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  • Finding File WIth Fixed File Size (>0) in Unix/Linux

    - by neversaint
    I have a list of file that looks like this 4 -rw-r--r-- 1 neversaint hgc0746 53 May 1 10:37 SRX016372-SRR037477.est_count 4 -rw-r--r-- 1 neversaint hgc0746 53 May 1 10:34 SRX016372-SRR037478.est_count 4 -rw-r--r-- 1 neversaint hgc0746 53 May 1 10:41 SRX016372-SRR037479.est_count 0 -rw-r--r-- 1 neversaint hgc0746 0 Apr 27 11:16 SRX003838-SRR015096.est_count 0 -rw-r--r-- 1 neversaint hgc0746 0 Apr 27 11:32 SRX004765-SRR016565.est_count What I want to do is to find files that has exactly size 53. But why this command failed? $ find . -name "*.est_count" -size 53 -print It works well though if I just want to find file of size 0 with this command: $ find . -name "*.est_count" -size 0 -print

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  • Permission Problem While Installing Module With CPAN

    - by neversaint
    I tried to following module using CPAN, but the message I get is the "I have neither the -x permission ..." . How can I resolve that? cpan[3]> install List::MoreUtils is it OK to try to connect to the Internet? [yes] Fetching with LWP: http://www.perl.org/CPAN/authors/id/V/VP/VPARSEVAL/List-MoreUtils-0.22.tar.gz CPAN: Digest::SHA loaded ok (v5.48) Fetching with LWP: http://www.perl.org/CPAN/authors/id/V/VP/VPARSEVAL/CHECKSUMS Checksum for /home/ewijaya/.cpan/sources/authors/id/V/VP/VPARSEVAL/List-MoreUtils-0.22.tar.gz ok Scanning cache /home/neversaint/.cpan/build for sizes .....I have neither the -x permission nor the permission to change the permission; cannot estimate disk usage of '/home/neversaint/.cpan/build/Module-Build-0.3607-Kvb1Vq' .I have neither the -x permission nor the permission to change the permission; cannot estimate disk usage of '/home/neversaint/.cpan/build/ExtUtils-ParseXS-2.2205-zuX4x2' ^CCaught SIGINT, trying to continue

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  • Howto unzip ".xz" file with 7z and lzma

    - by neversaint
    I tried to uncompressed a "*.xz" file with both 7z and lzma. But they gave me such message: $ 7z x myfile.fq.xz 7-Zip 4.57 Copyright (c) 1999-2007 Igor Pavlov 2007-12-06 p7zip Version 4.57 (locale=C,Utf16=off,HugeFiles=on,4 CPUs) Processing archive: myfile.fq.xz Error: Can not open file as archive $ 7z x myfile.fq.xz 7-Zip 4.57 Copyright (c) 1999-2007 Igor Pavlov 2007-12-06 p7zip Version 4.57 (locale=C,Utf16=off,HugeFiles=on,4 CPUs) Processing archive: myfile.fq.xz Error: Can not open file as archive and with lzma $ lzma -d myfile.fq.xz J_12.fq.xz: unknown suffix -- unchanged with other option: $ lzma -S .xz -d myfile.fq.xz lzma: SetDecoderProperties() error

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  • Running CGI With Perl under Apache Permission Problem

    - by neversaint
    I have the following entry under apache2.conf in my Debian box. AddHandler cgi-script .cgi .pl Options +ExecCGI ScriptAlias /cgi-bin/ /var/www/mychosendir/cgi-bin/ Then I have a perl cgi script stored under these directories and permissions: [email protected]:/var/www/mychosendir$ ls -lhR .: total 12K drwxr-xr-x 2 nvs nvs 4.0K 2010-04-21 13:42 cgi-bin ./cgi-bin: total 4.0K -rwxr-xr-x 1 nvs nvs 90 2010-04-21 13:40 test.cgi However when I tried to access it in the web browser: http://myhost.com/mychosendir/cgi-bin/test.cgi They gave me this error: Forbidden You don't have permission to access /mychosendir/cgi-bin/test.cgi on this server. What's wrong with it? Update: I also have the following entry in my apache2.conf: <Files ~ "^\.ht"> Order allow,deny Deny from all </Files>

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  • Running CGI With Perl under Apache Permission Problem

