.
>

Hmm, I'll take a look at the Newick parser. I think I've used numeric taxon
labels before without a problem, but PyCogent wasn't involved.

It might work if you can coax PyCogent into writing the Newick files with
an extra colon:
((((:41:0.01494,:44:0.00014):0.604:0...



> Problem 2: I would like to store multiple confidence values per node, but I
> can't figure out how to do it.
>
> I can get the plain old 'confidence' attribute set by:
>
>   clade.confidence = .05
>
> but can't figure out how to add and set new confidence types. Any
> suggestions?
>

The confidence types are instances of the Bio.Phylo.PhyloXML.Confidence
class.

In PhyloXML trees, the attribute "clade.confidence" is actually a Python
property pointing to the first element of "clade.confidences", a list of
Confidence objects. It's syntax sugar to keep compatibility with Newick,
which just has a numeric value there.

You can use it like this:

from Bio.Phylo import PhyloXML

# Create new Confidence instances
a_bootstrap_value = PhyloXML.Confidence(83, type="bootstrap")
# The second argument is optional
a_posterior_probability = PhyloXML.Confidence(0.99)

# Select a clade from your tree to modify
a_clade = mytree.clade[...]

# Modify the list of Confidences directly
a_clade.confidences.append(a_bootstrap_value)
a_clade.confidences.append(a_posterior_probability)


If you've assigned multiple confidence values to a clade, using the
PhyloXML class, then the "clade.confidence" shortcut won't work anymore
because it's not clear which confidence you mean. So you'll have to use
e.g. clade.confidences[0] or clade.confidences[1], and save it the tree in
PhyloXML format to preserve the extra data.

Hope that helps.

Best regards,
Eric


From jsanders at oeb.harvard.edu  Tue Dec 13 18:17:09 2011
From: jsanders at oeb.harvard.edu (Jon Sanders)
Date: Tue, 13 Dec 2011 13:17:09 -0500
Subject: [Biopython] help with confidence values on PhyloXML tree
	objects?
In-Reply-To: <CAMC681nxCD9L9pA+_6A5GfhXpK8fzvVDPyyc9aH9QXemRDRPqw@mail.gmail.com>
References: <CALHM1CE0Nu2AVqf2R32GhTHiW2aPfXNcPFAf2XCCY89bWhGC-g@mail.gmail.com>
	<CAMC681nxCD9L9pA+_6A5GfhXpK8fzvVDPyyc9aH9QXemRDRPqw@mail.gmail.com>
Message-ID: <CALHM1CGv4=UMOPjNhSXm+U9BWd_fbMQZQ=SYw3oYhH0yJLB70Q@mail.gmail.com>

Thanks Eric! I got the hang of the PhyloXML confidence objects now, so
that's straightened out.

Still having issues with the tree parsing. I tried throwing in extra colons
with a regex, both before and after the tip/edge label, but that didn't
change the behavior of the parser, and all the tip/edge labels were still
imported as confidence values. Poking around some documentation on the
newick format, it seems like the edge labels might be tricking the parser
into thinking there are confidence values present, since there's no clear
way to distinguish between them. I'll try playing around with supressing
the edge labels in PyCogent and see if I can't pass a decent tree to
BioPython side for proper PhyloXML output.

Ugh.

-j

On Fri, Dec 9, 2011 at 6:26 PM, Eric Talevich <eric.talevich at gmail.com>wrote:

> Hi Jon,
>
> On Fri, Dec 9, 2011 at 4:53 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>
>> So I have two problems.
>>
>>
>> Problem 1: when importing my newick-formatted trees, which were generated
>> in PyCogent, the terminal labels and branch labels are read in as
>> confidence values because they're numerical. So
>>
>>    ((((41:0.01494,44:0.00014)0.604:0...
>>
>> is read in with blank name='' values and 41, 44, 0.605, etc. as
>> 'confidence' values.
>>
>
> Hmm, I'll take a look at the Newick parser. I think I've used numeric
> taxon labels before without a problem, but PyCogent wasn't involved.
>
> It might work if you can coax PyCogent into writing the Newick files with
> an extra colon:
> ((((:41:0.01494,:44:0.00014):0.604:0...
>
>
>
>> Problem 2: I would like to store multiple confidence values per node, but
>> I
>> can't figure out how to do it.
>>
>> I can get the plain old 'confidence' attribute set by:
>>
>>   clade.confidence = .05
>>
>> but can't figure out how to add and set new confidence types. Any
>> suggestions?
>>
>
> The confidence types are instances of the Bio.Phylo.PhyloXML.Confidence
> class.
>
> In PhyloXML trees, the attribute "clade.confidence" is actually a Python
> property pointing to the first element of "clade.confidences", a list of
> Confidence objects. It's syntax sugar to keep compatibility with Newick,
> which just has a numeric value there.
>
> You can use it like this:
>
> from Bio.Phylo import PhyloXML
>
> # Create new Confidence instances
> a_bootstrap_value = PhyloXML.Confidence(83, type="bootstrap")
> # The second argument is optional
> a_posterior_probability = PhyloXML.Confidence(0.99)
>
> # Select a clade from your tree to modify
> a_clade = mytree.clade[...]
>
> # Modify the list of Confidences directly
> a_clade.confidences.append(a_bootstrap_value)
> a_clade.confidences.append(a_posterior_probability)
>
>
> If you've assigned multiple confidence values to a clade, using the
> PhyloXML class, then the "clade.confidence" shortcut won't work anymore
> because it's not clear which confidence you mean. So you'll have to use
> e.g. clade.confidences[0] or clade.confidences[1], and save it the tree in
> PhyloXML format to preserve the extra data.
>
> Hope that helps.
>
> Best regards,
> Eric
>



