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  • Sphinx - Python modules, classes and functions documentation

    - by user343934
    Hi everyone, I am trying to document my small project through sphinx which im recently trying to get familiar with. I read some tutorials and sphinx documentation but couldn't make it. Setup and configurations are ok! just have problems in using sphinx in a technical way. My table of content should look like this --- Overview .....Contents ----Configuration ....Contents ---- System Requirements .....Contents ---- How to use .....Contents ---- Modules ..... Index ......Display ----Help ......Content Moreover my focus is on Modules with docstrings. Details of Modules are Directory:- c:/wamp/www/project/ ----- Index.py >> Class HtmlTemplate: .... def header(): .... def body(): .... def form(): .... def header(): .... __init_main: ##inline function ----- display.py >> Class MainDisplay: .... def execute(): .... def display(): .... def tree(): .... __init_main: ##inline function My Documentation Directory:- c:/users/abc/Desktop/Documentation/doc/ --- _build --- _static --- _templates --- conf.py --- index.rst I have added Modules directory to the system environment and edited index.rst with following codes just to test Table of content. But i couldn't extract docstring directly Index.rst T-Alignment Documentation The documentation covers general overview of the application covering functionalities and requirements in details. To know how to use application its better to go through the documentation. .. _overview: Overview .. _System Requirement: System Requirement Seq-alignment tools can be used in varied systems base on whether all intermediary applications are available or not like in Windows, Mac, Linux and UNIX. But, it has been tested on the Windows working under a beta version. System Applications Server .. _Configuration:: Configuration Basic steps in configuration involves in following categories Environment variables Apache setting .. _Modules:: Modules How can i continue from here... Moreover, i am just a beginner to sphinx documentation tool I need your suggestions to brings my modules docstring to my documentation page Thanks

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  • Subprocess fails to catch the standard output

    - by user343934
    I am trying to generate tree with fasta file input and Alignment with MuscleCommandline import sys,os, subprocess from Bio import AlignIO from Bio.Align.Applications import MuscleCommandline cline = MuscleCommandline(input="c:\Python26\opuntia.fasta") child= subprocess.Popen(str(cline), stdout = subprocess.PIPE, stderr=subprocess.PIPE, shell=(sys.platform!="win32")) align=AlignIO.read(child.stdout,"fasta") outfile=open('c:\Python26\opuntia.phy','w') AlignIO.write([align],outfile,'phylip') outfile.close() I always encounter with these problems Traceback (most recent call last): File "<string>", line 244, in run_nodebug File "C:\Python26\muscleIO.py", line 11, in <module> align=AlignIO.read(child.stdout,"fasta") File "C:\Python26\Lib\site-packages\Bio\AlignIO\__init__.py", line 423, in read raise ValueError("No records found in handle") ValueError: No records found in handle

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  • 50 sequences in one line

    - by user343934
    I have alignment file and long record in it. Suppose while displaying to an end user i want to show Sequence ID and 50 sequences in each line and continue further till the end of file. Can anyone suggest me algorithm or example code in python. Thanks in advance

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  • 50 sequences in one line

    - by user343934
    I have Muttiple sequence alignment (clustal) file and i want to read this file and arrange sequences in a such a way that in looks more clear and precise in order. I am doing this from biopython using AlignIO object. My codes like this alignment = AlignIO.read("opuntia.aln", "clustal") print "Number of rows: %i" % len(align) for record in alignment: print "%s - %s" % (record.id, record.seq) My Output-- http://i48.tinypic.com/ae48ew.jpg , it looks messy and long scrolling. What i want to do is print only 50 sequences in each line and continue till the end of alignment file. I wish to have output like this---http://i45.tinypic.com/4vh5rc.jpg from --http://www.ebi.ac.uk/Tools/clustalw2/, sorry two links are just a text due to my reputation. Any suggestions, algorithm and sample code is appreciated Thanks in advance Br,

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  • importing class and its function from another file

    - by user343934
    Hi everyone, I am having little problem with importing classes in python. My work flow goes like this index.py class Template: def header(): def body(): def form(): def footer(): display.py I want to call function header(), body() and footer () in my display.py page. Will anyone make me clear about this issue in python. Thanks for your concern.

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  • File management

    - by user343934
    I am working on python and biopython right now. I have a file upload form and whatever file is uploaded suppose(abc.fasta) then i want to pass same name in execute (abc.fasta) function parameter and display function parameter (abc.aln). Right now i am changing file name manually, but i want to have it automatically. Workflow goes like this. ----If submit is not true then display only header and form part --- if submit is true then call execute() and get file name from form input --- Then display the save file result in the same page. File name is same as input. My raw code is here -- http://pastebin.com/FPUgZSSe Any suggestions, changes and algorithm is appreciated Thanks

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  • Can anyone tell me why these lines are not working?

