Category: github

The newer versions of emacs include JavaScript and other user modes useful for modern app development:

$ git clone git://git.savannah.gnu.org/emacs.git
$ sudo yum groupinstall "Development Tools"
$ wget ftp://ftp.gnu.org/gnu/autoconf/autoconf-2.68.tar.bz2
$ tar jxvf autoconf-2.68.tar.bz2
$ cd autoconf-2.68
$ ./configure; make; sudo make install
$ sudo yum install texinfo libXpm-devel giflib-devel libtiff-devel libotf-devel  
$ cd ../emacs
$ make bootstrap; sudo make install

This process can take upwards of 20-30 minutes.

With the git repo state as of 24 March 2015:

$ emacs --version
GNU Emacs 25.0.50.1
Copyright (C) 2015 Free Software Foundation, Inc.
GNU Emacs comes with ABSOLUTELY NO WARRANTY.
You may redistribute copies of GNU Emacs
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING.

Via: http://haulynjason.net/weblog/?p=1592

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Finishing touches are in place for my convert2bed tool (GitHub site).

This utility converts common genomics data formats (BAM, GFF, GTF, PSL, SAM, VCF, WIG) to lexicographically-sorted UCSC BED format. It offers two benefits over alternatives:

  • It runs about 3-10x as fast as bedtools *ToBed equivalents
  • It converts all input fields in as non-lossy a way as possible, to allow recovery of data to the original format

As an example, here we use convert2bed on a 14M-read, indexed BAM file to a sorted BED file (data are piped to /dev/null) on a 4 GB, dual-Core 2 (2.4 GHz) workstation running RHEL 6:

$ samtools view -c ../DS27127A_GTTTCG_L001.uniques.sorted.bam
14090028

Conversion is performed with default options (sorted BED as output, using BEDOPS sort-bed):

$ time ./convert2bed -i bam < ../DS27127A_GTTTCG_L001.uniques.sorted.bam > /dev/null
[bam_header_read] EOF marker is absent. The input is probably truncated.

real 3m5.508s
user 0m25.702s
sys 0m8.602s

Here is the same conversion, performed with bedtools v2.22 bamToBed and sortBed:

$ time ../bedtools2/bin/bamToBed -i ../DS27127A_GTTTCG_L001.uniques.sorted.bam | ../bedtools2/bin/sortBed -i stdin > /dev/null

real    28m22.057s
user    2m58.579s
sys     0m41.605s

The use of convert2bed for this file offers a 9.1x speed improvement. Other large BAM files show similar conversion speedups.

Further time reductions are conferred with use of bam2bedcluster and bam2starchcluster scripts (TBA) which make use of GNU Parallel or a Sun Grid Engine job scheduler, reducing conversion time even further by breaking conversion tasks down by chromosome.

When testing is complete, code will be wrapped into the upcoming BEDOPS v2.4.3 release. Source is now available via GitHub.

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