-- 
"If you hold a cat by the tail you learn things you cannot learn any other
way."
                         --Mark Twain


From jsanders at oeb.harvard.edu  Tue Dec 13 18:55:20 2011
From: jsanders at oeb.harvard.edu (Jon Sanders)
Date: Tue, 13 Dec 2011 13:55:20 -0500
Subject: [Biopython] help with confidence values on PhyloXML tree
	objects?
In-Reply-To: <CALHM1CGv4=UMOPjNhSXm+U9BWd_fbMQZQ=SYw3oYhH0yJLB70Q@mail.gmail.com>
References: <CALHM1CE0Nu2AVqf2R32GhTHiW2aPfXNcPFAf2XCCY89bWhGC-g@mail.gmail.com>
	<CAMC681nxCD9L9pA+_6A5GfhXpK8fzvVDPyyc9aH9QXemRDRPqw@mail.gmail.com>
	<CALHM1CGv4=UMOPjNhSXm+U9BWd_fbMQZQ=SYw3oYhH0yJLB70Q@mail.gmail.com>
Message-ID: <CALHM1CECo+233yRCus4CHxqRUhzAq7qZM1HYcefs0vM5AFjH_g@mail.gmail.com>

Update: yup, seems to be a problem with numeric tip names.

1) getting rid of internal edge name doesn't help
2) appending 'a' to tip names fixes it
3) this tree: (((1,2),(3,4)),5); loads the numeric tip names as branch
lengths
4) this tree: (((1:0.01,2:0.01):0.01,(3:0.01,4:0.01):0.01):0.01,5:0.03);
loads the numeric tip names as confidence values and branch lenghts
correctly

I might try poking around the parser too, although my python foo has little
bar.

-j

On Tue, Dec 13, 2011 at 1:17 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:

> Thanks Eric! I got the hang of the PhyloXML confidence objects now, so
> that's straightened out.
>
> Still having issues with the tree parsing. I tried throwing in extra
> colons with a regex, both before and after the tip/edge label, but that
> didn't change the behavior of the parser, and all the tip/edge labels were
> still imported as confidence values. Poking around some documentation on
> the newick format, it seems like the edge labels might be tricking the
> parser into thinking there are confidence values present, since there's no
> clear way to distinguish between them. I'll try playing around with
> supressing the edge labels in PyCogent and see if I can't pass a decent
> tree to BioPython side for proper PhyloXML output.
>
> Ugh.
>
> -j
>
>
> On Fri, Dec 9, 2011 at 6:26 PM, Eric Talevich <eric.talevich at gmail.com>wrote:
>
>> Hi Jon,
>>
>> On Fri, Dec 9, 2011 at 4:53 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>>
>>> So I have two problems.
>>>
>>>
>>> Problem 1: when importing my newick-formatted trees, which were generated
>>> in PyCogent, the terminal labels and branch labels are read in as
>>> confidence values because they're numerical. So
>>>
>>>    ((((41:0.01494,44:0.00014)0.604:0...
>>>
>>> is read in with blank name='' values and 41, 44, 0.605, etc. as
>>> 'confidence' values.
>>>
>>
>> Hmm, I'll take a look at the Newick parser. I think I've used numeric
>> taxon labels before without a problem, but PyCogent wasn't involved.
>>
>> It might work if you can coax PyCogent into writing the Newick files with
>> an extra colon:
>> ((((:41:0.01494,:44:0.00014):0.604:0...
>>
>>
>>
>>> Problem 2: I would like to store multiple confidence values per node,
>>> but I
>>> can't figure out how to do it.
>>>
>>> I can get the plain old 'confidence' attribute set by:
>>>
>>>   clade.confidence = .05
>>>
>>> but can't figure out how to add and set new confidence types. Any
>>> suggestions?
>>>
>>
>> The confidence types are instances of the Bio.Phylo.PhyloXML.Confidence
>> class.
>>
>> In PhyloXML trees, the attribute "clade.confidence" is actually a Python
>> property pointing to the first element of "clade.confidences", a list of
>> Confidence objects. It's syntax sugar to keep compatibility with Newick,
>> which just has a numeric value there.
>>
>> You can use it like this:
>>
>> from Bio.Phylo import PhyloXML
>>
>> # Create new Confidence instances
>> a_bootstrap_value = PhyloXML.Confidence(83, type="bootstrap")
>> # The second argument is optional
>> a_posterior_probability = PhyloXML.Confidence(0.99)
>>
>> # Select a clade from your tree to modify
>> a_clade = mytree.clade[...]
>>
>> # Modify the list of Confidences directly
>> a_clade.confidences.append(a_bootstrap_value)
>> a_clade.confidences.append(a_posterior_probability)
>>
>>
>> If you've assigned multiple confidence values to a clade, using the
>> PhyloXML class, then the "clade.confidence" shortcut won't work anymore
>> because it's not clear which confidence you mean. So you'll have to use
>> e.g. clade.confidences[0] or clade.confidences[1], and save it the tree in
>> PhyloXML format to preserve the extra data.
>>
>> Hope that helps.
>>
>> Best regards,
>> Eric
>>
>
>
>
> --
> "If you hold a cat by the tail you learn things you cannot learn any other
> way."
>                          --Mark Twain
>
>


