Search DaniWeb - genbank

Parsing multi-record Genbank file 10 Years Ago by perly Hi, I tried parsing a multi-record genbank file (from this site: http://biopython.org/DIST/docs/tutorial/… Parsing EMBL 13 Years Ago by Anthony Cameron … annotation and sequence sections from the first # record of a GenBank library use strict; use warnings; use BeginPerlBioinfo; # Declare and initialize… $dna = ''; my $record = ''; my $filename = 'sequence.gb'; my $save_input_separator = $/; # Open GenBank library file unless (open(GBFILE, $filename)) { print "Cannot open… GUI variables 12 Years Ago by zazga … [the file to open, and if it is a genbank or fasta file]. I want my GUI to use radiobuttons… for the genbank/fasta choice, and this works fine. But I want …? ").pack(pady=10) Radiobutton(root, text="GenBank", value="GenBank", variable=var, command = doOne).pack() Radiobutton(root… Re: Parsing EMBL 13 Years Ago by d5e5 … data #($annotation, $dna) = ($record =~ /^(LOCUS.*ORIGIN\s*\n)(.*)\/\/\n/s);#GenBank layout ($annotation, $dna) = ($record =~ /^(.*SQ\s*)(.*)\/\//s);#Trying to matchEMBL… Re: Parsing EMBL 13 Years Ago by Anthony Cameron … data #($annotation, $dna) = ($record =~ /^(LOCUS.*ORIGIN\s*\n)(.*)\/\/\n/s);#GenBank layout ($annotation, $dna) = ($record =~ /^(.*SQ\s*)(.*)\/\//s);#Trying to matchEMBL… Re: Parsing EMBL 13 Years Ago by Anthony Cameron … data #($annotation, $dna) = ($record =~ /^(LOCUS.*ORIGIN\s*\n)(.*)\/\/\n/s);#GenBank layout ($annotation, $dna) = ($record =~ /^(.*SQ\s*)(.*)\/\//s);#Trying to matchEMBL… How to skip a line ! 17 Years Ago by MojoS … do that??? This is a DNA seqeunce taken from the GenBank database. (the first line is not part of the sequence… problem extracting a sequence from a html page 12 Years Ago by nethero …;</ul></div> <pre class="genbank">LOCUS BAH23558 362 aa linear VRL 26-FEB… writing a program with biopython or python 11 Years Ago by eleiloon Hi All, I'm trying to make a tree and identify some 16s rRNA sequencing with genbank using biopython or python, but I have no Idea how can I start. Could you please help me? Re: biopython 17 Years Ago by G-Do …but you keep getting key collisions because you're using GenBank accession numbers as your primary keys? So you want to… add some number to the GenBank accessions - 1, 2, 3, and so on, yes? If…your database as well. You could always pull up the GenBank accessions later when displaying information (since everything is getting … Re: Help with an Exception please? 16 Years Ago by muppetjones … while($count < 5) { my $gb = Bio::DB::GenBank->new( # create new GenBank object -retrievaltype => 'tempfile' , -format => 'Fasta'); my… Re: Parsing tab separated .txt files with common and distinct attributes 13 Years Ago by haojam This is GenBank[COLOR="Red"]®[/COLOR] not GenBank@ Re: biopython 17 Years Ago by G-Do … needs a primary key, msaenz has (I think) chosen the GenBank accession (also a RefSeq ID, which is why you see… Re: Parsing tab separated .txt files with common and distinct attributes 13 Years Ago by haojam … an error while running the code at line number 86 GenBank[COLOR="red"]@[/COLOR]. When i remove [COLOR="… Re: multiple file argument 13 Years Ago by weblover …( parser, "select a subset of the features in the genbank file for calculations. " "(type can be tRNA, rRNA… Re: multiple file argument 13 Years Ago by Gribouillis …( parser, "select a subset of the features in the genbank file for calculations. " "(type can be tRNA, rRNA… Re: Parsing EMBL 13 Years Ago by d5e5 [QUOTE=Anthony Cameron;1406125]Hi, since I need to pring out the $ID, $SQ, $KW, AND $OC within the file should I declare them as variables and then print them out? Thanks[/QUOTE] Why declare four scalar variables just to store the four literal values you want to look for at the beginning of the lines? Also, I don't know why you want to follow the … Re: Parsing EMBL 13 Years Ago by Anthony Cameron [QUOTE=d5e5;1406764]Why declare four scalar variables just to store the four literal values