A Boycott for NPG journals?

NPG as in Nature Publishing Group for those not in the know, this includes the journal Nature. What might have sparked off this?
An impending price increase of 400% for journal subscription.

Michael Eisen, nailed it down it his blog post.
I totally agree with his view especially how he describes the situation as:
"Only one thing — short of outright insanity — can lead a company to think they can get away with this kind of behavior: a monopoly. And it is the monopolistic, and grossly unfair and irrational, business model that NPG and most other scientific publishers employ that should be the real target of any organized action from UC faculty."

Jonathan Eisen also has interesting things posted here

I think the price increase might be a good move to persuade researchers to use soft copies of journals instead of having to resorting to print. But as Michael rightly points out. It shouldn't be an issue of price. And price increase in this climate, I think NPG might be making a wrong move here.

What are your thoughts? Would you adhere to such a boycott if your department is against the idea?

Do you talk awk ?

Neat file! I have one of my own recipes but it pales in comparison to this .. anyway.. is it possible to write 2 lines of awk code? rofl.

HANDY ONE-LINE SCRIPTS FOR AWK                               30 April 2008
Compiled by Eric Pement - eric [at] pement.org               version 0.27

Latest version of this file (in English) is usually at:
   http://www.pement.org/awk/awk1line.txt

This file will also be available in other languages:
   Chinese  - http://ximix.org/translation/awk1line_zh-CN.txt   

USAGE:

   Unix: awk '/pattern/ {print "$1"}'    # standard Unix shells
DOS/Win: awk '/pattern/ {print "$1"}'    # compiled with DJGPP, Cygwin
         awk "/pattern/ {print \"$1\"}"  # GnuWin32, UnxUtils, Mingw

Note that the DJGPP compilation (for DOS or Windows-32) permits an awk
script to follow Unix quoting syntax '/like/ {"this"}'. HOWEVER, if the
command interpreter is CMD.EXE or COMMAND.COM, single quotes will not
protect the redirection arrows (<, >) nor do they protect pipes (|).
These are special symbols which require "double quotes" to protect them
from interpretation as operating system directives. If the command
interpreter is bash, ksh or another Unix shell, then single and double
quotes will follow the standard Unix usage.

Users of MS-DOS or Microsoft Windows must remember that the percent
sign (%) is used to indicate environment variables, so this symbol must
be doubled (%%) to yield a single percent sign visible to awk.

If a script will not need to be quoted in Unix, DOS, or CMD, then I
normally omit the quote marks. If an example is peculiar to GNU awk,
the command 'gawk' will be used. Please notify me if you find errors or
new commands to add to this list (total length under 65 characters). I
usually try to put the shortest script first. To conserve space, I
normally use '1' instead of '{print}' to print each line. Either one
will work.

FILE SPACING:

 # double space a file
 awk '1;{print ""}'
 awk 'BEGIN{ORS="\n\n"};1'

 # double space a file which already has blank lines in it. Output file
 # should contain no more than one blank line between lines of text.
 # NOTE: On Unix systems, DOS lines which have only CRLF (\r\n) are
 # often treated as non-blank, and thus 'NF' alone will return TRUE.
 awk 'NF{print $0 "\n"}'

 # triple space a file
 awk '1;{print "\n"}'

NUMBERING AND CALCULATIONS:

 # precede each line by its line number FOR THAT FILE (left alignment).
 # Using a tab (\t) instead of space will preserve margins.
 awk '{print FNR "\t" $0}' files*

 # precede each line by its line number FOR ALL FILES TOGETHER, with tab.
 awk '{print NR "\t" $0}' files*

 # number each line of a file (number on left, right-aligned)
 # Double the percent signs if typing from the DOS command prompt.
 awk '{printf("%5d : %s\n", NR,$0)}'

 # number each line of file, but only print numbers if line is not blank
 # Remember caveats about Unix treatment of \r (mentioned above)
 awk 'NF{$0=++a " :" $0};1'
 awk '{print (NF? ++a " :" :"") $0}'