-- 
"If you hold a cat by the tail you learn things you cannot learn any other
way."
                         --Mark Twain


From eric.talevich at gmail.com  Tue Dec 13 22:28:11 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Tue, 13 Dec 2011 17:28:11 -0500
Subject: [Biopython] help with confidence values on PhyloXML tree
	objects?
In-Reply-To: <CALHM1CECo+233yRCus4CHxqRUhzAq7qZM1HYcefs0vM5AFjH_g@mail.gmail.com>
References: <CALHM1CE0Nu2AVqf2R32GhTHiW2aPfXNcPFAf2XCCY89bWhGC-g@mail.gmail.com>
	<CAMC681nxCD9L9pA+_6A5GfhXpK8fzvVDPyyc9aH9QXemRDRPqw@mail.gmail.com>
	<CALHM1CGv4=UMOPjNhSXm+U9BWd_fbMQZQ=SYw3oYhH0yJLB70Q@mail.gmail.com>
	<CALHM1CECo+233yRCus4CHxqRUhzAq7qZM1HYcefs0vM5AFjH_g@mail.gmail.com>
Message-ID: <CAMC681nG8ThRvAXCzRSAwn0TnzpH47AG99+8TvHTYjrBCug1NQ@mail.gmail.com>

On Tue, Dec 13, 2011 at 1:55 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:

> Update: yup, seems to be a problem with numeric tip names.
>
> 1) getting rid of internal edge name doesn't help
> 2) appending 'a' to tip names fixes it
> 3) this tree: (((1,2),(3,4)),5); loads the numeric tip names as branch
> lengths
> 4) this tree: (((1:0.01,2:0.01):0.01,(3:0.01,4:0.01):0.01):0.01,5:0.03);
> loads the numeric tip names as confidence values and branch lenghts
> correctly
>
> I might try poking around the parser too, although my python foo has
> little bar.
>
> -j
>

All right, sounds like you've got it working then -- thanks for sharing
your investigations. Looking back at my own work, I see that when I used
numbered taxon labels earlier, I prefixed them with the letter "t"; I never
actually used plain integers, so I didn't hit this issue. For now, I
suppose your best bet is to temporarily add a letter prefix or suffix to
the names when transferring between PyCogent and Biopython.

According to the spec for the Nexus format (
http://www.ncbi.nlm.nih.gov/pubmed/11975335), which includes Newick,
all-numeric taxon names are illegal. So, I suppose the Biopython parser's
behavior is technically correct -- at least for parsing the tree section of
Nexus files.

In any case, this behavior is surprising and at least deserves a mention in
a docstring or an error message. I'll try to take a look at PyCogent's
parser to see how they handle ambiguous cases like the ones you listed.

