hi to everyone,
does anyone help me about giving command line arguments in windows?
thanks.
biter
Do You Yahoo!?
HotJobs, a Yahoo! service - Search Thousands of New Jobs --0-395188809-1028901067=:79907-- From katel@worldpath.net Fri Aug 9 19:48:40 2002 From: katel@worldpath.net (Katharine Lindner) Date: Fri, 09 Aug 2002 14:48:40 -0400 Subject: [BioPython] LocusLink Message-ID: <3D540E88.1090600@worldpath.net> Is there a need for an HTTP parser for LocusLink in addition to the flat file? I'd especially like to have Sagar's perspective because he is a user. Although memory is cheap in places like Boston and California, biopython has an international user base. Researchers from emerging technologies may not have the resources to store flat files locally. An alternate solution for public domain databases might be mindyized mirror sites. Cayte From simple4u2do@hotmail.com Fri Aug 9 13:58:19 2002 From: simple4u2do@hotmail.com (simple4u2do@hotmail.com) Date: Fri, 9 Aug 2002 08:58:19 -0400 Subject: [BioPython] IT'S SO SIMPLE...... 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Fred Dellaca, Westport, New Zealand ========================================= ORDER YOUR REPORTS TODAY AND GET STARTED ON YOUR ROAD TO FINANCIAL FREEDOM! ========================================= If you have any questions of the legality of this program contact the Office of Associate Director for Marketing Practices, Federal Trade Commission, Bureau of Consumer Protection, and Washington, D.C. ========================================= ONE TIME MAILING, NO NEED TO REMOVE ======================================== From sagar@caltech.edu Sun Aug 11 04:09:31 2002 From: sagar@caltech.edu (Sagar Damle) Date: Sat, 10 Aug 2002 20:09:31 -0700 Subject: [BioPython] Re: LocusLink In-Reply-To: <3D540E88.1090600@worldpath.net> References: <3D540E88.1090600@worldpath.net> Message-ID: <20020810200932.3d6f34ef.sagar@caltech.edu> hi cayte, > Researchers from emerging > technologies may not have the resources to store flat files locally. you may be right. I also want to point out that maintaining an up-to-date annotations database (from several sources) might be well- suited for a larger user-base, but an HTTP-parser still seems more convenient for the lone, casual scripter. On the other hand, I hadn't fully appreciated the flat-file parser till recently. It might be nice if someone would save us all the work and set up a local annotations database (using biopython's flat-file parsers) and attach to it a cron-job that updates flat-files on a month-to-month basis. So, I think I still need the locus-link parser, but maybe there's a more general/more useful project that deserves a higher priority. -sagar On Fri, 09 Aug 2002 14:48:40 -0400 Katharine Lindner
hi everybody,
i am to write a program that makes gapless multiple alignments with 17 sequences. i attempted to use clustalw within biopyhon. but even the example program at
http://bioweb.pasteur.fr/docs/doc-gensoft/biopython/Doc/examples/clustal_run.py
gave errors as:
Traceback (most recent call last):
File "<pyshell#2>", line 1, in ?
execfile('clustal_run.py')
File "clustal_run.py", line 24, in ?
alignment = Clustalw.do_alignment(cline)
File "C:\Python22\Lib\site-packages\Bio\Clustalw\__init__.py", line 86, in do_alignment
raise ValueError("Bad command line option in the command: %s"
ValueError: Bad command line option in the command: clustalw .\opuntia.fasta -OUTFILE=test.aln
it is not mentioned in the cookbook that i should download a software for running clustalw. i think the problem is not the files(opuntia.fasta or test.aln) but clustalw since i dowloaded opuntia.fasta.
has anyone got idea about the problem?
thanks
biter
Do You Yahoo!?