 # count lines (emulates "wc -l")
 awk 'END{print NR}'

 # print the sums of the fields of every line
 awk '{s=0; for (i=1; i<=NF; i++) s=s+$i; print s}'

 # add all fields in all lines and print the sum
 awk '{for (i=1; i<=NF; i++) s=s+$i}; END{print s}'

 # print every line after replacing each field with its absolute value
 awk '{for (i=1; i<=NF; i++) if ($i < 0) $i = -$i; print }'
 awk '{for (i=1; i<=NF; i++) $i = ($i < 0) ? -$i : $i; print }'

 # print the total number of fields ("words") in all lines
 awk '{ total = total + NF }; END {print total}' file

 # print the total number of lines that contain "Beth"
 awk '/Beth/{n++}; END {print n+0}' file

 # print the largest first field and the line that contains it
 # Intended for finding the longest string in field #1
 awk '$1 > max {max=$1; maxline=$0}; END{ print max, maxline}'

 # print the number of fields in each line, followed by the line
 awk '{ print NF ":" $0 } '

 # print the last field of each line
 awk '{ print $NF }'

 # print the last field of the last line
 awk '{ field = $NF }; END{ print field }'

 # print every line with more than 4 fields
 awk 'NF > 4'

 # print every line where the value of the last field is > 4
 awk '$NF > 4'

STRING CREATION:

 # create a string of a specific length (e.g., generate 513 spaces)
 awk 'BEGIN{while (a++<513) s=s " "; print s}'

 # insert a string of specific length at a certain character position
 # Example: insert 49 spaces after column #6 of each input line.
 gawk --re-interval 'BEGIN{while(a++<49)s=s " "};{sub(/^.{6}/,"&" s)};1'

ARRAY CREATION:

 # These next 2 entries are not one-line scripts, but the technique
 # is so handy that it merits inclusion here.
 
 # create an array named "month", indexed by numbers, so that month[1]
 # is 'Jan', month[2] is 'Feb', month[3] is 'Mar' and so on.
 split("Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec", month, " ")

 # create an array named "mdigit", indexed by strings, so that
 # mdigit["Jan"] is 1, mdigit["Feb"] is 2, etc. Requires "month" array
 for (i=1; i<=12; i++) mdigit[month[i]] = i

TEXT CONVERSION AND SUBSTITUTION:

 # IN UNIX ENVIRONMENT: convert DOS newlines (CR/LF) to Unix format
 awk '{sub(/\r$/,"")};1'   # assumes EACH line ends with Ctrl-M

 # IN UNIX ENVIRONMENT: convert Unix newlines (LF) to DOS format
 awk '{sub(/$/,"\r")};1'

 # IN DOS ENVIRONMENT: convert Unix newlines (LF) to DOS format
 awk 1

 # IN DOS ENVIRONMENT: convert DOS newlines (CR/LF) to Unix format
 # Cannot be done with DOS versions of awk, other than gawk:
 gawk -v BINMODE="w" '1' infile >outfile

 # Use "tr" instead.
 tr -d \r outfile            # GNU tr version 1.22 or higher

 # delete leading whitespace (spaces, tabs) from front of each line
 # aligns all text flush left
 awk '{sub(/^[ \t]+/, "")};1'

 # delete trailing whitespace (spaces, tabs) from end of each line
 awk '{sub(/[ \t]+$/, "")};1'

 # delete BOTH leading and trailing whitespace from each line
 awk '{gsub(/^[ \t]+|[ \t]+$/,"")};1'
 awk '{$1=$1};1'           # also removes extra space between fields

 # insert 5 blank spaces at beginning of each line (make page offset)
 awk '{sub(/^/, "     ")};1'

 # align all text flush right on a 79-column width
 awk '{printf "%79s\n", $0}' file*

 # center all text on a 79-character width
 awk '{l=length();s=int((79-l)/2); printf "%"(s+l)"s\n",$0}' file*

 # substitute (find and replace) "foo" with "bar" on each line
 awk '{sub(/foo/,"bar")}; 1'           # replace only 1st instance
 gawk '{$0=gensub(/foo/,"bar",4)}; 1'  # replace only 4th instance
 awk '{gsub(/foo/,"bar")}; 1'          # replace ALL instances in a line