-E


On Fri, Dec 9, 2011 at 6:26 PM, Eric Talevich <eric.talevich at gmail.com>wrote:
>
>> Hi Jon,
>>
>> On Fri, Dec 9, 2011 at 4:53 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>>
>>> So I have two problems.
>>>
>>>
>>> Problem 1: when importing my newick-formatted trees, which were generated
>>> in PyCogent, the terminal labels and branch labels are read in as
>>> confidence values because they're numerical. So
>>>
>>>    ((((41:0.01494,44:0.00014)0.604:0...
>>>
>>> is read in with blank name='' values and 41, 44, 0.605, etc. as
>>> 'confidence' values.
>>>
>>
>> Hmm, I'll take a look at the Newick parser. I think I've used numeric
>> taxon labels before without a problem, but PyCogent wasn't involved.
>>
>> It might work if you can coax PyCogent into writing the Newick files with
>> an extra colon:
>> ((((:41:0.01494,:44:0.00014):0.604:0...
>>
>>
>>
>>> Problem 2: I would like to store multiple confidence values per node,
>>> but I
>>> can't figure out how to do it.
>>>
>>> I can get the plain old 'confidence' attribute set by:
>>>
>>>   clade.confidence = .05
>>>
>>> but can't figure out how to add and set new confidence types. Any
>>> suggestions?
>>>
>>
>> The confidence types are instances of the Bio.Phylo.PhyloXML.Confidence
>> class.
>>
>> In PhyloXML trees, the attribute "clade.confidence" is actually a Python
>> property pointing to the first element of "clade.confidences", a list of
>> Confidence objects. It's syntax sugar to keep compatibility with Newick,
>> which just has a numeric value there.
>>
>> You can use it like this:
>>
>> from Bio.Phylo import PhyloXML
>>
>> # Create new Confidence instances
>> a_bootstrap_value = PhyloXML.Confidence(83, type="bootstrap")
>> # The second argument is optional
>> a_posterior_probability = PhyloXML.Confidence(0.99)
>>
>> # Select a clade from your tree to modify
>> a_clade = mytree.clade[...]
>>
>> # Modify the list of Confidences directly
>> a_clade.confidences.append(a_bootstrap_value)
>> a_clade.confidences.append(a_posterior_probability)
>>
>>
>> If you've assigned multiple confidence values to a clade, using the
>> PhyloXML class, then the "clade.confidence" shortcut won't work anymore
>> because it's not clear which confidence you mean. So you'll have to use
>> e.g. clade.confidences[0] or clade.confidences[1], and save it the tree in
>> PhyloXML format to preserve the extra data.
>>
>> Hope that helps.
>>
>> Best regards,
>> Eric
>>
>
>


From jsanders at oeb.harvard.edu  Fri Dec 16 18:44:07 2011
From: jsanders at oeb.harvard.edu (Jon Sanders)
Date: Fri, 16 Dec 2011 13:44:07 -0500
Subject: [Biopython] Bug in Phylo.write('phyloxml')?
Message-ID: <CALHM1CEjeYomEiidxjS0UC0JLjGfqmx_GNbfHvtdYjGn1sk-OQ@mail.gmail.com>

My XML trees exported in biopython (with confidence values, thanks Eric!)
don't open in most XML tree viewing programs.

The problem seems to be a spurious <name /> tag at the beginning of the
tree.

<phy:phyloxml xmlns:phy="http://www.phyloxml.org">
  <phy:phylogeny rooted="false">
    <phy:name />
    <phy:clade>

If I delete this tag they open fine.


-- 
"If you hold a cat by the tail you learn things you cannot learn any other
way."
                         --Mark Twain


From eric.talevich at gmail.com  Sun Dec 18 05:03:51 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Sun, 18 Dec 2011 00:03:51 -0500
Subject: [Biopython] Bug in Phylo.write('phyloxml')?
In-Reply-To: <CALHM1CEjeYomEiidxjS0UC0JLjGfqmx_GNbfHvtdYjGn1sk-OQ@mail.gmail.com>
References: <CALHM1CEjeYomEiidxjS0UC0JLjGfqmx_GNbfHvtdYjGn1sk-OQ@mail.gmail.com>
Message-ID: <CAMC681kgx14Bd+gfQwHZew9KYhn3+qJXzUvRrx9C8ddN7CzNHQ@mail.gmail.com>

On Fri, Dec 16, 2011 at 1:44 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:

> My XML trees exported in biopython (with confidence values, thanks Eric!)
> don't open in most XML tree viewing programs.
>
> The problem seems to be a spurious <name /> tag at the beginning of the
> tree.
>
> <phy:phyloxml xmlns:phy="http://www.phyloxml.org">
>  <phy:phylogeny rooted="false">
>    <phy:name />
>    <phy:clade>
>
> If I delete this tag they open fine.
>
>
Hi Jon,

Thanks for reporting this. I'll check the spec to see if an empty 'name'
tag is even valid. Can you give me the name of one or two programs that are
supposed to handle phyloXML, but don't like this input? Is Archaeopteryx
one of them?

