search

immunomind / immunarch

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
https://immunarch.com
Apache License 2.0
303 stars 65 forks source link

repLoad question for MiXCR #123

Closed parkjaeming closed 10 months ago

parkjaeming commented 3 years ago

Hi, I am working with immunarch to analyse my paired RNA data, and I am facing a technical issue.

I used MiXCR to get full TCR/IG sequence using "assembleContigs" parameter. After that, I have loaded my dataset using "repLoad" function.

However, I was only able to retrieve data on CDR3 gene region such as aa sequences, leaving out other gene region information in my MiXCR data. Is there a possible way to get other gene region information through immunarch? Or is it not possible yet?

I would be grateful if you can help for this problem, Thank you.

Alexander230 commented 3 years ago

Hi, I am working with immunarch to analyse my paired RNA data, and I am facing a technical issue.

I used MiXCR to get full TCR/IG sequence using "assembleContigs" parameter. After that, I have loaded my dataset using "repLoad" function.

However, I was only able to retrieve data on CDR3 gene region such as aa sequences, leaving out other gene region information in my MiXCR data. Is there a possible way to get other gene region information through immunarch? Or is it not possible yet?

I would be grateful if you can help for this problem, Thank you.

Hi, could you, please, provide a sample of your data? I want to test how it will look after loading in Immunarch.

parkjaeming commented 3 years ago

Hi, I'm so sorry for replying late.

Actually, Immunarch works very well. But, after Immunarch::repLoad() function, only CDR3 sequence data have been included in the R environment. I attached one of my data named 'test_sample1_clonotypes.TRA.txt' below. As you can see, my MiXCR data has columns named 'nseqCDR1', 'nseqCDR2', 'nseqCDR3', and so on. Is there any way to gain those CDR1, CDR2 seq information? That is my question.

Thank you.