 # substitute "foo" with "bar" ONLY for lines which contain "baz"
 awk '/baz/{gsub(/foo/, "bar")}; 1'

 # substitute "foo" with "bar" EXCEPT for lines which contain "baz"
 awk '!/baz/{gsub(/foo/, "bar")}; 1'

 # change "scarlet" or "ruby" or "puce" to "red"
 awk '{gsub(/scarlet|ruby|puce/, "red")}; 1'

 # reverse order of lines (emulates "tac")
 awk '{a[i++]=$0} END {for (j=i-1; j>=0;) print a[j--] }' file*

 # if a line ends with a backslash, append the next line to it (fails if
 # there are multiple lines ending with backslash...)
 awk '/\\$/ {sub(/\\$/,""); getline t; print $0 t; next}; 1' file*

 # print and sort the login names of all users
 awk -F ":" '{print $1 | "sort" }' /etc/passwd

 # print the first 2 fields, in opposite order, of every line
 awk '{print $2, $1}' file

 # switch the first 2 fields of every line
 awk '{temp = $1; $1 = $2; $2 = temp}' file

 # print every line, deleting the second field of that line
 awk '{ $2 = ""; print }'

 # print in reverse order the fields of every line
 awk '{for (i=NF; i>0; i--) printf("%s ",$i);print ""}' file

 # concatenate every 5 lines of input, using a comma separator
 # between fields
 awk 'ORS=NR%5?",":"\n"' file

SELECTIVE PRINTING OF CERTAIN LINES:

 # print first 10 lines of file (emulates behavior of "head")
 awk 'NR < 11'

 # print first line of file (emulates "head -1")
 awk 'NR>1{exit};1'

  # print the last 2 lines of a file (emulates "tail -2")
 awk '{y=x "\n" $0; x=$0};END{print y}'

 # print the last line of a file (emulates "tail -1")
 awk 'END{print}'

 # print only lines which match regular expression (emulates "grep")
 awk '/regex/'

 # print only lines which do NOT match regex (emulates "grep -v")
 awk '!/regex/'

 # print any line where field #5 is equal to "abc123"
 awk '$5 == "abc123"'

 # print only those lines where field #5 is NOT equal to "abc123"
 # This will also print lines which have less than 5 fields.
 awk '$5 != "abc123"'
 awk '!($5 == "abc123")'

 # matching a field against a regular expression
 awk '$7  ~ /^[a-f]/'    # print line if field #7 matches regex
 awk '$7 !~ /^[a-f]/'    # print line if field #7 does NOT match regex

 # print the line immediately before a regex, but not the line
 # containing the regex
 awk '/regex/{print x};{x=$0}'
 awk '/regex/{print (NR==1 ? "match on line 1" : x)};{x=$0}'

 # print the line immediately after a regex, but not the line
 # containing the regex
 awk '/regex/{getline;print}'

 # grep for AAA and BBB and CCC (in any order on the same line)
 awk '/AAA/ && /BBB/ && /CCC/'

 # grep for AAA and BBB and CCC (in that order)
 awk '/AAA.*BBB.*CCC/'

 # print only lines of 65 characters or longer
 awk 'length > 64'

 # print only lines of less than 65 characters
 awk 'length < 64'

 # print section of file from regular expression to end of file
 awk '/regex/,0'
 awk '/regex/,EOF'

 # print section of file based on line numbers (lines 8-12, inclusive)
 awk 'NR==8,NR==12'

 # print line number 52
 awk 'NR==52'
 awk 'NR==52 {print;exit}'          # more efficient on large files

 # print section of file between two regular expressions (inclusive)
 awk '/Iowa/,/Montana/'             # case sensitive

SELECTIVE DELETION OF CERTAIN LINES:

 # delete ALL blank lines from a file (same as "grep '.' ")
 awk NF
 awk '/./'

 # remove duplicate, consecutive lines (emulates "uniq")
 awk 'a !~ $0; {a=$0}'

 # remove duplicate, nonconsecutive lines
 awk '!a[$0]++'                     # most concise script
 awk '!($0 in a){a[$0];print}'      # most efficient script

CREDITS AND THANKS:

Special thanks to the late Peter S. Tillier (U.K.) for helping me with
the first release of this FAQ file, and to Daniel Jana, Yisu Dong, and
others for their suggestions and corrections.