-Eric


From jsanders at oeb.harvard.edu  Sun Dec 18 05:08:14 2011
From: jsanders at oeb.harvard.edu (Jon Sanders)
Date: Sun, 18 Dec 2011 00:08:14 -0500
Subject: [Biopython] Bug in Phylo.write('phyloxml')?
In-Reply-To: <CAMC681kgx14Bd+gfQwHZew9KYhn3+qJXzUvRrx9C8ddN7CzNHQ@mail.gmail.com>
References: <CALHM1CEjeYomEiidxjS0UC0JLjGfqmx_GNbfHvtdYjGn1sk-OQ@mail.gmail.com>
	<CAMC681kgx14Bd+gfQwHZew9KYhn3+qJXzUvRrx9C8ddN7CzNHQ@mail.gmail.com>
Message-ID: <CALHM1CFPurXY5U=qsu5=b0uHNVJoBs7eUus-aMsJ0YUdy6Hwog@mail.gmail.com>

Archaeopteryx is the one program that read the trees fine. I also tried
HyperTree, TreeGraph2, and Treevolution, which failed.

-j

On Sun, Dec 18, 2011 at 12:03 AM, Eric Talevich <eric.talevich at gmail.com>wrote:

> On Fri, Dec 16, 2011 at 1:44 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>
>> My XML trees exported in biopython (with confidence values, thanks Eric!)
>> don't open in most XML tree viewing programs.
>>
>> The problem seems to be a spurious <name /> tag at the beginning of the
>> tree.
>>
>> <phy:phyloxml xmlns:phy="http://www.phyloxml.org">
>>  <phy:phylogeny rooted="false">
>>    <phy:name />
>>    <phy:clade>
>>
>> If I delete this tag they open fine.
>>
>>
> Hi Jon,
>
> Thanks for reporting this. I'll check the spec to see if an empty 'name'
> tag is even valid. Can you give me the name of one or two programs that are
> supposed to handle phyloXML, but don't like this input? Is Archaeopteryx
> one of them?
>
> -Eric
>



-- 
"If you hold a cat by the tail you learn things you cannot learn any other
way."
                         --Mark Twain


From eric.talevich at gmail.com  Mon Dec 19 05:31:48 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Sun, 18 Dec 2011 21:31:48 -0800
Subject: [Biopython] Bug in Phylo.write('phyloxml')?
In-Reply-To: <CALHM1CFPurXY5U=qsu5=b0uHNVJoBs7eUus-aMsJ0YUdy6Hwog@mail.gmail.com>
References: <CALHM1CEjeYomEiidxjS0UC0JLjGfqmx_GNbfHvtdYjGn1sk-OQ@mail.gmail.com>
	<CAMC681kgx14Bd+gfQwHZew9KYhn3+qJXzUvRrx9C8ddN7CzNHQ@mail.gmail.com>
	<CALHM1CFPurXY5U=qsu5=b0uHNVJoBs7eUus-aMsJ0YUdy6Hwog@mail.gmail.com>
Message-ID: <CAMC681mSsQcMooQzGq_zmbxiH0b17wrRmdpNCq5yqcXa3H3avw@mail.gmail.com>

Alrighty,

I think the main problem in your case is that the Newick parser creates
trees with the 'name' attribute set to the empty string "" instead of None.
When converting to PhyloXML, that value stays in place and gets serialized
as an empty element. The author of the phyloXML spec is the author of
Archaeopteryx, so all of that makes sense.

For your case, Jon, and others having this problem: before writing a tree
as phyloXML, set the tree name to None if it's not already named.

if tree.name == "":
    tree.name = None
Phylo.write(tree, 'example.xml', 'newick')


For the future, I guess the best approach is to change the Newick parser to
set the tree name to None instead of "" by default. Any issues with that
solution?

-Eric


On Sat, Dec 17, 2011 at 9:08 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:

> Archaeopteryx is the one program that read the trees fine. I also tried
> HyperTree, TreeGraph2, and Treevolution, which failed.
>
> -j
>
>
> On Sun, Dec 18, 2011 at 12:03 AM, Eric Talevich <eric.talevich at gmail.com>wrote:
>
>> On Fri, Dec 16, 2011 at 1:44 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>>
>>> My XML trees exported in biopython (with confidence values, thanks Eric!)
>>> don't open in most XML tree viewing programs.
>>>
>>> The problem seems to be a spurious <name /> tag at the beginning of the
>>> tree.
>>>
>>> <phy:phyloxml xmlns:phy="http://www.phyloxml.org">
>>>  <phy:phylogeny rooted="false">
>>>    <phy:name />
>>>    <phy:clade>
>>>
>>> If I delete this tag they open fine.
>>>
>>>
>> Hi Jon,
>>
>> Thanks for reporting this. I'll check the spec to see if an empty 'name'
>> tag is even valid. Can you give me the name of one or two programs that are
>> supposed to handle phyloXML, but don't like this input? Is Archaeopteryx
>> one of them?
>>
>> -Eric
>>
>
>
>
> --
> "If you hold a cat by the tail you learn things you cannot learn any other
> way."
>                          --Mark Twain
>
>


