User:Lindenb/Notebook/UMR915/20110221

=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