cloneId cloneCount cloneFraction targetSequences targetQualities allVHitsWithScore allDHitsWithScore allJHitsWithScore allCHitsWithScore allVAlignments allDAlignments allJAlignments allCAlignments nSeqFR1 minQualFR1 nSeqCDR1 minQualCDR1 nSeqFR2 minQualFR2 nSeqCDR2 minQualCDR2 nSeqFR3 minQualFR3 nSeqCDR3 minQualCDR3 nSeqFR4 minQualFR4 aaSeqFR1 aaSeqCDR1 aaSeqFR2 aaSeqCDR2 aaSeqFR3 aaSeqCDR3 aaSeqFR4 refPoints 229 23.0 0.1013215859030837 GGAACCCCGGTGCTGCTGAGGTGCAACTACTCATCTTCTTATTCACCATCTCTCTTCTGGTATGTGCAACACCCCAACAAAGGACTCCAGCTTCTCCTGAA,ATCAGCGGCCACCCTGGTTAAAGGCATCAACGGTTTTGAGGCTGAATTTAAGAAGAGTGAAACCTCCTTCCACCTGACGAAACCCTCAGCCCATATGAGCGACGCGGCTGAGTACTTCTGTGTTGTGAATGCCTACAAATACATCTTTGGAACAGGCACCAGGCTGAAGGTTTTAGCAAATATCCAGAACCCTGA,TGTACCAGCTGAGAGACTCTAAATCCAGTGACAAGTCTGTCTGCCTATTCAC [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[,[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[-[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[333333333333333333333333333333[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[)[))))[))[[))))[,[[[[[[0[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV8-200(439.3) TRAJ4000(235.5) TRAC00(224.7) 202|303|461|0|101||505.0,309|437|461|0|128||640.0, ,33|81|81|131|179||240.0, ,, TCTTCTTATTCACCATCT 58 AAAGGCATCAACGGTTTTGAGGCTGAATTTAAGAAGAGTGAAACCTCCTTCCACCTGACGAAACCCTCAGCCCATATGAGCGACGCGGCTGAGTACTTC 12 TGTGTTGTGAATGCCTACAAATACATCTTT 18 GGAACAGGCACCAGGCTGAAGGTTTTAGCAA 58 SSYSPS KGINGFEAEFKKSETSFHLTKPSAHMSDAAEYF CVVNAYKYIF GTGTRLKVLA_ :::::33:51:::::::::::::::,::::::::19:118:-4:128:::::131:-13:148:179::,::::::::::::::::::::: 300 17.0 0.07488986784140969 CTGGTACAGACAGGATTGCAGGAAAGAACCTAAGTTGCTGATGTCCGTATACTCCAGTGGTAATGAAGATGGAAGGTTTACAGCACAGCTCAATAGAGCCAGCCAGTATATTTCCCTGCTCATCAGAGACTCCAAGCTCAGTGATTCAGCCACCTACCTCTGTGTGGTGACCAGCCCTATGGATAGCAACTATCAGTTAATCTGGGGCGCTGGGACCAAGCTAATTATAAAGCCAGG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV12-100(640.3) TRAJ3300(262.9) 264|434|457|0|170||850.0 19|77|77|178|236||290.0 GTATACTCCAGTGGT 58 AATGAAGATGGAAGGTTTACAGCACAGCTCAATAGAGCCAGCCAGTATATTTCCCTGCTCATCAGAGACTCCAAGCTCAGTGATTCAGCCACCTACCTC 58 TGTGTGGTGACCAGCCCTATGGATAGCAACTATCAGTTAATCTGG 58 GGCGCTGGGACCAAGCTAATTATAAAGCCAG 58 VYSSG NEDGRFTAQLNRASQYISLLIRDSKLSDSATYL CVVTSPMDSNYQLIW GAGTKLIIKP_ :::::::46:61:160:-3:170:::::178:1:205:236:: 411 12.0 0.05286343612334802 ACCAGACATCTGGGTTCAACGGGCTGTTCTGGTACCAGCAACATGCTGGCGAAGCACCCACATTTCTGTCTTACAATGTTCTGGATGGTTTGGAGGAGAAA,CTAAAGGGTACAGTTACCTCCTTTTGAAGGAGCTCCAGATGAAAGACTCTGCCTCTTACCTCTGTGCTGTCCCTTCTTATAACCAGGGAGGAAAGCTTATCTTCGGACAGGGAACGGAGTTATCTGTGAAACCCAATATCCAGAACCCTGACCCTGCCGTGTACCAGCT [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[,[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[%[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV1-200(445.8) TRAJ2300(245.6) TRAC00(70.8) 221|322|446|0|101||505.0,350|420|446|0|70||350.0 ,24|83|83|76|135||295.0 , ACATCTGGGTTCAACGGG 58 CTGTTCTGGTACCAGCAACATGCTGGCGAAGCACCCACATTTCTGTCTTAC 58 AATGTTCTGGATGGTTTG 58 TGTGCTGTCCCTTCTTATAACCAGGGAGGAAAGCTTATCTTC 58 GGACAGGGAACGGAGTTATCTGTGAAACCCA 4 TSGFNG LFWYQQHAGEAPTFLSY NVLDGL CAVPSYNQGGKLIF GQGTELSVKP_ :::::5:23:74:92:::::::::::::,:::::::::62:-6:70:::::76:-4:104:135:: 498 10.0 0.04405286343612335 AGAAGACAGAAAGTCCAGCACCTTGATCCTGCCCCACGCTACGCTGAGAGACACTGCTGTGTACTATTGCATCGTCAGAGCCGGGCAGGCAACAAGCTAACTTTTGGAGGAGGAACCAGGGTGCTAGTTAAACCAAGTGAGTACTGGGG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV26-100(400) TRAJ1700(260) 345|425|448|0|80||400.0 31|83|83|84|136||260.0 TGCATCGTCAGAGCCGGGCAGGCAACAAGCTAACTTTT 58 GGAGGAGGAACCAGGGTGCTAGTTAAACCAA 58 CIVRAGGNKLTF GGGTRVLVKP :::::::::67:-3:80:::::84:-11:105:136:: 538 9.0 0.039647577092511016 CAGCTCCGTTATAAACTGCACTTACACAGACAGCTCCTCCACCTACTTATACTGGTATAAGCAAGAACCTGGAGCAGGTCTCCAGTTGCTGACGTATATTT,GGGACTCAGCTATCTACTTCTGTGCAGAGAGACCGAGCAACACAGGCAAACTAATCTTTGGGCAAGGGACAACTTTACAAGTAAAACCAGATATCCAGAACCCTGACCCTGCCGTG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[,[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[/[[[[/[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV500(480) TRAJ3700(266.4) TRAC00(80) 210|311|460|0|101||505.0,407|438|460|0|31||155.0 ,28|82|82|36|90||270.0 , GACAGCTCCTCCACCTAC 58 TTATACTGGTATAAGCAAGAACCTGGAGCAGGTCTCCAGTTGCTGACGTAT 58 TGTGCAGAGAGACCGAGCAACACAGGCAAACTAATCTTT 58 GGGCAAGGGACAACTTTACAAGTAAAACCAG 14 DSSSTY LYWYKQEPGAGLQLLTY CAERPSNTGKLIF GQGTTLQVKP_ :::::28:46:97::::::::::::::,:::::::::20:-2:31:::::36:-8:59:90:: 546 9.0 0.039647577092511016 GTCACCGTTTTATTGAATAAGACAGTGAAACATCTCTCTCTGCAAATTGCAGCTACTCAACCTGGAGACTCAGCTGTCTACTTTTGTGCAGCCGCGCAAGGAAATGAGAAATTAACCTTTGGGACTGG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV13-200(455) TRAJ4800(145) 343|434|460|0|91||455.0 31|60|83|99|128||145.0 TGTGCAGCCGCGCAAGGAAATGAGAAATTAACCTTT 58 CAAAQGNEKLTF :::::::::84:-6:91:::::99:-11:120::: 577 8.0 0.03524229074889868 AGTGATTCAGCCACCTACCTCTGTGCCGTGATTAGGAGGGGGTCTAACCAGGGAGGAAAGCTTATCTTCGGACAGGGAACGGAGTTATCTGTGAAACCCAG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV12-200(155) TRAJ2300(280) 409|440|463|0|31||155.0 27|83|83|44|100||280.0 TGTGCCGTGATTAGGAGGGGGTCTAACCAGGGAGGAAAGCTTATCTTC 58 GGACAGGGAACGGAGTTATCTGTGAAACCCA 58 CAVIRRGSNQGGKLIF GQGTELSVKP_ :::::::::21:-3:31:::::44:-7:69:100:: 586 8.0 0.03524229074889868 CCTCAGTCCATATAAGCGACACGGCTGAGTACTTCTGTGCTGTGAGTCCCAGTGGAGGTAGCAACTATAAACTGACATTTGGAAAAGGAACTCTCTTAACCGTGAATCCAAATATCCAGAACCCTGACCCTGCCGTGTACCAGCTGAGAGACTCTAAATCCAGTGACG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV8-600(235) TRAJ5300(305) TRAC00(269) 392|439|461|0|47||235.0 25|86|86|50|111||305.0 TGTGCTGTGAGTCCCAGTGGAGGTAGCAACTATAAACTGACATTT 58 GGAAAAGGAACTCTCTTAACCGTGAATCCAA 58 CAVSPSGGSNYKLTF GKGTLLTVNP :::::::::35:-2:47:::::50:-5:80:111:: 661 7.0 0.030837004405286344 