From jsanders at oeb.harvard.edu  Mon Dec 19 15:44:51 2011
From: jsanders at oeb.harvard.edu (Jon Sanders)
Date: Mon, 19 Dec 2011 10:44:51 -0500
Subject: [Biopython] Bug in Phylo.write('phyloxml')?
In-Reply-To: <CAMC681mSsQcMooQzGq_zmbxiH0b17wrRmdpNCq5yqcXa3H3avw@mail.gmail.com>
References: <CALHM1CEjeYomEiidxjS0UC0JLjGfqmx_GNbfHvtdYjGn1sk-OQ@mail.gmail.com>
	<CAMC681kgx14Bd+gfQwHZew9KYhn3+qJXzUvRrx9C8ddN7CzNHQ@mail.gmail.com>
	<CALHM1CFPurXY5U=qsu5=b0uHNVJoBs7eUus-aMsJ0YUdy6Hwog@mail.gmail.com>
	<CAMC681mSsQcMooQzGq_zmbxiH0b17wrRmdpNCq5yqcXa3H3avw@mail.gmail.com>
Message-ID: <CALHM1CEYOEzc-MTJX9rDnjvN5fy7imYUVGH15C-=J3=z+_XeTQ@mail.gmail.com>

Yup, that seems to work just fine, and it's way easier and safer than
writing a script to open the tree file and kill the tag, which is what I
was going to do. Thanks again!

-j

On Mon, Dec 19, 2011 at 12:31 AM, Eric Talevich <eric.talevich at gmail.com>wrote:

> Alrighty,
>
> I think the main problem in your case is that the Newick parser creates
> trees with the 'name' attribute set to the empty string "" instead of None.
> When converting to PhyloXML, that value stays in place and gets serialized
> as an empty element. The author of the phyloXML spec is the author of
> Archaeopteryx, so all of that makes sense.
>
> For your case, Jon, and others having this problem: before writing a tree
> as phyloXML, set the tree name to None if it's not already named.
>
> if tree.name == "":
>     tree.name = None
> Phylo.write(tree, 'example.xml', 'newick')
>
>
> For the future, I guess the best approach is to change the Newick parser
> to set the tree name to None instead of "" by default. Any issues with that
> solution?
>
> -Eric
>
>
>
> On Sat, Dec 17, 2011 at 9:08 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>
>> Archaeopteryx is the one program that read the trees fine. I also tried
>> HyperTree, TreeGraph2, and Treevolution, which failed.
>>
>> -j
>>
>>
>> On Sun, Dec 18, 2011 at 12:03 AM, Eric Talevich <eric.talevich at gmail.com>wrote:
>>
>>> On Fri, Dec 16, 2011 at 1:44 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>>>
>>>> My XML trees exported in biopython (with confidence values, thanks
>>>> Eric!)
>>>> don't open in most XML tree viewing programs.
>>>>
>>>> The problem seems to be a spurious <name /> tag at the beginning of the
>>>> tree.
>>>>
>>>> <phy:phyloxml xmlns:phy="http://www.phyloxml.org">
>>>>  <phy:phylogeny rooted="false">
>>>>    <phy:name />
>>>>    <phy:clade>
>>>>
>>>> If I delete this tag they open fine.
>>>>
>>>>
>>> Hi Jon,
>>>
>>> Thanks for reporting this. I'll check the spec to see if an empty 'name'
>>> tag is even valid. Can you give me the name of one or two programs that are
>>> supposed to handle phyloXML, but don't like this input? Is Archaeopteryx
>>> one of them?
>>>
>>> -Eric
>>>
>>
>>
>>
>> --
>> "If you hold a cat by the tail you learn things you cannot learn any
>> other way."
>>                          --Mark Twain
>>
>>
>


-- 
"If you hold a cat by the tail you learn things you cannot learn any other
way."
                         --Mark Twain


From benjamin.ys.li at gmail.com  Tue Dec 20 08:25:00 2011
From: benjamin.ys.li at gmail.com (Benjamin Li)
Date: Tue, 20 Dec 2011 16:25:00 +0800
Subject: [Biopython] To do Blast alignment of two proteins by biopython
Message-ID: <CAAgdehyjEOVj6JA8rjYf1Xocc+9Q4w8TyFkCNMnudMGGF_T=zw@mail.gmail.com>

Hi all,

I have posted the same question on BioStar, but I think some of the
Biopython users may not check Biostar so I also post it to the mail list.

I am new to biopython and I am not sure if it is a stupid question.

I would like to perform the same task as the one can be done on the web
based blast.

I am trying to align two protein by providing their GIs and receive the
e-value. But I can only find examples to blast one protein in the biopython
tutorial.

How can I align two protein using the qblast function?

I have tried the command

result_handle = NCBIWWW.qblast("blastp", "pat", "330186","118881")

But it returns me a lot of alignments and a lot of e-values.

I also found that it takes a few minutes for my computer to complete the
query, where if I use the web based blast only takes a few seconds.

Is my query anything wrong?