For additional syntax instructions, including the way to apply editing
commands from a disk file instead of the command line, consult:

  "sed & awk, 2nd Edition," by Dale Dougherty and Arnold Robbins
  (O'Reilly, 1997)

  "UNIX Text Processing," by Dale Dougherty and Tim O'Reilly (Hayden
  Books, 1987)

  "GAWK: Effective awk Programming," 3d edition, by Arnold D. Robbins
  (O'Reilly, 2003) or at http://www.gnu.org/software/gawk/manual/

To fully exploit the power of awk, one must understand "regular
expressions." For detailed discussion of regular expressions, see
"Mastering Regular Expressions, 3d edition" by Jeffrey Friedl (O'Reilly,
2006).

The info and manual ("man") pages on Unix systems may be helpful (try
"man awk", "man nawk", "man gawk", "man regexp", or the section on
regular expressions in "man ed").

USE OF '\t' IN awk SCRIPTS: For clarity in documentation, I have used
'\t' to indicate a tab character (0x09) in the scripts.  All versions of
awk should recognize this abbreviation.

#---end of file---

Yet another fasta splitter in perl

I love Miguel's explanation of bioinformatics "another way to torture biological data"
For me, I just massage them into the myriad of input formats that programs declare they require.. I never torture them!
Anyway to check out his variant on splitting fasta (I currently have python, csplit(linux), bioperl versions of fasta splitters)

Miguel's fasta splitter (into batches of fasta) requires BioPerl

More Documentation for Bioscope v1.2 ?

Jacob whom I presume is a bioscope developer blogs about how he intends to write a book entitled Bioscope for dummies. I think the title so ripe with double meanings that I think they should work on a campaign with that as a slogan!
Jokes for those in the know aside, Bioscope is sorely lacking in documentation. While the idea has been to make it a single click = analysed data I feel that there's a lot of scripts and binaries within the software framework that can be utilised by its own or with combination of other tools. For example, it's mapper (named mapreads i believe ) might be a good standalone colorspace mapping tool that one might use instead of BWA or BFAST or Bowtie if one so inclines to. But actually I am more interested to use the downstream SNP reporting tools after I have gotten my BAM file from another aligner. Sadly, I only just realised I might not be able to use Bioscope that way just recently.
By limiting the number of people getting the software and by limiting people who gets the software with no documentation to use it the way they want just creates frustration for users trying to use SOLiD for its accuracy. Not a bright thing to do when you are jostling for 2nd position in the game.

Illumina Cuts Price of Personal Genome Sequencing Service by At Least 60 Percent

For individuals, the new price will be $19,500, while groups of five or more participants using the same ordering physician will pay $14,500 per person. In addition, individuals with serious medical conditions for whom whole-genome sequencing could be of clinical value will pay $9,500 to have their genome sequenced. Read full article

Sequence Variant Analyzer SVA

The rapidly evolving high-throughput DNA sequencing technologies have now allowed the fast generation of large amount of sequence data for the purpose of performing such whole-genome sequencing studies, at a reasonable cost. S equence V ariant A nalyzer, or SVA , is a software tool that we have been developing to analyze the genetic variants identified from such studies.

SVA is designed for two specific aims:

(1) To annotate the biological functions of the identified genetic variants, visualize and organize them;
(2) To help find the genetic variants associated with or responsible for the biological traits or medical outcomes of interest.

SVA is:
a program designed to run on a LINUX platform, with a graphical user interface (GUI), meaning that the main functions of this program can be done with clicking buttons.

a program specifically designed for analyzing genetic variants that have already been called (identified) from a whole genome sequencing study. So do not try to find a function here to align short reads and call variants - SVA is not designed for those purposes - many other software tools, for example, BWA and SAMTOOLS , were developed for those purposes.

How it  works