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  • Installing Python without root http stackoverflow com questions…

    http://petangueules.fr/wp-json/wp/v2/pages/225873 Installing Python without root.

    http://stackoverflow.com/questions/622744/unable-to-install-python-without-sudo-access

  • Quick and easy submission of R on Sun…

    Quick and easy submission of R on Sun Grid Engine

    Easiest way to submit R jobs

    Here are two scripts and a symlink I created to make it easy as possible to submit R jobs to your Grid:

    qsub-R

    If you normally do something along the lines of:

    user@exec:~$ nohup nice R CMD BATCH toodles.R
    Now all you need to do is:

    user@submit:~$ qsub-R toodles.R
    Your job 3540 (“toodles.R”) has been submitted
    qsub-R is linked to submit-R, a script I wrote. It calls qsub and submits a simple shell wrapper with the R file as an argument. It ends up in the queue and eventually your output arrives in the current directory: toodles.R.o3540

    Download it and install it. You’ll need to make the ‘qsub-R’ symlink to ‘3rd_party/uoa-dos/submit-R’ yourself, although there is one in the package already for lx24-x86: qsub-R.tar (10 KiB, tar)

    http://www.stat.auckland.ac.nz/~kimihia/sun-grid#submitting

  • When Mendeley bibliography duplicates instead of refreshing Check…

    When Mendeley bibliography duplicates instead of refreshing.

    Check whether the following option is set in Word 2007:
    Office button->Word Options->Advanced->General->Confirm file format conversion on open

    http://feedback.mendeley.com/forums/4941-mendeley-feedback/suggestions/1384943-bug-refresh-bibliography-in-word-creates-duplicat

  • Remove the first line in Perl $first line…

    Remove the first line in Perl

    $first_line = <>;

while (<>) {
    do_something();
}

  • Mask repetitive region using BEDtools intersectBed a reads…

    Mask repetitive region using BEDtools.

    intersectBed -a reads.bed -b repeat_region.bed -v

  • Viewing huge text files between specific lines $…

    Viewing huge text files; between specific lines

    $ sed -n 101,110p /var/log/cron

    10 Awesome Examples for Viewing Huge Log Files in Unix

  • Subsetting ranged data with its values Example subset…

    Subsetting ranged data with its values.
    Example
    subset reads according to the width

    > paired.read.rd
RangedData with 997111 rows and 1 value column across 1 space
          space             ranges   |   strand
                    | 
1          chr4 [ 146855,  146898]   |        +
2          chr4 [1322462, 1322493]   |        -
3          chr4 [ 135547,  135703]   |        +
4          chr4 [ 965138,  965228]   |        -
5          chr4 [ 614464,  614606]   |        +
6          chr4 [ 274244,  274297]   |        +
7          chr4 [1191851, 1191994]   |        -
8          chr4 [ 310251,  310393]   |        +
9          chr4 [ 524981,  525273]   |        +
...         ...                ... ...      ...
997103     chr4 [1071785, 1071930]   |        -
997104     chr4 [ 819270,  819409]   |        -
997105     chr4 [ 951987,  952139]   |        +
997106     chr4 [ 327573,  327659]   |        -
997107     chr4 [ 343265,  343289]   |        -
997108     chr4 [ 615827,  615992]   |        +
997109     chr4 [ 615402,  615423]   |        -
997110     chr4 [ 128254,  128323]   |        +
997111     chr4 [ 659492,  659641]   |        -


> paired.read.rd[width(paired.read.rd) > 100, ]
RangedData with 623327 rows and 1 value column across 1 space
          space             ranges   |   strand
                    | 
1          chr4 [ 135547,  135703]   |        +
2          chr4 [ 614464,  614606]   |        +
3          chr4 [1191851, 1191994]   |        -
4          chr4 [ 310251,  310393]   |        +
5          chr4 [ 524981,  525273]   |        +
6          chr4 [1174028, 1174189]   |        -
7          chr4 [1174480, 1174655]   |        +
8          chr4 [ 869049,  869191]   |        -
9          chr4 [ 595415,  595565]   |        +
...         ...                ... ...      ...
623319     chr4 [ 646433,  646588]   |        +
623320     chr4 [ 227923,  228078]   |        -
623321     chr4 [1204606, 1204767]   |        -
623322     chr4 [1013562, 1013741]   |        -
623323     chr4 [1071785, 1071930]   |        -
623324     chr4 [ 819270,  819409]   |        -
623325     chr4 [ 951987,  952139]   |        +
623326     chr4 [ 615827,  615992]   |        +
623327     chr4 [ 659492,  659641]   |        -

    Or subset() works, too.

  • Exchange current window with the next on Ctrl…

    Exchange current window with the next on.
    Ctrl-w x

  • The Minus File Again following the lead of…

    The Minus File
    Again following the lead of the standard shell utilities, Perl’s open function treats a file whose name is a single minus, “-“, in a special way. If you open minus for reading, it really means to access the standard input. If you open minus for writing, it really means to access the standard output.

    UPDATE
    ========
    The minus file is not working with 3-argument open.

    Bryan> How can I use the “safe” 3-argument open and still be able to read off a
    Bryan> pipe?

    You don’t. 2-arg open has to be good for something.

    And 2-arg open is perfectly safe if the second arg is a literal:

    open OTHER, “<-" or die; open my $handle, "<-" or die; Don't let anyone tell you "Always use 3-arg open" unless they also footnote it with "unless you have no variables involved". -- Randal L. Schwartz - Stonehenge Consulting Services, Inc. - +1 503 777 0095
    Smalltalk/Perl/Unix consulting, Technical writing, Comedy, etc. etc.
    See http://methodsandmessages.posterous.com/ for Smalltalk discussion

  • Finding nearby genes using MySQL query to the…

    Finding nearby genes using MySQL query to the public server of USCS.

    http://genomewiki.ucsc.edu/index.php/Finding_nearby_genes