Mr/ Mrs,
I am running a perl script for mapping the genomic positions i.e. the start and end positions to retrieve positions within the start and end. The script runs correctly in smaller text files, but it was running slowly for almost 4 days, how it could be run faster by rectifying the script attach here. The size for [COLOR="Red"]snp129.txt is 1.60 GB[/COLOR] and [COLOR="red"]TARGETSCAN is 2.20 MB[/COLOR] I would be...
haobijam
Last Activity: Sep 9 '11, 09:50 AM
Joined: Oct 11 '10
Location:
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mapping of genomic positions within start and end positions
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map attributes between three columns and extract common
Hi,
I am running a perl script to retrieve common values in columns at mysql tables. I am mapping three columns for finding same $chr, $start, $end or values within $start and $end. I have attached the text files for two tables earlier. I would be glad to see your positive response.
Regards,
Rocky
...Code:#!/usr/bin/perl -w use strict; use DBI; my $user = 'root'; my $password
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map and extract common numbers between two columns
Hello,
I would like to map columns chr, start, end for dbSNP with chr, start, end for mirna and extract common lines with same chr, start, end positions and also considering within the start and end positions of chromosome (chr). So for this, I have written a perl script where I found an error while running. could you please check it out and suggest me some points or modify. I would be glad for your help.
Regards,
Rocky... -
Hello,
The output for this python code is attached here but the line number 86 in MINiML.xml file is not printed. This an error. Please see the output.
Regards,
Haobijam... -
Hello,
Thanks for your help. I do have assembled and run the script but there was an error while running it on Platform section at line number 86 in MINiML.xml file. When i remove this line and run the script it prints correctly what we want in the output. The error in output prints like -
>>>
Traceback (most recent call last):
File "C:\Users\haoja m\Desktop\GEO\G SE10006\test2.p y",...Leave a comment:
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Dear,
Could yo please tell me how could i parse the attributes and its values from the XML file (MINiML.txt). I would like to print output like below -
Contributoriid = "contrib1"
Person Yael Strulovici-Bare
Email yas2003@med.cor nell.edu
Phone 646-962-5560
Laboratory Crystal
Department Department of Genetic Medicine
Organization Weill Cornell Medical College
Line 1300...Leave a comment:
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Parsing tag names and values from XML files
Sir,
Could you please assist me in writing a python code for parsing values from XML files. I would like to extract Person, Email, Phone, Organization, Address, etc from the XML file. I have a written a code for it but could you please rectify. Please find the attached MINiML.txt file.
...Code:#!/usr/bin/python print "Content-Type: text/plain\n" print "<html><body>"
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Parsing attributes and extracting unique terms from adf.txt
Dear Sir,
I do have a query regarding parsing attributes and extracting unique terms from adf.txt files from ArrayExpress [ftp://ftp.ebi.ac.uk/pub/databases/mi...y/data/array/] .The python code written here is feasible for running individual file with similar starting term but it is infeasible for running around 2270 adf.txt files at one time. Could you please...Leave a comment:
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Parsing attributes from adf.txt files
Dear,
I would like to parse only the first line of each adf.txt files (i.e. attributes) . This python code could print individually for each file type, but i would like to run in one python code for all adf.txt files where the first line starts with only 4 different attribute terms like 'Composite Element Name | Block Column | Reporter Name | CompositeSequen ce Identifier' for all 35 different adf.txt files. I hereby attached only a zip file... -
Parsing attributes from sdrf.txt files and extracting unique terms for all sdrf.txt
Dear Sir,
I would like to extract only unique terms from all sdrf.txt files but this python code outputs unique terms for every file individually. Like Array Data File , Array Design REF ... are repeated in most of sdrf.txt files so i don't wanna print it as unique terms. Could you please tell me to hide case sensitive in python because...Leave a comment:
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...Code:#!/usr/bin/python import glob #import linecache outfile = open('output_att.txt' , 'w') files = glob.glob('*.sdrf.txt') for file in files: infile = open(file) #count = 0 for line in infile: lineArray = line.rstrip() if not line.startswith('Source Name') : continue #count = count + 1 lineArray = line.split('%s\t')Leave a comment:
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Parsing tab separated .txt files with distinct or unique attributes
Dear Sir,
I have written a script to extract the first line starting with Source Name AND ends with Comment [ArrayExpress Data Retrieval URI] and i have done it but i could not parse distinct or unique attributes which is not repeated in every files. I would like to parse only the first line attributes not the table values. Could you please rectify this script....Leave a comment:
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Dear,
What is wrong with this script? I could not print any output.
...Code:#!/usr/bin/python import glob outFile = open('output.txt', 'w') fileNameList = glob.glob('*.adf.txt') for file in fileNameList: f = open(file) output = [] for line in f: line = line.strip().split("\t") #lineArray = line.split('\t') if line:Last edited by bvdet; Oct 13 '10, 03:14 PM. Reason: Please use code tags when posting code. [code]....code goes here....[/code]Leave a comment:
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Dear,
Yes there is always a blank line separating the header information i want from the text data i do not want to extract in all the files.
Regards,
HaobijamLeave a comment:
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Parsing headers with \n\n separated
I would like to extract only the headers from the file parsed. Every files in header starts with Array Design Name but ends with unfix attribute. So i would like to extract headers with space (\n\n)separated gap which is attached in zip file format. I would like to extract only the RED encircled headers. I have attached the output for this script written. I would be glad for your support and cooperation....Leave a comment:
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Parsing headers with \n\n separated
Dear,
Please find the attached zip file. I would like to extract only the headers from the file parsed. Every files in header starts with Array Design Name but not fix attribute. So i would like to extract headers with space (\n\n)separated gap which is attached in zip file format. I would like to extract only the RED encircled headers. I would be glad for your support and cooperation....Leave a comment:
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