    - by neversaint
    I have the following entry under apache2.conf in my Debian box. AddHandler cgi-script .cgi .pl Options +ExecCGI ScriptAlias /cgi-bin/ /var/www/mychosendir/cgi-bin/ <Directory /var/www/mychosendir/cgi-bin> Options +ExecCGI -Indexes allow from all </Directory> Then I have a perl cgi script stored under these directories and permissions: [email protected]:/var/www/mychosendir$ ls -lhR .: total 12K drwxr-xr-x 2 nvs nvs 4.0K 2010-04-21 13:42 cgi-bin ./cgi-bin: total 4.0K -rwxr-xr-x 1 nvs nvs 90 2010-04-21 13:40 test.cgi However when I tried to access it in the web browser: http://myhost.com/mychosendir/cgi-bin/test.cgi They gave me this error: [Wed Apr 21 15:26:09 2010] [error] [client 150.82.219.158] (8)Exec format error: exec of '/var/www/mychosendir/cgi-bin/test.cgi' failed [Wed Apr 21 15:26:09 2010] [error] [client 150.82.219.158] Premature end of script headers: test.cgi What's wrong with it? Update: I also have the following entry in my apache2.conf: <Files ~ "^\.ht"> Order allow,deny Deny from all </Files> And the content of test.cgi is this: #!/usr/bin/perl -wT print "Content-type: text/html\n\n"; print "Hello, world!\n";

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  • Running CGI With Perl under Apache Permission Problem

    - by neversaint
    I have the following entry under apache2.conf in my Debian box. AddHandler cgi-script .cgi .pl Options +ExecCGI ScriptAlias /mychosendir/cgi-bin/ /var/www/mychosendir/cgi-bin/ <Directory /var/www/mychosendir/cgi-bin> Options +ExecCGI -Indexes allow from all </Directory> Then I have a perl cgi script stored under these directories and permissions: [email protected]:/var/www/mychosendir$ ls -lhR .: total 12K drwxr-xr-x 2 nvs nvs 4.0K 2010-04-21 13:42 cgi-bin ./cgi-bin: total 4.0K -rwxr-xr-x 1 nvs nvs 90 2010-04-21 13:40 test.cgi However when I tried to access it in the web browser: http://myhost.com/mychosendir/cgi-bin/test.cgi They gave me this error: [Wed Apr 21 15:26:09 2010] [error] [client 150.82.219.158] (8)Exec format error: exec of '/var/www/mychosendir/cgi-bin/test.cgi' failed [Wed Apr 21 15:26:09 2010] [error] [client 150.82.219.158] Premature end of script headers: test.cgi What's wrong with it? Update: I also have the following entry in my apache2.conf: <Files ~ "^\.ht"> Order allow,deny Deny from all </Files> And the content of test.cgi is this: #!/usr/bin/perl -wT print "Content-type: text/html\n\n"; print "Hello, world!\n";

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  • Joining Multiple Fields Using Unix Join

    - by neversaint
    How can I do it? I have a file that looks like this foo 1 scaf 3 bar 2 scaf 3.3 File2 looks like this foo 1 scaf 4.5 foo 1 boo 2.3 bar 2 scaf 1.00 What I want to do is to fine lines that co-occur in file1 and file2 when field 1,2,3 are the same. Is there a way to do it?

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  • Add URL link in CSS Background Image?

    - by neversaint
    I have a CSS entry that looks like this: .header { background-image: url("./images/recountLogo.png"); background-repeat: no-repeat; height:160px; padding-left:280px; padding-top:50px; width:470px; color: #eaeaea; border-bottom:1px solid #eaeaea; } How can I add the link to the the background image in that CSS? The full CSS can be found here and the html that uses is there.

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  • How can I extract paragaphs and selected lines with Perl?

