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  • How to include frameset under CGI.pm

    - by neversaint
    I want to have a cgi-script that does two things. Take the input from a form. Generate results base on the input values on a frame. Primarily I want the frame exist only after the results is generated/printed. Below is the simplified code of what I want to do. But somehow it doesn't work. What's the right way to do it? #!/usr/local/bin/perl use CGI ':standard'; print header; print start_html('A Simple Example'), h1('A Simple Example'), start_form, "What's your name? ",textfield('name'), p, "What's the combination?", p, checkbox_group(-name=>'words', -values=>['eenie','meenie','minie','moe'], -defaults=>['eenie','minie']), p, "What's your favorite color? ", popup_menu(-name=>'color', -values=>['red','green','blue','chartreuse']), p, submit, end_form, hr; if (param()) { # begin create the frame print <<EOF; <html><head><title>$TITLE</title></head> <frameset rows="10,90"> <frame src="$script_name/query" name="query"> <frame src="$script_name/response" name="response"> </frameset> EOF # Finish creating frame print "Your name is: ",em(param('name')), p, "The keywords are: ",em(join(", ",param('words'))), p, "Your favorite color is: ",em(param('color')), hr; } print end_html;

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  • Pipeline For Downloading and Processing Files In Unix/Linux Environment With Perl

    - by neversaint
    I have a list of files URLS where I want to download them: http://somedomain.com/foo1.gz http://somedomain.com/foo2.gz http://somedomain.com/foo3.gz What I want to do is the following for each file: Download foo1,2.. in parallel with wget and nohup. Every time it complete download process them with myscript.sh What I have is this: #! /usr/bin/perl @files = glob("foo*.gz"); foreach $file (@files) { my $downurls = "http://somedomain.com/".$file; system("nohup wget $file &"); system("./myscript.sh $file >> output.txt"); } The problem is that I can't tell the above pipeline when does the file finish downloading. So now it myscript.sh doesn't get executed properly. What's the right way to achieve this?

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  • Regex for capturing number in brackets

    - by neversaint
    I have a lines like this NF419andZNF773 (e=10^-92,). ZNF571 (e=2 10^-14,) What's the regex for extracting the results above so that it gives NF419andZNF773 - 10^-92 ZNF571 - 2 10^-14 I tried this but fail. $line =~ /(\w+)\s\(e=\s(.*),\)/; print "$1 - $2\n";

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  • Parsing Chunk of Data into Hash of Array With Perl

    - by neversaint
    I have data that looks like this: #info #info2 1:SRX004541 Submitter: UT-MGS, UT-MGS Study: Glossina morsitans transcript sequencing project(SRP000741) Sample: Glossina morsitans(SRS002835) Instrument: Illumina Genome Analyzer Total: 1 run, 8.3M spots, 299.9M bases Run #1: SRR016086, 8330172 spots, 299886192 bases 2:SRX004540 Submitter: UT-MGS Study: Anopheles stephensi transcript sequencing project(SRP000747) Sample: Anopheles stephensi(SRS002864) Instrument: Solexa 1G Genome Analyzer Total: 1 run, 8.4M spots, 401M bases Run #1: SRR017875, 8354743 spots, 401027664 bases 3:SRX002521 Submitter: UT-MGS Study: Massive transcriptional start site mapping of human cells under hypoxic conditions.(SRP000403) Sample: Human DLD-1 tissue culture cell line(SRS001843) Instrument: Solexa 1G Genome Analyzer Total: 6 runs, 27.1M spots, 977M bases Run #1: SRR013356, 4801519 spots, 172854684 bases Run #2: SRR013357, 3603355 spots, 129720780 bases Run #3: SRR013358, 3459692 spots, 124548912 bases Run #4: SRR013360, 5219342 spots, 187896312 bases Run #5: SRR013361, 5140152 spots, 185045472 bases Run #6: SRR013370, 4916054 spots, 176977944 bases What I want to do is to create a hash of array with first line of each chunk as keys and SR## part of lines with "^Run" as its array member: $VAR = { 'SRX004541' => ['SRR016086'], # etc } But why my construct doesn't work. And it must be a better way to do it. use Data::Dumper; my %bighash; my $head = ""; my @temp = (); while ( <> ) { chomp; next if (/^\#/); if ( /^\d{1,2}:(\w+)/ ) { print "$1\n"; $head = $1; } elsif (/^Run \#\d+: (\w+),.*/){ print "\t$1\n"; push @temp, $1; } elsif (/^$/) { push @{$bighash{$head}}, [@temp]; @temp =(); } } print Dumper \%bighash ;

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  • How do I include a frameset under CGI.pm?