you want to look for at the beginning of the lines? Also, I don't know why you want to follow the same route as illustrated in the script you posted. That script reads two mult-line records into two variables: $annotation and $dna, which it then prints. Why … Re: GUI variables 12 Years Ago by askandstudy Use thread,what do you think? [URL="http://code.google.com/p/my-study-code/source/browse/trunk/python2/tk_dialog.py"]http://code.google.com/p/my-study-code/source/browse/trunk/python2/tk_dialog.py[/URL] [URL="http://code.google.com/p/my-study-code/source/browse/trunk/python2/dosomework.py"]http://code.google.com/p/my-study-… Re: How to skip a line ! 17 Years Ago by Mushy-pea Say your data is in a variable called $page. You can use the split function to split on the first line break only and then only apply your data processing code to the text that appears after that. Take a look at this: [code=perl] @stuff = split(/\\n/, $page, 2); [/code] You can find out how the split function works here: [URL]http://perldoc.… Re: How to skip a line ! 17 Years Ago by KevinADC [CODE]#!/usr/bin/perl use strict; use warnings; open(IN, '<',"dna.dat") or die "Can't read file\n $!"; my $first_line = <IN>; my $dna = ''; while(my $line=<IN>){ chomp $line; $dna .= $line; } close IN; my $cdna = ''; for my $i (0 .. length($dna)-1){ $_ = substr($dna, $i, 1); if (!/[TAGC]/) {die "… Re: How to skip a line ! 17 Years Ago by KevinADC this line: $rdna = reverse $cdna; should be: [B]my[/B] $rdna = reverse $cdna; Re: How to skip a line ! 17 Years Ago by MojoS Hi guys .... Thanxs alot for ur big help! Kevin I have tried the following but when I want to write the data into a file I get problems with displaying the first line without repeating itself for every new data line (because of loop): How do I display the first line only once and followed by the dataset I have tried this: open(IN, '<',"… Re: How to skip a line ! 17 Years Ago by KevinADC print it outside the loop. [CODE]open(OUT,'>' , "revdna.fsa") or die "Can't write file\n $!"; print OUT "$first_line\n"; for($i=0; $i < length($rdna);$i+=60){ $base =substr($rdna, $i, 60); print OUT "$base\n"; } close OUT;[/CODE] Re: How to skip a line ! 17 Years Ago by MojoS Hmmm I had tried that, and its still wouldnt work when I nedit revdna.dat, only the sequence is showing!!!!! the first line apperently cant be seen in the texteditor .....! Re: How to skip a line ! 17 Years Ago by KevinADC hard to say why it's not working because in the code you posted it never prints $first_line to a file and you print to a file called "revdna.fsa" but then in your last post you mention "revdna.dat". This line in your last code post: substr($first_line, -1, 0)= "ComplementStrand"; is simpler written as: $first_line… Re: problem extracting a sequence from a html page 12 Years Ago by predator78 It's hard to tell without seeing the exact page and code your using what the problem is. If there is an issue with providing that information I would suggest doing what you seem to have done already again which is to navigate the sight manually first and take good note of how you are reaching the page you are requesting. Is it some sort of popup?… Re: problem extracting a sequence from a html page 12 Years Ago by TrustyTony Use access instructions here [url]http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html[/url] or ftp access. [url]http://www.ncbi.nlm.nih.gov/guide/data-software/#downloads_[/url] Re: problem extracting a sequence from a html page 12 Years Ago by nethero Thanks for the help guys. I did not figure out how to fix my problem; however, I did find a different way of doing it. I found the link to the [URL="http://www.ncbi.nlm.nih.gov/books/NBK25501/"]http API of NCBI[/URL] (thanks tonyjv for the suggestion). I wrote some python code with a couple of urllib2.urlopen calls to retreive the data… Re: writing a program with biopython or python 11 Years Ago by rubberman Do you have any programming experience? Do you know python at all?