Merry Christmas!

Benjamin Li


From p.j.a.cock at googlemail.com  Tue Dec 20 10:10:06 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 20 Dec 2011 10:10:06 +0000
Subject: [Biopython] To do Blast alignment of two proteins by biopython
In-Reply-To: <CAAgdehyjEOVj6JA8rjYf1Xocc+9Q4w8TyFkCNMnudMGGF_T=zw@mail.gmail.com>
References: <CAAgdehyjEOVj6JA8rjYf1Xocc+9Q4w8TyFkCNMnudMGGF_T=zw@mail.gmail.com>
Message-ID: <CAKVJ-_7jvNHsh2fnmkRJjeCBKw_jXGHxgx=xs-pSA8KRS67Jcw@mail.gmail.com>

On Tue, Dec 20, 2011 at 8:25 AM, Benjamin Li <benjamin.ys.li at gmail.com> wrote:
> Hi all,
>
> I have posted the same question on BioStar, but I think some of the
> Biopython users may not check Biostar so I also post it to the mail list.
>
> I am new to biopython and I am not sure if it is a stupid question.
>
> I would like to perform the same task as the one can be done on the web
> based blast.
>
> I am trying to align two protein by providing their GIs and receive the
> e-value. But I can only find examples to blast one protein in the biopython
> tutorial.
>
> How can I align two protein using the qblast function?

I don't think you can. The main BLAST webpage is actually very
advanced, doing things like trying to guide you with parameter
choices and so on. The QBLAST URL API is much simpler.
http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html

> I have tried the command
>
> result_handle = NCBIWWW.qblast("blastp", "pat", "330186","118881")
>
> But it returns me a lot of alignments and a lot of e-values.
>
> I also found that it takes a few minutes for my computer to complete the
> query, where if I use the web based blast only takes a few seconds.
>
> Is my query anything wrong?

Probably not. The Biopython qblast function uses a 3 second
delay between checking for results, which may partly explain
this. Also the NCBI may give priority to the website.

Have you considered downloading the sequences and running
standalone BLAST on your computer?

Peter


From member at linkedin.com  Sun Dec 25 21:36:34 2011
From: member at linkedin.com (Justinas Daugmaudis via LinkedIn)
Date: Sun, 25 Dec 2011 21:36:34 +0000 (UTC)
Subject: [Biopython] Invitation to connect on LinkedIn
Message-ID: <2000945239.20014961.1324848994821.JavaMail.app@ela4-app0130.prod>

LinkedIn
------------




    Justinas Daugmaudis requested to add you as a connection on LinkedIn:
  

------------------------------------------

Michele,

I'd like to add you to my professional network on LinkedIn.

- Justinas

Accept invitation from Justinas Daugmaudis
http://www.linkedin.com/e/l8bh8w-gwmkvuv5-4/qqAvDr0lR7bVZ5oUF-GdFl1c_dfVGAwasCwqz9Wv-gP/blk/I66984156_16/pmpxnSRJrSdvj4R5fnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_dz5vdzkNd3wVdzp9bQZKiCFvdCRDbPgTcPATc3cOcPkLrCBxbOYWrSlI/EML_comm_afe/?hs=false&tok=3Hoj7CCzUMXl01

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-- 
(c) 2011, LinkedIn Corporation


From mmokrejs at fold.natur.cuni.cz  Mon Dec 26 17:55:09 2011
From: mmokrejs at fold.natur.cuni.cz (Martin Mokrejs)
Date: Mon, 26 Dec 2011 18:55:09 +0100
Subject: [Biopython] GO parsers in biopython
Message-ID: <4EF8B4FD.6050601@fold.natur.cuni.cz>

Hi,
  I would like to parse some OBO/OWL files in python. I searched
for some existing code and found http://biopython.org/wiki/Gene_Ontology
pointing to some OWL parser from Ed Cannon (follow a link on the page
listed above). Unfortunately, the code is gone? :((

  I also discovered an OBO parser at http://hal.elte.hu/~nepusz/development,
the sources can be fetched from

http://bazaar.launchpad.net/~ntamas/+junk/go-parser/tarball/7?start_revid=7

  It can open the .obo files for me although I do not see much methods available.

  Finally, I found https://github.com/gotgenes/biopython/tree/a4824ceb71f3a687b3eb5e1fefd0ad3c278bf185/Bio/GO so my question is when will this be available in released biopython
and what are your opinions/suggestions now. Does it offer more than the
go-parser from ~ntamas?

  I want to cluster some sequences based on anatomical terms, so
I think what I want is to be able to lookup easily all parents
(probably except the very root node or so) and compare whether
they overlap with any parent of another sequence.