    - by neversaint
    I want to have a cgi-script that does two things. Take the input from a form. Generate results base on the input values on a frame. I also want the frame to exist only after the result is generated/printed. Below is the simplified code of what I want to do. But somehow it doesn't work. What's the right way to do it? #!/usr/local/bin/perl use CGI ':standard'; print header; print start_html('A Simple Example'), h1('A Simple Example'), start_form, "What's your name? ",textfield('name'), p, "What's the combination?", p, checkbox_group(-name=>'words', -values=>['eenie','meenie','minie','moe'], -defaults=>['eenie','minie']), p, "What's your favorite color? ", popup_menu(-name=>'color', -values=>['red','green','blue','chartreuse']), p, submit, end_form, hr; if (param()) { # begin create the frame print <<EOF; <html><head><title>$TITLE</title></head> <frameset rows="10,90"> <frame src="$script_name/query" name="query"> <frame src="$script_name/response" name="response"> </frameset> EOF # Finish creating frame print "Your name is: ",em(param('name')), p, "The keywords are: ",em(join(", ",param('words'))), p, "Your favorite color is: ",em(param('color')), hr; } print end_html;

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  • Perl standard input with argument inside Bash

    - by neversaint
    I want to have such pipe in bash #! /usr/bin/bash cut -f1,2 file1.txt | myperl.pl foo | sort -u Now in myperl.pl it has content like this my $argv = $ARG[0] || "foo"; while (<>) { chomp; if ($argv eq "foo") { # do something with $_ } else { # do another } } But why the Perl script can't recognize the parameter passed through bash? Namely the code break with this message: Can't open foo: No such file or directory at myperl.pl line 15. What the right way to do it so that my Perl script can receive standard input and parameter at the same time?

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  • How to Implement Web Based Find File Database Text Search

    - by neversaint
    I have series of files like this: foo1.txt.gz foo2.txt.gz bar1.txt.gz ..etc.. and a tabular format files that describe the file foo1 - Explain foo1 foo2 - Explain foo2 bar1 - Explain bar1 ..etc.. What I want to do is to have a website with a simple search bar and allow people to type foo1 or just foo and finally return the gzipped file(s) and the explanation of the file(s). What's the best way to implement this. Sorry I am totally new in this area.

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  • Howto Plot "Reverse" Cumulative Frequency Graph With ECDF

    - by neversaint
    I have no problem plotting the following cumulative frequency graph plot like this. library(Hmisc) pre.test <- rnorm(100,50,10) post.test <- rnorm(100,55,10) x <- c(pre.test, post.test) g <- c(rep('Pre',length(pre.test)),rep('Post',length(post.test))) Ecdf(x, group=g, what="f", xlab='Test Results', label.curves=list(keys=1:2)) But I want to show the graph in forms of the "reverse" cumulative frequency of values x ? (i.e. something equivalent to what="1-f"). Is there a way to do it? Other suggestions in R other than using Hmisc are also very much welcomed.

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  • How to Implement Web Based Find File Database Via Text Search

    - by neversaint
    I have series of files like this: foo1.txt.gz foo2.txt.gz bar1.txt.gz ..etc.. and a tabular format file that describe those files: foo1 - Explain foo1 foo2 - Explain foo2 bar1 - Explain bar1 ..etc.. What I want to do is to have a website with a simple search bar and allow people to type foo1 or just foo and finally return the gzipped file(s) and the related explanation of the file(s). What's the best way to implement this and what kind of tools should I use. Sorry I am totally new in this area.