    - by neversaint
    I have a text where I need to: to extract the whole paragraph under the section "Aceview summary" until the line that starts with "Please quote" (not to be included). to extract the line that starts with "The closest human gene". to store them into array with two elements. The text looks like this (also on pastebin): AceView: gene:1700049G17Rik, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView. <META NAME="title" CONTENT=" AceView: gene:1700049G17Rik a comprehensive annotation of human, mouse and worm genes with mRNAs or EST"> <META NAME="keywords" CONTENT=" AceView, genes, Acembly, AceDB, Homo sapiens, Human, nematode, Worm, Caenorhabditis elegans , WormGenes, WormBase, mouse, mammal, Arabidopsis, gene, alternative splicing variant, structure, sequence, DNA, EST, mRNA, cDNA clone, transcript, transcription, genome, transcriptome, proteome, peptide, GenBank accession, dbest, RefSeq, LocusLink, non-coding, coding, exon, intron, boundary, exon-intron junction, donor, acceptor, 3'UTR, 5'UTR, uORF, poly A, poly-A site, molecular function, protein annotation, isoform, gene family, Pfam, motif ,Blast, Psort, GO, taxonomy, homolog, cellular compartment, disease, illness, phenotype, RNA interference, RNAi, knock out mutant expression, regulation, protein interaction, genetic, map, antisense, trans-splicing, operon, chromosome, domain, selenocysteine, Start, Met, Stop, U12, RNA editing, bibliography"> <META NAME="Description" CONTENT= " AceView offers a comprehensive annotation of human, mouse and nematode genes reconstructed by co-alignment and clustering of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes, their functions, alternative variants, expression, regulation and interactions, in the hope to stimulate further validating experiments at the bench "> <meta name="author" content="Danielle Thierry-Mieg and Jean Thierry-Mieg, NCBI/NLM/NIH, [email protected]"> <!-- var myurl="av.cgi?db=mouse" ; var db="mouse" ; var doSwf="s" ; var classe="gene" ; //--> However I am stuck with the following script logic. What's the right way to achieve that? #!/usr/bin/perl -w my $INFILE_file_name = $file; # input file name open ( INFILE, '<', $INFILE_file_name ) or croak "$0 : failed to open input file $INFILE_file_name : $!\n"; my @allsum; while ( <INFILE> ) { chomp; my $line = $_; my @temp1 = (); if ( $line =~ /^ AceView summary/ ) { print "$line\n"; push @temp1, $line; } elsif( $line =~ /Please quote/) { push @allsum, [@temp1]; @temp1 = (); } elsif ($line =~ /The closest human gene/) { push @allsum, $line; } } close ( INFILE ); # close input file # Do something with @allsum There are many files like that I need to process.

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  • Unzipping ".xz" file with 7z and lzma

    - by neversaint
    I tried to uncompressed a "*.xz" file with both 7z and lzma. But they gave me such message: $ 7z x J_12.fq.xz 7-Zip 4.57 Copyright (c) 1999-2007 Igor Pavlov 2007-12-06 p7zip Version 4.57 (locale=C,Utf16=off,HugeFiles=on,4 CPUs) Processing archive: J_12.fq.xz Error: Can not open file as archive $ 7z x J_12.fq.xz 7-Zip 4.57 Copyright (c) 1999-2007 Igor Pavlov 2007-12-06 p7zip Version 4.57 (locale=C,Utf16=off,HugeFiles=on,4 CPUs) Processing archive: J_12.fq.xz Error: Can not open file as archive and with lzma $ lzma -d J_12.fq.xz J_12.fq.xz: unknown suffix -- unchanged

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  • Running CGI With Perl under Apache Permission Problem

    - by neversaint
    I have the following entry under apache2.conf in my Debian box. AddHandler cgi-script .cgi .pl Options +ExecCGI ScriptAlias /cgi-bin/ /var/www/mychosendir/cgi-bin/ Then I have a perl cgi script stored under these directories and permissions: [email protected]:/var/www/mychosendir$ ls -lhR .: total 12K drwxr-xr-x 2 nvs nvs 4.0K 2010-04-21 13:42 cgi-bin ./cgi-bin: total 4.0K -rwxr-xr-x 1 nvs nvs 90 2010-04-21 13:40 test.cgi However when I tried to access it in the web browser: http://myhost.com/mychosendir/cgi-bin/test.cgi They gave me this error: Forbidden You don't have permission to access /mychosendir/cgi-bin/test.cgi on this server. What's wrong with it?

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  • AWK If/ElseConditional Problem

    - by neversaint
    I have a data that looks like this: foo foo scaffold_7 1 4845 6422 4845 bar bar scaffold_7 -1 14689 16310 16310 What I want to do is to process the above lines where I just want to print column 1,2,3, 7 and one more column after 7th. But with condition when printing column 7 onwards. Below is my awk script: awk '{ if ($4=="+") { {end=$6-$5}{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $7 "\t" end+$7} } else {end=$6-$5}{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $7-end "\t" $7} }' But why it doesn't achieve the desired result like this? foo foo scaffold_7 1 4845 6422 bar bar scaffold_7 -1 14689 16310 Note that the arithmetic (e.g. $7-end or end+$7) is a must. So we can't just swap column from input file. Furthermore this AWK will be inside a bash script.