Thank you for your comments,
Martin
P.S.: I want to parse OBO from http://www.evocontology.org/


From eric.talevich at gmail.com  Mon Dec 26 20:34:28 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Mon, 26 Dec 2011 12:34:28 -0800
Subject: [Biopython] Bug in Phylo.write('phyloxml')?
In-Reply-To: <CALHM1CEYOEzc-MTJX9rDnjvN5fy7imYUVGH15C-=J3=z+_XeTQ@mail.gmail.com>
References: <CALHM1CEjeYomEiidxjS0UC0JLjGfqmx_GNbfHvtdYjGn1sk-OQ@mail.gmail.com>
	<CAMC681kgx14Bd+gfQwHZew9KYhn3+qJXzUvRrx9C8ddN7CzNHQ@mail.gmail.com>
	<CALHM1CFPurXY5U=qsu5=b0uHNVJoBs7eUus-aMsJ0YUdy6Hwog@mail.gmail.com>
	<CAMC681mSsQcMooQzGq_zmbxiH0b17wrRmdpNCq5yqcXa3H3avw@mail.gmail.com>
	<CALHM1CEYOEzc-MTJX9rDnjvN5fy7imYUVGH15C-=J3=z+_XeTQ@mail.gmail.com>
Message-ID: <CAMC681krw1cxjjNXfckOuA=4SbxD0GyaQOCP6i=BtyM82PmVqg@mail.gmail.com>

Here's the fix:
https://github.com/biopython/biopython/commit/85c3f5d35a0ae349cc35ea94754037f5c329b9b3

The 'name' attribute for clades already defaulted to None instead of the
empty string (""), so I think it was just an oversight that the Tree 'name'
attribute defaulted to "" before this patch.

That should fix your problem, Jon. I'm not so concerned about the empty
<name /> tag crashing other tree viewers because it's valid XML, it fits
the phyloXML spec, and Archaeopteryx accepts it. This patch should keep
that troublesome attribute value from arising inadvertently, though.


Cheers & best wishes,
Eric


On Mon, Dec 19, 2011 at 7:44 AM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:

> Yup, that seems to work just fine, and it's way easier and safer than
> writing a script to open the tree file and kill the tag, which is what I
> was going to do. Thanks again!
>
> -j
>
>
> On Mon, Dec 19, 2011 at 12:31 AM, Eric Talevich <eric.talevich at gmail.com>wrote:
>
>> Alrighty,
>>
>> I think the main problem in your case is that the Newick parser creates
>> trees with the 'name' attribute set to the empty string "" instead of None.
>> When converting to PhyloXML, that value stays in place and gets serialized
>> as an empty element. The author of the phyloXML spec is the author of
>> Archaeopteryx, so all of that makes sense.
>>
>> For your case, Jon, and others having this problem: before writing a tree
>> as phyloXML, set the tree name to None if it's not already named.
>>
>> if tree.name == "":
>>     tree.name = None
>> Phylo.write(tree, 'example.xml', 'newick')
>>
>>
>> For the future, I guess the best approach is to change the Newick parser
>> to set the tree name to None instead of "" by default. Any issues with that
>> solution?
>>
>> -Eric
>>
>>
>>
>> On Sat, Dec 17, 2011 at 9:08 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>>
>>> Archaeopteryx is the one program that read the trees fine. I also tried
>>> HyperTree, TreeGraph2, and Treevolution, which failed.
>>>
>>> -j
>>>
>>>
>>> On Sun, Dec 18, 2011 at 12:03 AM, Eric Talevich <eric.talevich at gmail.com
>>> > wrote:
>>>
>>>> On Fri, Dec 16, 2011 at 1:44 PM, Jon Sanders <jsanders at oeb.harvard.edu>wrote:
>>>>
>>>>> My XML trees exported in biopython (with confidence values, thanks
>>>>> Eric!)
>>>>> don't open in most XML tree viewing programs.
>>>>>
>>>>> The problem seems to be a spurious <name /> tag at the beginning of the
>>>>> tree.
>>>>>
>>>>> <phy:phyloxml xmlns:phy="http://www.phyloxml.org">
>>>>>  <phy:phylogeny rooted="false">
>>>>>    <phy:name />
>>>>>    <phy:clade>
>>>>>
>>>>> If I delete this tag they open fine.
>>>>>
>>>>>
>>>> Hi Jon,
>>>>
>>>> Thanks for reporting this. I'll check the spec to see if an empty
>>>> 'name' tag is even valid. Can you give me the name of one or two programs
>>>> that are supposed to handle phyloXML, but don't like this input? Is
>>>> Archaeopteryx one of them?
>>>>
>>>> -Eric
>>>>
>>>
>>>
>>>
>>> --
>>> "If you hold a cat by the tail you learn things you cannot learn any
>>> other way."
>>>                          --Mark Twain
>>>
>>>
>>
>
>
> --
> "If you hold a cat by the tail you learn things you cannot learn any other
> way."
>                          --Mark Twain
>
>