Yahoo! Finance - Get real-time stock quotes --0-105930084-1030182013=:69359-- From letondal@pasteur.fr Mon Aug 26 19:28:58 2002 From: letondal@pasteur.fr (Catherine Letondal) Date: Mon, 26 Aug 2002 20:28:58 +0200 Subject: [BioPython] Pise client Message-ID: <200208261828.g7QISxLq208805@electre.pasteur.fr> Hi, I have written a Python package to run jobs on a Pise Web server from a python program (Pise is a tool to generate user interfaces for programs running under Unix described here: http://www-alt.pasteur.fr/~letondal/Pise). For example, the following script run a toppred job on a SeqRecord instance, displays the standard output of this job, and save the graphical output in a file. Sequences or alignments can be input either as Seq, SeqRecord, files or just strings. from Pise import PiseFactory import Bio.Fasta import sys factory = PiseFactory(email='user@domain') program = factory.program("toppred", graph_output=1, profile_format="ps") handle = open(sys.argv[1]) it = Bio.Fasta.Iterator(handle, Bio.Fasta.SequenceParser()) seq = it.next() job = program.run(query=seq) if job.error(): print job.error_message() else: print "url of the job: " + job.jobid() print job.stdout() print "Results: ", job.get_results() job.save('.ps') The package is available at: http://www-alt.pasteur.fr/~letondal/Pise/#pisepython The package is organized in 4 main classes (the package is organized about the same way as in the bioperl API in fact): PiseFactory ----------- builds PiseApplication instances program() | | v PiseApplication PiseJob PiseJobParser --------------- ------- ------------- object --> actual job (an xml.sax.handler) to parse to set (methods to XHTML server output parameters actually submit and launch the http request jobs via httplib, get job state | and results) | +----------------------------------------------+ | toppred fasta hmmbuild nnssp blast2 clustalw | | genscan tacg dnapars wublast2 ... | | | +----------------------------------------------+ I'm aware about the Bio.Application framework, but I have understood it's more for local run. For instance, AbstractCommandline would have been useful on a server, but there is no such thing in the client, which does not deal with command lines. It should be possible to wrap PiseApplication classes in Bio.Application classes though (and ApplicationResult sub-class could re-use PiseJob methods for instance). I have tried to put the minimum information in the numerous files that belongs to this package (there is a small file for each program, and there are about 287 programs). I would be very happy to get some feedback about this code! -- Catherine Letondal -- Pasteur Institute Computing Center From biterbilen@yahoo.com Tue Aug 27 09:17:02 2002 From: biterbilen@yahoo.com (biter bilen) Date: Tue, 27 Aug 2002 01:17:02 -0700 (PDT) Subject: [BioPython] do_alignment Message-ID: <20020827081702.94218.qmail@web10101.mail.yahoo.com> --0-1275916588-1030436222=:94121 Content-Type: multipart/alternative; boundary="0-15017384-1030436222=:94121" --0-15017384-1030436222=:94121 Content-Type: text/plain; charset=us-ascii hi to everyone. my aim for learning python is its bio libraries. i use windows. i want to run clustalw (a multiple alignment program) within it. it requires the clustalx program to be downloaded (it is said so in the python help documents). i downloaded it. the program is as in the attacments. --------------------------------- Do You Yahoo!? Yahoo! Health - Feel better, live better --0-15017384-1030436222=:94121 Content-Type: text/html; charset=us-ascii
hi to everyone.
my aim for learning python is its bio libraries. i use windows. i want to run clustalw (a multiple alignment program) within it. it requires the clustalx program to be downloaded (it is said so in the python help documents). i downloaded it. the program is as in the attacments.
Do You Yahoo!?
