User:Lindenb/Notebook/UMR915/20110221

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20110218‎        Top        20110222       


Contents

Ensembl prediction API

setting PERL conf:

export PERL5LIB=${PWD}/bioperl-1.2.3:${PWD}/ensembl/modules:${PWD}/ensembl-compara/modules:${PWD}/ensembl-variation/modules:${PWD}/ensembl-functgenomics/modules

Problem:

-------------------- EXCEPTION --------------------
MSG: Start must be less than or equal to end+1
STACK Bio::EnsEMBL::Feature::new /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Feature.pm:139
STACK Bio::EnsEMBL::Variation::VariationFeature::new /home/lindenb/tmp/ENSEMBL/ensembl-variation/modules/Bio/EnsEMBL/Variation/VariationFeature.pm:177
STACK toplevel ./variant_effect_predictor.pl:309
Ensembl API version = 61

Belgium

Calling with mpileup:

/usr/local/package/samtools-0.1.10/samtools mpileup -uf /GENOTYPAGE/data/pubdb/ucsc/hg18/chromosomes/hg18.fa sample1.bam | /usr/local/package/samtools-0.1.10/bcftools/bcftools view -bvcg - > sample1.raw.bcf

/usr/local/package/samtools-0.1.10/samtools mpileup -uf /GENOTYPAGE/data/pubdb/ucsc/hg18/chromosomes/hg18.fa sample2.bam | /usr/local/package/samtools-0.1.10/bcftools/bcftools view -bvcg - > sample2.raw.bcf


/usr/local/package/samtools-0.1.10/bcftools/bcftools view sample1.raw.bcf  > sample1.20110221.bcf.vcf
/usr/local/package/samtools-0.1.10/bcftools/bcftools view sample2.raw.bcf  > sample2.20110221.bcf.vcf

Awk for pileup

/^chr4/	{
	$2=int($2)-219449
	print $0;
	next;
	}


/^chr19/	{
	$2=int($2)+49000
	print $0;
	next;
	}

	{
	print $0;
	}

TABIX

bunzip2  tabix-0.2.3.tar.bz2 
tar xf tabix-0.2.3.tar
cd tabix-0.2.3
tabix-0.2.3$ make
make[1]: Entering directory `/home/lindenb/package/tabix-0.2.3'
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  bgzf.c -o bgzf.o
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  kstring.c -o kstring.o
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  knetfile.c -o knetfile.o
knetfile.c: In function ‘kftp_send_cmd’:
knetfile.c:239: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
knetfile.c: In function ‘khttp_connect_file’:
knetfile.c:418: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  index.c -o index.o
ar -cru libtabix.a bgzf.o kstring.o knetfile.o index.o
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  main.c -o main.o
gcc -g -Wall -O2 -fPIC  -o tabix main.o -lm  -lz -L. -ltabix
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  bgzip.c -o bgzip.o
bgzip.c: In function ‘write_open’:
bgzip.c:57: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
bgzip.c: In function ‘main’:
bgzip.c:198: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
gcc -g -Wall -O2 -fPIC  -o bgzip bgzip.o bgzf.o knetfile.o -lz
make[1]: Leaving directory `/home/lindenb/package/tabix-0.2.3

~/package/tabix-0.2.3/bgzip knownGene.txt
~/package/tabix-0.2.3/tabix -s 2 -b 4 -e 5 knownGene.txt.gz

~/package/tabix-0.2.3/tabix   -s 2 -b 4 -e 5 knownGene.txt.gz -l
chr1
chr10
chr11
chr12
chr13
chr13_random
chr14
chr15
chr15_random
chr16
chr16_random
chr17
chr17_random
chr18
chr19
chr19_random
chr1_random
chr2
chr20
chr21
chr21_random
chr22
chr22_h2_hap1
chr22_random
chr2_random
chr3
chr3_random
chr4
chr4_random
chr5
chr5_h2_hap1
chr5_random
chr6
chr6_cox_hap1
chr6_qbl_hap2
chr6_random
chr7
chr7_random
chr8
chr8_random
chr9
chr9_random
chrM
chrX
chrX_random
chrY

lindenb@yokofakun:~/tmp$ ~/package/tabix-0.2.3/tabix  knownGene.txt.gz chr2:200000-250000
uc002qvu.1	chr2	-	208154	239852	208154	208154	8	208154,214863,219965,221022,223100,224159,237537,239730,	209001,214920,220044,221191,223229,224272,237602,239852,		uc002qvu.1
uc002qvv.1	chr2	-	208154	246690	208810	232800	12	208154,214863,219965,221022,223100,224159,232797,233502,237537,239730,243004,246206,	209001,214920,220044,221191,223229,224272,232871,233562,237602,239844,243115,246690,	Q96HL8-3	uc002qvv.1
uc002qvw.1	chr2	-	208154	250702	208154	208154	11	208154,219965,220546,223100,224159,232797,233502,237537,239730,243004,250084,	209001,220044,221191,223229,224272,232871,233562,237602,239844,243115,250702,		uc002qvw.1
uc002qvx.1	chr2	-	208154	254024	208810	253984	10	208154,214863,219965,221022,223100,224159,237537,239730,243004,253983,	209001,214920,220044,221191,223229,224272,237602,239844,243115,254024,	Q96HL8	uc002qvx.1
uc002qvy.1	chr2	-	208154	254024	208810	253984	9	208154,219965,221022,223100,224159,237537,239730,243004,253983,	209001,220044,221191,223229,224272,237602,239844,243115,254024,	Q96HL8-2	uc002qvy.1
uc002qvz.1	chr2	-	208154	254392	208154	208154	10	208154,214867,219965,221022,223100,224159,237537,239730,243004,254083,	209001,214920,220044,221191,223229,224272,237602,239844,243115,254392,		uc002qvz.1
uc002qwa.1	chr2	-	208154	254743	208154	208154	12	208154,214863,219965,221022,223100,224159,237537,239730,243004,250084,252200,254702,	209001,214920,220044,221191,223229,224272,237602,239844,243115,251130,252786,254743,		uc002qwa.1
uc010ewe.1	chr2	-	208154	254810	208810	232800	11	208154,219965,221022,223100,224159,232797,233502,237537,239730,243004,254781,	209001,220044,221191,223229,224272,232871,233562,237602,239844,243115,254810,	Q96HL8-4	uc010ewe.1
uc002qwb.2	chr2	-	229562	232178	229562	229562	1	229562,	232178,		uc002qwb.2
uc002qwc.1	chr2	-	233502	252786	233502	233502	6	233502,237537,239730,243004,250084,252630,	233562,237602,239844,243115,250702,252786,		uc002qwc.1

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