User:Lindenb/Notebook/UMR915/20110221
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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