Yahoo! Health - Feel better, live better --0-15017384-1030436222=:94121-- --0-1275916588-1030436222=:94121 Content-Type: text/plain; name="clustal_run.py" Content-Description: clustal_run.py Content-Disposition: inline; filename="clustal_run.py" # !/usr/bin/env python """clustal_run.py Example code to show how to create a clustalw command line, run clustalw and parse the results into an object that can be dealt with easily.""" # standard library import os # biopython from Bio.Alphabet import IUPAC from Bio import Clustalw from Bio.Clustalw import MultipleAlignCL from Bio.Align import AlignInfo from Bio.SubsMat import FreqTable # create the command line to run clustalw # this assumes you've got clustalw somewhere on your path, otherwise # you need to pass a second argument to MultipleAlignCL with the complete # path to clustalw cline = MultipleAlignCL(os.path.join(os.curdir, 'opuntia.fasta')) cline.set_output('test.aln') # actually perform the alignment and get back an alignment object alignment = Clustalw.do_alignment(cline) # get the records in the alignment all_records = alignment.get_all_seqs() print 'description:', all_records[0].description print 'sequence:', all_records[0].seq # get the length of the alignment print 'length', alignment.get_alignment_length() print alignment # print out interesting information about the alignment summary_align = AlignInfo.SummaryInfo(alignment) consensus = summary_align.dumb_consensus() print 'consensus', consensus my_pssm = summary_align.pos_specific_score_matrix(consensus, chars_to_ignore = ['N']) print my_pssm expect_freq = { 'A' : .3, 'G' : .2, 'T' : .3, 'C' : .2} freq_table_info = FreqTable.FreqTable(expect_freq, FreqTable.FREQ, IUPAC.unambiguous_dna) info_content = summary_align.information_content(5, 30, chars_to_ignore = ['N'], e_freq_table = \ freq_table_info) print "relative info content:", info_content --0-1275916588-1030436222=:94121-- From biterbilen@yahoo.com Tue Aug 27 09:31:25 2002 From: biterbilen@yahoo.com (biter bilen) Date: Tue, 27 Aug 2002 01:31:25 -0700 (PDT) Subject: [BioPython] error about do_alignment function in Clustalw module Message-ID: <20020827083125.95463.qmail@web10101.mail.yahoo.com> --0-324068416-1030437085=:95037 Content-Type: text/plain; charset=us-ascii hi everybody, i wanted to test clustal_run.py at http://bioweb.pasteur.fr/docs/doc-gensoft/biopython/Doc/examples/clustal_run.py this uses do_alignment function and i see an error as: raise ValueError("Bad command line option in the command: %s" ValueError: Bad command line option in the command: clustalw .\opuntia.fasta -OUTFILE=test.aln i downloaded clustalx 1.81 (sorry for the previous message) as said in the help documentation. can the error happen due to not seeing the path of clustalw? i realised that no clustalw executable file exists in the said (clustalx 1.81) package. can anyone help me about it? special thanks biter --------------------------------- Do You Yahoo!? Yahoo! Health - Feel better, live better --0-324068416-1030437085=:95037 Content-Type: text/html; charset=us-ascii
hi everybody,
i wanted to test clustal_run.py at
http://bioweb.pasteur.fr/docs/doc-gensoft/biopython/Doc/examples/clustal_run.py
this uses do_alignment function and i see an error as:
raise ValueError("Bad command line option in the command: %s"
ValueError: Bad command line option in the command: clustalw .\opuntia.fasta -OUTFILE=test.aln
i downloaded clustalx 1.81 (sorry for the previous message) as said in the help documentation.
can the error happen due to not seeing the path of clustalw? i realised that no clustalw executable file exists in the said (clustalx 1.81) package. can anyone help me about it? 