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  • Create File Speedily From Individual Column

    - by neversaint
    I have a data that looks like this: -1 1:-0.394668 2:-0.794872 3:-1 4:-0.871341 5:0.9365 6:0.75597 1 1:-0.463641 2:-0.897436 3:-1 4:-0.871341 5:0.44378 6:0.121824 1 1:-0.469432 2:-0.897436 3:-1 4:-0.871341 5:0.32668 6:0.302529 -1 1:-0.241547 2:-0.538462 3:-1 4:-0.871341 5:0.9994 6:0.987166 1 1:-0.757233 2:-0.948718 3:-1 4:-0.871341 5:-0.33904 6:0.915401 1 1:-0.167147 2:-0.589744 3:-1 4:-0.871341 5:0.95078 6:0.991566 The first column is class, and next 6 columns are features. I want to create 6 files for individual features. For example feat1_file.txt will contain -1 1:-0.394668 1 1:-0.463641 ... 1 1:-0.757233 1 1:-0.167147 feat2_file.txt will contain -1 2:-0.794872 ... 1 2:-0.589744 and so on. I have a Perl code that does this but it is horribly slow. Is there a way to do it faster? Typically the input files will contain 100K lines. use strict; use Data::Dumper; use Carp; my $input = $ARGV[0] || "myinput.txt"; my $INFILE_file_name = $input; # input file name open ( INFILE, '<', $INFILE_file_name ) or croak "$0 : failed to open input file $INFILE_file_name : $!\n"; my $out1 = $input."_feat_1.txt"; my $out2 = $input."_feat_2.txt"; my $out3 = $input."_feat_3.txt"; my $out4 = $input."_feat_4.txt"; my $out5 = $input."_feat_5.txt"; my $out6 = $input."_feat_6.txt"; unlink($out1); unlink($out2); unlink($out3); unlink($out4); unlink($out5); unlink($out6); print "$out1\n"; while ( <INFILE> ) { chomp; my @els = split(/\s+/,$_); my $lbl = $els[0]; my $OUTFILE1_file_name = $out1; # output file name open ( OUTFILE1, '>>', $OUTFILE1_file_name ) or croak "$0 : failed to open output file $OUTFILE1_file_name : $!\n"; print OUTFILE1 "$lbl $els[1]\n"; close ( OUTFILE1 ); # close output file my $OUTFILE2_file_name = $out2; # output file name open ( OUTFILE2, '>>', $OUTFILE2_file_name ) or croak "$0 : failed to open output file $OUTFILE2_file_name : $!\n"; print OUTFILE2 "$lbl $els[2]\n"; close ( OUTFILE2 ); # close output file # Etc.. until OUTFILE 6 } close (INFILE);

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  • Parsing line with delimiter in Python

    - by neversaint
    I have lines of data which I want to parse. The data looks like this: a score=216 expect=1.05e-06 a score=180 expect=0.0394 What I want to do is to have a subroutine that parse them and return 2 values (score and expect) for each line. However this function of mine doesn't seem to work: def scoreEvalFromMaf(mafLines): for word in mafLines[0]: if word.startswith("score="): theScore = word.split('=')[1] theEval = word.split('=')[2] return [theScore, theEval] raise Exception("encountered an alignment without a score") Please advice what's the right way to do it?

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  • How to enable 'wget' to download the whole content of HTML with Javascript

    - by neversaint
    I have a site which I want to download using Unix wget. If you look at the source code and content of the file it contain section called SUMMARY. However after issuing a wget command like this: wget -O downdloadedtext.txt http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=mouse&c=gene&a=fiche&l=2610008E11Rik The content of the downdloadedtext.txt is incomplete and different with the source code of that site. For example it doesn't contain SUMMARY section. Is there a correct way to obtain the full content correctly? The reason I ask this because I want to automate the download from different values in that HTML.

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  • Create Directory, 'cd' to it and download a file pipeline in Perl

    - by neversaint
    I have a file that looks like this: ftp://url1/files1.tar.gz dir1 ftp://url2/files2.txt dir2 .... many more... What I want to do are these steps: Create directory based on column 2 Unix 'cd' to that directory Download file with 'wget' based on column1 But how come this approach of mine doesn't work while(<>) { chomp; my ($url,$dir) = split(/\t/,$_); system("mkdir $dir"); system("cd $dir"); # Fail here system("wget $url"); # here too } What's the right way to do it?

