cjfields

[cjfields@cjfields-imac comp-fail]$ cat Bar.pm6
role Bar {
    has Str $.my-str handles <lines words>
};

[cjfields@cjfields-imac comp-fail]$ cat Foo.pm6
use lib '.';

use Bar;

cjfields

[cjfields@cjfields-imac panda (master)]$ perl6 -v
This is perl6 version 2014.11-65-gdfcf9fc built on MoarVM version 2014.11-64-g650333f
[cjfields@cjfields-imac panda (master)]$ panda install NativeCall
==> Fetching NativeCall
==> Building NativeCall
Compiling lib/NativeCall.pm6 to mbc
==> Testing NativeCall
t/01-argless.t ......... ok
t/02-simple-args.t ..... ok
t/03-simple-returns.t .. ok

cjfields

[cjfields@Chriss-MacBook-Pro bioperl6]$ cat test.fasta
>roa1_drome Rea guano receptor type III >> 0.1
MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVV
VMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVK
KLFVGALKDDHDEQSIRDYFQHFGNIVDNIVIDKETGKKRGFAFVEFDDYDPVDKVVLQK
QHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGN
NWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGND
FGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY
>roa2_drome Rea guano ligand
MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVV

cjfields

[cjfields@Chriss-MacBook-Pro bioperl6 (master)]$ prove6 -l -v t/Role/Aliased.t
t/Role/Aliased.t ..
ok 1 -
not ok 2 - adds alias

# Failed test 'adds alias'
# at t/Role/Aliased.t line 23
ok 3 -
1..3
# Looks like you failed 1 tests of 3

cjfields

use v6;

use Test;

use Bio::Tools::CodonTable; 
use Bio::PrimarySeq; 

done();

cjfields

-system-specific-4.1$ samtools view -h Control_Input_2_GAGTGG_L008_R1_001.trimmed.sorted.bam | head -n 100
@HD	VN:1.0	SO:coordinate
@PG	ID:novoalign	PN:novoalign	VN:V3.02.00	CL:novoalign -c 7 -d /home/mirrors/igenome/Homo_sapiens/UCSC/hg19/Sequence/NovoalignIndex/WholeGenomeFasta.nvi -f /home/groups/hpcbio/projects/longley/2014-08-04/results/2014-08-06-alignment/Control_Input_2_GAGTGG_L008_R1_001.trimmed.fastq.gz -l 15 -r RANDOM -o SAM
@SQ	SN:chrM	LN:16571	AS:WholeGenomeFasta.nvi
@SQ	SN:chr1	LN:249250621	AS:WholeGenomeFasta.nvi
@SQ	SN:chr2	LN:243199373	AS:WholeGenomeFasta.nvi
@SQ	SN:chr3	LN:198022430	AS:WholeGenomeFasta.nvi
@SQ	SN:chr4	LN:191154276	AS:WholeGenomeFasta.nvi
@SQ	SN:chr5	LN:180915260	AS:WholeGenomeFasta.nvi
@SQ	SN:chr6	LN:171115067	AS:WholeGenomeFasta.nvi

cjfields

From bce13df624f703ac7501aaa83f87fe644f187c1a Mon Sep 17 00:00:00 2001
From: Chris Fields <cjfields@illinois.edu>
Date: Tue, 7 Jan 2014 14:31:47 -0600
Subject: [PATCH] API change in kent utils; not sure how to check for the
 version yet, so this branch will need a little more work

---
 Bio-BigFile/lib/Bio/DB/BigFile.xs | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

cjfields

==25851== Memcheck, a memory error detector
==25851== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
==25851== Using Valgrind-3.6.1-Debian and LibVEX; rerun with -h for copyright info
==25851== Command: lumpy -mw 4 -tt 1e-3 -sr bam_file:JHU_926_5_sr.sorted.bam,back_distance:20,weight:1,min_mapping_threshold:1,id:1
==25851== 
--25851-- Valgrind options:
--25851--    --suppressions=/usr/lib/valgrind/debian-libc6-dbg.supp
--25851--    -v
--25851--    --leak-check=yes
--25851-- Contents of /proc/version:

cjfields

#!/usr/bin/env perl
use Modern::Perl;
use Bio::DB::EUtilities;
# set optional history queue
my $factory = Bio::DB::EUtilities->new(-eutil      => 'esearch',
                                       -email      => 'cjfields@bioperl.org',
                                       -db         => 'nuccore',
                                       -term       => 'Nasonia vitripennis[organism] NOT 13660[BioProject] NOT WGS[Keyword]',
                                       -usehistory => 'y');
 

cjfields

#!/usr/bin/perl
use strict;
use warnings;
use Bio::DB::EUtilities;
use Bio::SeqIO;

# this needs to be a list of EntrezGene unique IDs
my @gene_ids = @ARGV;

my $eutil   = Bio::DB::EUtilities->new(-eutil => 'esummary',