special thanks
biter
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Yahoo! Health - Feel better, live better --0-324068416-1030437085=:95037-- From biterbilen@yahoo.com Tue Aug 27 09:33:52 2002 From: biterbilen@yahoo.com (biter bilen) Date: Tue, 27 Aug 2002 01:33:52 -0700 (PDT) Subject: [BioPython] do_alignment In-Reply-To: <20020827081702.94218.qmail@web10101.mail.yahoo.com> Message-ID: <20020827083352.94763.qmail@web10107.mail.yahoo.com> --0-1010516694-1030437232=:94753 Content-Type: text/plain; charset=us-ascii sorry for this mail to clog your mailboxes. biter bilen wrote: hi to everyone. my aim for learning python is its bio libraries. i use windows. i want to run clustalw (a multiple alignment program) within it. it requires the clustalx program to be downloaded (it is said so in the python help documents). i downloaded it. the program is as in the attacments. --------------------------------- Do You Yahoo!? Yahoo! Health - Feel better, live better# !/usr/bin/env python """clustal_run.py Example code to show how to create a clustalw command line, run clustalw and parse the results into an object that can be dealt with easily.""" # standard library import os # biopython from Bio.Alphabet import IUPAC from Bio import Clustalw from Bio.Clustalw import MultipleAlignCL from Bio.Align import AlignInfo from Bio.SubsMat import FreqTable # create the command line to run clustalw # this assumes you've got clustalw somewhere on your path, otherwise # you need to pass a second argument to MultipleAlignCL with the complete # path to clustalw cline = MultipleAlignCL(os.path.join(os.curdir, 'opuntia.fasta')) cline.set_output('test.aln') # actually perform the alignment and get back an alignment object alignment = Clustalw.do_alignment(cline) # get the records in the alignment all_records = alignment.get_all_seqs() print 'description:', all_records[0].description print 'sequence:', all_records[0].seq # get the length of the alignment print 'length', alignment.get_alignment_length() print alignment # print out interesting information about the alignment summary_align = AlignInfo.SummaryInfo(alignment) consensus = summary_align.dumb_consensus() print 'consensus', consensus my_pssm = summary_align.pos_specific_score_matrix(consensus, chars_to_ignore = ['N']) print my_pssm expect_freq = { 'A' : .3, 'G' : .2, 'T' : .3, 'C' : .2} freq_table_info = FreqTable.FreqTable(expect_freq, FreqTable.FREQ, IUPAC.unambiguous_dna) info_content = summary_align.information_content(5, 30, chars_to_ignore = ['N'], e_freq_table = \ freq_table_info) print "relative info content:", info_content --------------------------------- Do You Yahoo!? Yahoo! Finance - Get real-time stock quotes --0-1010516694-1030437232=:94753 Content-Type: text/html; charset=us-ascii
sorry for this mail to clog your mailboxes.
biter bilen
hi to everyone.
my aim for learning python is its bio libraries. i use windows. i want to run clustalw (a multiple alignment program) within it. it requires the clustalx program to be downloaded (it is said so in the python help documents). i downloaded it. the program is as in the attacments.
Do You Yahoo!?
Yahoo! Health - Feel better, live better# !/usr/bin/env python
"""clustal_run.py
Example code to show how to create a clustalw command line, run clustalw
and parse the results into an object that can be dealt with easily."""
# standard library
import os
# biopython
from Bio.Alphabet import IUPAC
from Bio import Clustalw
from Bio.Clustalw import MultipleAlignCL
from Bio.Align import AlignInfo
from Bio.SubsMat import FreqTable
# create the command line to run clustalw
# this assumes you've got clustalw somewhere on your path, otherwise
# you need to pass a second argument to MultipleAlignCL with the complete
# path to clustalw
cline = MultipleAlignCL(os.path.join(os.curdir, 'opuntia.fasta'))
cline.set_output('test.aln')
# actually perform the alignment and get back an alignment object
alignment = Clustalw.do_alignment(cline)
# get the records in the alignment
all_records = alignment.get_all_seqs()
print 'description:', all_records[0].description
print 'sequence:', all_records[0].seq
# get the length of the alignment
print 'length', alignment.get_alignment_length()
print alignment
# print out interesting information about the alignment
summary_align = AlignInfo.SummaryInfo(alignment)
consensus = summary_align.dumb_consensus()
print 'consensus', consensus
my_pssm = summary_align.pos_specific_score_matrix(consensus,
chars_to_ignore = ['N'])
print my_pssm
expect_freq = {
'A' : .3,
'G' : .2,
'T' : .3,
'C' : .2}
freq_table_info = FreqTable.FreqTable(expect_freq, FreqTable.FREQ,
IUPAC.unambiguous_dna)
info_content = summary_align.information_content(5, 30,
chars_to_ignore = ['N'],
e_freq_table = \
freq_table_info)
print "relative info content:", info_content
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