    - by user343934
    I am trying to generate tree with fasta file input and Alignment with MuscleCommandline import sys,os, subprocess from Bio import AlignIO from Bio.Align.Applications import MuscleCommandline cline = MuscleCommandline(input="c:\Python26\opuntia.fasta") child= subprocess.Popen(str(cline), stdout = subprocess.PIPE, stderr=subprocess.PIPE, shell=(sys.platform!="win32")) align=AlignIO.read(child.stdout,"fasta") outfile=open('c:\Python26\opuntia.phy','w') AlignIO.write([align],outfile,'phylip') outfile.close() I always encounter with these problems Traceback (most recent call last): File "", line 244, in run_nodebug File "C:\Python26\muscleIO.py", line 11, in align=AlignIO.read(child.stdout,"fasta") File "C:\Python26\Lib\site-packages\Bio\AlignIO_init_.py", line 423, in read raise ValueError("No records found in handle") ValueError: No records found in handle

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  • saving file name from html form input

    - by user343934
    I am working on python and biopython right now. I have a file upload form and whatever file is uploaded suppose(abc.fasta) then i want to pass same name in execute (abc.fasta) function parameter and display function parameter (abc.aln). Workflow goes like this. ----If submit is not true then display only header and form part --- if submit is true then call execute() and get file name from form input --- Then display the save file result in the same page. File name is same as input. My raw code is here -- http://pastebin.com/FPUgZSSe Any suggestions, changes and algorithm is appreciated Thanks

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  • Time Calculation in Python

    - by user343934
    Hi everyone, I have two python cgi pages (index, display), what i need to do is calculate time frame between the execution. Work flow: Index.py (submit) After submit it redirect to display.py page display.py page has got class with execute(),display() &init_main() functions In init_main() i have created class object which access to above functions I need to calculate time interval between the submit (index.py) to execute() end, so i can show user how much time does different weighted file takes on real time. Hoping to see your suggestions Thanks

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  • Python modules, classs, functions documentation through Sphinx

    - by user343934
    Hi everyone, I am trying to document my small project through sphinx which im recently trying to get familiar with. I read some tutorials and sphinx documentation but couldn't make it. Setup and configurations are ok! just have problems in using sphinx in a technical way. My table of content should look like this --- Overview .....Contents ----Configuration ....Contents ---- System Requirements .....Contents ---- How to use .....Contents ---- Modules ..... Index ......Display ----Help ......Content Moreover my focus is on Modules with docstrings. Details of Modules are Directory:- c:/wamp/www/project/ ----- Index.py >> Class HtmlTemplate: .... def header(): .... def body(): .... def form(): .... def header(): .... __init_main: ----- display.py >> Class MainDisplay: .... def execute(): .... def display(): .... def tree(): .... __init_main: My Documentation Directory:- c:/users/abc/Desktop/Documentation/doc/ --- _build --- _static --- _templates --- conf.py --- index.rst I have added Modules directory to the system environment and edited index.rst with following codes Welcome to Seq-alignment's documentation! Contents: .. toctree:: :maxdepth: 2 .. automodule:: index.py .. autoclass:: HtmlTemplate :members:Header,Body,Form,Footer,CloseHtml .. automodule:: display.py .. autoclass:: MainDisplay :members:execute,display,tree Indices and tables :ref:genindex :ref:modindex :ref:search When i make html file and view it, apparently i dont get Modules in the content tables but just there is show record and when i click it just i get "index.txt" version in another window. I need your suggestions Thanks

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  • Create unique file name and fetching it to commandline argument

    - by user343934
    Hi everyone, I am working on python right now and i am little bit stuck in performing some tricks. I have web form with two options- File upload and textarea, i can easily pass file name with file upload options but have problem when it's textarea. Because when i use textarea then first i have to save values passed from textarea to some files and save it on the working directory. After that i can execute commandline argument and pass same saved filename name. For this problem i have to generate unique file first and save the values passed from textarea in it. Can anybody give me some tips to solve my problem. Any algorithms, suggestions and lines of code are appreciated. Thanks for your concern

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  • importing class and its function from another file [Python]

    - by user343934
    Hi everyone, I am having little bit problem in importing classes in python. My work flow goes like this -index.py ---class template: ------def header(): ------def body(): ------def footer(): -display.py I want to call function header(), body() and footer () in my display.py page. Will anyone make me clear about this issue in python. Thanks for your concern.

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