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  • Convert Chunk of Data into Tabular Format Using Perl

    - by neversaint
    I have a data that looks like this 1:SRX000566 Submitter: WoldLab Study: RNASeq expression profiling for ENCODE project(SRP000228) Sample: Human cell line GM12878(SRS000567) Instrument: Solexa 1G Genome Analyzer Total: 4 runs, 62.7M spots, 2.1G bases Run #1: SRR002055, 11373440 spots, 375323520 bases Run #2: SRR002063, 22995209 spots, 758841897 bases Run #3: SRR005091, 13934766 spots, 459847278 bases Run #4: SRR005096, 14370900 spots, 474239700 bases 2:SRX000565 Submitter: WoldLab Study: RNASeq expression profiling for ENCODE project(SRP000228) Sample: Human cell line GM12878(SRS000567) Instrument: Solexa 1G Genome Analyzer Total: 3 runs, 51.2M spots, 1.7G bases Run #1: SRR002052, 12607931 spots, 416061723 bases Run #2: SRR002054, 12880281 spots, 425049273 bases Run #3: SRR002060, 25740337 spots, 849431121 bases 3:SRX012407 Submitter: GEO Study: GSE17153: Illumina sequencing of small RNAs from C. elegans embryos(SRP001363) Sample: Caenorhabditis elegans(SRS006961) Instrument: Illumina Genome Analyzer II Total: 1 run, 3M spots, 106.8M bases Run #1: SRR029428, 2965597 spots, 106761492 bases Is there a compact way to convert them into tabular format (tab separated). Hence 1 entry/row per chunk. In these case 3 rows. I tried this but doesn't seem to work. perl -laF/\n/ -000ne"print join chr(9),@F" myfile.txt

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  • Converting FASTQ to FASTA with SED/AWK

    - by neversaint
    I have a data in that always comes in block of four in the following format (called FASTQ): @SRR018006.2016 GA2:6:1:20:650 length=36 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGN +SRR018006.2016 GA2:6:1:20:650 length=36 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!+! @SRR018006.19405469 GA2:6:100:1793:611 length=36 ACCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +SRR018006.19405469 GA2:6:100:1793:611 length=36 7);;).;);;/;*.2>/@@7;@77<..;)58)5/>/ Is there a simple sed/awk/bash way to convert them into this format (called FASTA): >SRR018006.2016 GA2:6:1:20:650 length=36 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGN >SRR018006.19405469 GA2:6:100:1793:611 length=36 ACCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC In principle we want to extract the first two lines in each block-of-4 and replace @ with >.

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  • Inserting text to a file with Sed within Bash Script

    - by neversaint
    I tried to insert a text to the first line of a file using sed. I do this inside a bash script. But why it hangs at the line of sed execution? #! /bin/bash # Command to execute # ./mybashcode.sh test.nbq nbqfile=$1 nbqbase=$(basename $nbqfile nbq) taglistfiletemp="${nbqbase}taglist_temp" taglistfile="${nbqbase}taglist" ./myccode $nbqfile | sort | uniq -c | awk '{print $2}' > $taglistfiletemp noftags=$(wc -l $taglistfiletemp | awk '{print $1}') echo $noftags # We want to append output of noftags # to the first line of taglistfile sed '1i\ $noftags' > $taglistfile # why it hangs here # the content of taglistfile is NIL

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  • How to embedd cgi in html

    - by neversaint
    I have no problem executing a cgi file under the normal url like this: http://www.myhost.com/mydir/cgi-bin/test.cgi However when I tried to embedd it into HTML file (called index.html) like this: <HTML> <BODY> <P>Here's the output from my program: <FORM ACTION="/var/www/mydir/cgi-bin/test.cgi" METHOD=POST> </FORM> </P> </BODY> </HTML> The CGI doesn't get executed when I do: http://www.myhost.com/mydir/index.html The CGI file (test.cgi) simply looks like this: #!/usr/bin/perl -wT use CGI::Carp qw(fatalsToBrowser); print "Test cgi!\n"; What's the right way to do it?

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  • Replacing Part of Text Using Sed

    - by neversaint
    I have the following text file Eif2ak1.aSep07 Eif2ak1.aSep07 LOC100042862.aSep07-unspliced NADH5_C.0.aSep07-unspliced LOC100042862.aSep07-unspliced NADH5_C.0.aSep07-unspliced What I want to do is to remove all the text starting from period (.) to the end. But why this command doesn't do it? sed 's/\.*//g' myfile.txt What's the right way to do it?

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  • How to extract paragaph and selected lines with Perl

    - by neversaint
    I have a text that looks like this. What I want to do is to extract the whole paragraph under the section "Aceview summary" until the line that starts with "Please quote". extract the line that starts with "The closest human gene". And store them into array with two elements. However I am stuck with the following script logic. What's the right way to achieve that? #!/usr/bin/perl -w my $INFILE_file_name = $file; # input file name open ( INFILE, '<', $INFILE_file_name ) or croak "$0 : failed to open input file $INFILE_file_name : $!\n"; my @allsum; while ( <INFILE> ) { chomp; my $line = $_; my @temp1 = (); if ( $line =~ /^ AceView summary/ ) { print "$line\n"; push @temp1, $line; } elsif( $line =~ /Please quote/) { push @allsum, [@temp1]; @temp1 = (); } } close ( INFILE ); # close input file

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