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  • Howto plot two cumulative frequency graph together

    - by neversaint
    I have data that looks like this: #val Freq1 Freq2 0.000 178 202 0.001 4611 5300 0.002 99 112 0.003 26 30 0.004 17 20 0.005 15 20 0.006 11 14 0.007 11 13 0.008 13 13 ...many more lines.. Full data can be found here: http://dpaste.com/173536/plain/ What I intend to do is to have a cumulative graph with "val" as x-axis with "Freq1" & "Freq2" as y-axis, plot together in 1 graph. I have this code. But it creates two plots instead of 1. dat <- read.table("stat.txt",header=F); val<-dat$V1 freq1<-dat$V2 freq2<-dat$V3 valf1<-rep(val,freq1) valf2<-rep(val,freq2) valfreq1table<- table(valf1) valfreq2table<- table(valf2) cumfreq1=c(0,cumsum(valfreq1table)) cumfreq2=c(0,cumsum(valfreq2table)) plot(cumfreq1, ylab="CumFreq",xlab="Loglik Ratio") lines(cumfreq1) plot(cumfreq2, ylab="CumFreq",xlab="Loglik Ratio") lines(cumfreq2) What's the right way to approach this?

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  • How can I read and parse chunks of data into a Perl hash of arrays?

    - by neversaint
    I have data that looks like this: #info #info2 1:SRX004541 Submitter: UT-MGS, UT-MGS Study: Glossina morsitans transcript sequencing project(SRP000741) Sample: Glossina morsitans(SRS002835) Instrument: Illumina Genome Analyzer Total: 1 run, 8.3M spots, 299.9M bases Run #1: SRR016086, 8330172 spots, 299886192 bases 2:SRX004540 Submitter: UT-MGS Study: Anopheles stephensi transcript sequencing project(SRP000747) Sample: Anopheles stephensi(SRS002864) Instrument: Solexa 1G Genome Analyzer Total: 1 run, 8.4M spots, 401M bases Run #1: SRR017875, 8354743 spots, 401027664 bases 3:SRX002521 Submitter: UT-MGS Study: Massive transcriptional start site mapping of human cells under hypoxic conditions.(SRP000403) Sample: Human DLD-1 tissue culture cell line(SRS001843) Instrument: Solexa 1G Genome Analyzer Total: 6 runs, 27.1M spots, 977M bases Run #1: SRR013356, 4801519 spots, 172854684 bases Run #2: SRR013357, 3603355 spots, 129720780 bases Run #3: SRR013358, 3459692 spots, 124548912 bases Run #4: SRR013360, 5219342 spots, 187896312 bases Run #5: SRR013361, 5140152 spots, 185045472 bases Run #6: SRR013370, 4916054 spots, 176977944 bases What I want to do is to create a hash of array with first line of each chunk as keys and SR## part of lines with "^Run" as its array member: $VAR = { 'SRX004541' => ['SRR016086'], # etc } But why my construct doesn't work. And it must be a better way to do it. use Data::Dumper; my %bighash; my $head = ""; my @temp = (); while ( <> ) { chomp; next if (/^\#/); if ( /^\d{1,2}:(\w+)/ ) { print "$1\n"; $head = $1; } elsif (/^Run \#\d+: (\w+),.*/){ print "\t$1\n"; push @temp, $1; } elsif (/^$/) { push @{$bighash{$head}}, [@temp]; @temp =(); } } print Dumper \%bighash ;

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  • How to enable `geom_text` to recognize `aes` in QPLOT (R programming)

    - by neversaint
    I have a data that looks like this ensg mirna_hgc time value perc id ENSG00000211521 MIR665 x 89 2.07612456747405 1 ENSG00000207787 MIR98 x 73 1.73010380622837 2 ... ENSG00000207827 MIR30A y 99 21.4532871972318 288 ENSG00000207757 MIR93 y 94 1.73010380622837 289 What I'm trying to do is to create a facet plot with label on top of it. The label can be easily called from the perc column. Using this code: dat.m <- read.delim("http://dpaste.com/1271039/plain/",header=TRUE,sep=" ") qplot(value, data=dat.m,facets=time~.,binwidth=1,main="")+ xlab("Value")+ ylab("Count")+ theme(legend.position="none")+ stat_bin(aes(value,label=sprintf("%.01f",perc)),geom="text") But it gave me this error: Error: geom_text requires the following missing aesthetics: label What I'm trying to do is to generate this plot:

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