wt12318 / tcep

Package preforming T cell epitope prediction

tcep's Issues

添加 IEDB 的 api

包括 MHC-I, MHC-II, MHC-I process 的 api：http://tools.iedb.org/main/tools-api/

各种方法的 HLA allele 在 api 返回的和 local 不一样

以 Local 为准，因为虽然某些 allele 在 API 上是支持的，但是实际使用的时候还是会报错

添加其他的预测工具

除了IEDB外其他常用的预测工具

增加其他文件格式的输入

• VCF，使用 annovar 进行注释, 先判断有没有注释，如果没有注释就调用 annovar 进行注释，然后提取注释后的信息（多肽）
• MAF， 先用 maf2vaf 进行转化（不要运行 VEP），然后进行注释
• TXT，用 anaovar 进行注释

对于 VCF ,MAF, TXT 增加对所有转录本的预测

同一个突变位点在不同的转录本上可能会产生不同的氨基酸的改变，需要增加不同转录本的预测，annovar 默认选第一个，pvacseq的处理：

pVACseq only makes predictions for those transcripts of a variant that were annotated as missense_variant, inframe_insertion, inframe_deletion, inframe protein_altering_variant, or frameshift_variant by VEP as long as the transcript was not also annotated as start_lost.

不同格式的数据整合

VCF MAF TXT 函数整合

ANNOVAR 注释改成 table_annovar

table_annovar 更加方便，还支持多线程

Annovar 注释的 exonic_variant_function 中的氨基酸改变和 coding change 中不一样

示例文件：

chr7	55155850	55155850	C	T

运行代码：

~/software/annovar/annotate_variation.pl -out ~/tmp/mhcbinding/test/test -build hg38 ~/tmp/mhcbinding/test/test.txt ~/software/annovar/humandb/ -hgvs -dbtype ensGene

~/software/annovar/coding_change.pl ~/tmp/mhcbinding/test/test.exonic_variant_function ~/software/annovar/humandb/hg38_ensGene.txt ~/software/annovar//humandb/hg38_ensGeneMrna.fa -includesnp -onlyAltering --alltranscript --outfile ~/tmp/mhcbinding/test/coding.txt

两个文件在 ENST00000638463.1 c.292C>T 的注释不一样：

line1	nonsynonymous SNV	EGFR:ENST00000420316.6:exon8:c.910C>T:p.H304Y,EGFR:ENST00000638463.1:exon4:c.292C>T:p.H98Y,EGFR:ENST00000344576.6:exon8:c.910C>T:p.H304Y,EGFR:ENST00000455089.5:exon7:c.775C>T:p.H259Y,EGFR:ENST00000342916.7:exon8:c.910C>T:p.H304Y,EGFR:ENST00000275493.6:exon8:c.910C>T:p.H304Y,EGFR:ENST00000454757.6:exon7:c.775C>T:p.H259Y,	chr7	55155850	55155850	C	T

>line1 ENST00000638463.1 c.292C>T p.H98_R464delinsYGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCNLLEGEPREFVENSECIQCHPECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTLVWKYADAGHVCHLCHPNCTYGCTGPGLEGCPTNGPKIPSIATGMVGALLLLLVVALGIGLFMRRRHIVRKRTLRRLLQERELVEPLTPSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGFFSSPSTSRTPLLSSLSATSNNSTVACIDRNGLQSCPIKEDSFLQRYSSDPTGALTEDSIDDTFLPVPEYINQSVPKRPAGSVQNPVYHNQPLNPAPSRDPHYQDPHSTAVGNPEYLNTVQPTCVNSTFDSPAHWAQKGSHQISLDNPDYQQDFFPKEAKPNGIFKGSTAENAEYLRVAPQSSEFIGA* protein-altering  (position 98-464 changed from HGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCNLLEGEPREFVENSECIQCHPECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTLVWKYADAGHVCHLCHPNCTYGCTGPGLEGCPTNGPKIPSIATGMVGALLLLLVVALGIGLFMRR to YGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCNLLEGEPREFVENSECIQCHPECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTLVWKYADAGHVCHLCHPNCTYGCTGPGLEGCPTNGPKIPSIATGMVGALLLLLVVALGIGLFMRRRHIVRKRTLRRLLQERELVEPLTPSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGFFSSPSTSRTPLLSSLSATSNNSTVACIDRNGLQSCPIKEDSFLQRYSSDPTGALTEDSIDDTFLPVPEYINQSVPKRPAGSVQNPVYHNQPLNPAPSRDPHYQDPHSTAVGNPEYLNTVQPTCVNSTFDSPAHWAQKGSHQISLDNPDYQQDFFPKEAKPNGIFKGSTAENAEYLRVAPQSSEFIGA*)
MSSLTKIICAQQCSGRCRGKSPSDCCHNQCAAGCTGPRESDCLVCRKFRDEATCKDTCPPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYVVTDYGS
CVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLL
IQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQVC
HALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCNLLEGEPREFVENSECIQCHPECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTL
VWKYADAGHVCHLCHPNCTYGCTGPGLEGCPTNGPKIPSIATGMVGALLLLLVVALGIGLFMRRRHIVRKRTLRRLLQERELVEPLTPSGEAPNQALLRI
LKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHK
DNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWE
LMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEED
MDDVVDADEYLIPQQGFFSSPSTSRTPLLSSLSATSNNSTVACIDRNGLQSCPIKEDSFLQRYSSDPTGALTEDSIDDTFLPVPEYINQSVPKRPAGSVQ
NPVYHNQPLNPAPSRDPHYQDPHSTAVGNPEYLNTVQPTCVNSTFDSPAHWAQKGSHQISLDNPDYQQDFFPKEAKPNGIFKGSTAENAEYLRVAPQSSE
FIGA*

添加本地的IEDB预测工具

IEDB 的 API 只适用于数据量较少的情况，在数据量比较大时还是要使用本地的预测工具，因此在函数中加入 get_method 参数，可以选择 api 或者 client