AAACCCTCAGCCCATATGAGCGACGCGGCTGAGTACTTCTGTGTTGTGAGTGAGGAAAGGACCGGGGGAGGAAAGCTTATCTTCGGACAGGGAACGGAGTTATCTGTGAAACCCAATATCCAGAACCCTGACCCTGCCGTGTACCAGCTGAGAG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV8-400(266),TRAV8-200(265) TRAJ2300(250) TRAC00(195) 388|441|461|0|53|SC431T|249.0;427|441|461|39|53||70.0 33|83|83|65|115||250.0 TGTGTTGTGAGTGAGGAAAGGACCGGGGGAGGAAAGCTTATCTTC 58 GGACAGGGAACGGAGTTATCTGTGAAACCCA 58 CVVSEERTGGGKLIF GQGTELSVKP :::::::::39:0:53:::::65:-13:84:115:: 665 7.0 0.030837004405286344 GATTCACTGTCTTCTTAAACAAAAGTGCCAAGCACCTCTCTCTGCACATTGTGCCCTCCCAGCCTGGAGACTCTGCAGTGTACTTCTGTGCAGCAACTTTTACTCTGGCAACACAGGCAAACTAATCTTTGGGCAAGGGACAACTTTACAAGTAAAACCAGGTAGGTCTGGAT [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV29DV500(480) TRAJ3700(295) 359|455|478|0|96||480.0 23|82|82|102|161||295.0 TGTGCAGCAACTTTTACTCTGGCAACACAGGCAAACTAATCTTT 58 GGGCAAGGGACAACTTTACAAGTAAAACCAG 58 CAATFTLNTGKLIF GQGTTLQVKP :::::::::86:-3:96:::::102:-3:130:161:: 714 7.0 0.030837004405286344 AAGAAAGACTGAAGGTCACCTTTGATACCACCCTTAAACAGAGTTTGTTTCATATCACAGCCTCCCAGCCTGCAGACTCAGCTACCTACCTCTCATATGACAGCTGGGGGAAATTGCAGTTTGGAGCAGGGACCCAGGTTGTGGTCACCCCAGG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV600(465) TRAJ2400(280) 335|428|460|0|93||465.0 27|83|83|97|153||280.0 TCATATGACAGCTGGGGGAAATTGCAGTTT 58 GGAGCAGGGACCCAGGTTGTGGTCACCCCAG 58 SYDSWGKLQF GAGTQVVVTP_ :::::::::92:-12:93:::::97:-7:122:153:: 746 6.0 0.02643171806167401 ACCTCCTTCCACCTGAAGAAACCATCTGCCCTTGTGAGCGACTCCGCTTTGTACTTCTGTGCTGTGAGACCTCCCCTCCTGGCTCTAGCAACACAGGCAAACTAATCTTTGGGCAAGG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV300(345) TRAJ3700(179) 370|439|463|0|69||345.0 20|59|82|79|118|SG27A|179.0 TGTGCTGTGAGACCTCCCCTCCTGGCTCTAGCAACACAGGCAAACTAATCTTT 58 CAVRPPLLA_SNTGKLIF :::::::::57:-4:69:::::79:0:110::: 828 6.0 0.02643171806167401 CTCTGACTGTGAAATGCACCTATTCAGTCTCTGGAAACCCTTATCTTTTTTGGTATGTTCAATACCCCAACCGAGGCCTCCAGTTCCTTCTGAAATACATC,CAAACCTCCTTCCACCTGAAGAAACCATCTGCCCTTGTGAGCGACTCCGCTTTGTACTTCTGTGTCTCTAGCAACACAGGCAAACTAATCTTTGGGCGAGG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[,[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV300(825) TRAJ3700(148) 209|310|463|0|101||505.0,367|431|463|0|64||320.0 ,23|59|82|65|101|SG27ASA55G|148.0 GTCTCTGGAAACCCTTAT 58 CTTTTTTGGTATGTTCAATACCCCAACCGAGGCCTCCAGTTCCTTCTGAAA 58 TGTGTCTCTAGCAACACAGGCAAACTAATCTTT 58 VSGNPY LFWYVQYPNRGLQFLLK CVSSNTGKLIF :::::26:44:95::::::::::::::,:::::::::60:-12:64:::::65:-3:93::: 873 5.0 0.022026431718061675 GTACTTTTGTGCTCTTGGGGACCGGTTCTAACTTTGGAAATGAGAAATTAACCTTTGGGACTGGAACAAGACTCACCATCATACCCAGTAAGTTCTTCATC [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRDV100(105) TRAJ4800(305) 423|444|467|0|21||105.0 22|83|83|26|87||305.0 TGTGCTCTTGGGGACCGGTTCTAACTTTGGAAATGAGAAATTAACCTTT 58 GGGACTGGAACAAGACTCACCATCATACCCA 58 CALGDRFFGNEKLTF GTGTRLTIIP :::::::::7:-3:21:::::26:-2:56:87:: 875 5.0 0.022026431718061675 CTCTGTGCATTGGAGTGATGCTGCTGAGTACTTCTGTGCTGTGGGTGGGAGATCAGGAGGAGGTGCTGACGGACTCACCTTTGGCAAAGGGACTCATCTAATCATCCAGCCC [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV8-300(235),TRAV8-500(205) TRAJ4500(300) 393|440|461|0|47||235.0;1504|1511|1538|34|41||35.0 25|85|86|52|112||300.0 TGTGCTGTGGGTGGGAGATCAGGAGGAGGTGCTGACGGACTCACCTTT 58 CAVGGRSGGGADGLTF :::::::::34:-1:47:::::52:-5:82::: 896 5.0 0.022026431718061675 CAGAAAGTCCAGCACTCTGAGCCTGCCCCGGGTTTCCCTGAGCGACACTGCTGTGTACTACTGCCTCGTGGTGGGGGGTTCAGGAAACACACCTCTTGTCTTTGGAAAGGGCACAAGACTTTCTGTGATTGCAAATATCCAGAACCCTGACCCTGCCGTGTACCAGCTGAGAGACTCTAAATCCAGT [[,[[[[[[[[[[[[,[[[[[[[[[[[[[[[[[[[[[[,[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[,[[[[[[[[[[[[[[[[[[[[[ TRAV400(345.4) TRAJ2900(280) TRAC00(261.8) 351|422|448|0|71||355.0 24|80|80|78|134||280.0 TGCCTCGTGGTGGGGGGTTCAGGAAACACACCTCTTGTCTTT 58 GGAAAGGGCACAAGACTTTCTGTGATTGCAA 58 CLVVGGSGNTPLVF GKGTRLSVIA_ :::::::::61:-6:71:::::78:-4:103:134:: 900 5.0 0.022026431718061675 GGAGGAGAAAGGTCGTTTTTCTTCATTCCTTAGTCGGTCTAAAGGGTACAGTTACCTCCTTTTGAAGGAGCTCCAGATGAAAGACTCTGCCTCTTACCTCTGTGCTGTGAACGGGGCTGCAGGCAACAAGCTAACTTTTGGAGGAG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV1-200(550) TRAJ1700(155) 312|422|446|0|110||550.0 28|59|83|115|146||155.0 GAGGAGAAAGGTCGTTTTTCTTCATTCCTTAGTCGGTCTAAAGGGTACAGTTACCTCCTTTTGAAGGAGCTCCAGATGAAAGACTCTGCCTCTTACCTC 58 TGTGCTGTGAACGGGGCTGCAGGCAACAAGCTAACTTTT 58 EEKGRFSSFLSRSKGYSYLLLKELQMKDSASYL CAVNGAAGNKLTF ::::::::1:100:-4:110:::::115:-8:139::: 901 5.0 0.022026431718061675 TGAACTCTTCTGGTATGTCCAGTACTCCAGACAACGCCTCCAGTTACTCTTGAGACACATCTCTAGAGAGAGCATCAAAGGCTTCACTGCTGACCTTAACA,AGACATCTTTCCACCTGAAGAAACCATTTGCTCAAGAGGAAGACTCAGCCATGTATTACTGTGCTCTAAGTCGAAAGACCGGTAACCAGTTCTATTTTGGG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[,[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV1600(860) TRAJ4900(120) 249|350|449|0|101||505.0,356|427|449|0|71||355.0 ,24|48|76|77|101||120.0 CTCTTCTGGTATGTCCAGTACTCCAGACAACGCCTCCAGTTACTCTTGAGA 58 CACATCTCTAGA 58 TGTGCTCTAAGTCGAAAGACCGGTAACCAGTTCTATTTT 58 LFWYVQYSRQRLQLLLR HISR CALSRKTGNQFYF ::::::4:55:67:::::::::::::,:::::::::59:-2:71:::::77:-4:98::: 908 5.0 0.022026431718061675 GACTCAGCCACCTACTTCTGTGCAGCAAGCAAGGGAGGAAGCTACATACCTACATTTGGAAGAGGAACCAGCCTTATTGTTCATCCGTATATCCAGAACCCTGACCCTGCCGTGTACCAGCTGAGAGACTCTAAATCCAGTGAC [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[,[[[[,[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV23DV600(155) TRAJ600(275) TRAC00(273.6) 433|464|484|0|31||155.0 27|82|82|33|88||275.0 TGTGCAGCAAGCAAGGGAGGAAGCTACATACCTACATTT 58 GGAAGAGGAACCAGCCTTATTGTTCATCCGT 58 CAASKGGSYIPTF GRGTSLIVHP_ :::::::::18:0:31:::::33:-7:57:88:: 1035 4.0 0.01762114537444934 AGAAAATCCGCCAACCTTGTCATCTCCGCTTCACAACTGGGGGACTCAGCAATGTACTTCTGTGCAATGAGAGAGGGTCTCTGGGGGTTACCAGAAAGTTACCTTTGGAACTGGAACAAAGCTCCAAGTCATCCCAAGTGAGTCCAATTTCCT [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV14DV400(369) TRAJ1300(274) 373|450|470|0|77|ST429C|369.0 25|83|83|79|137|ST56C|274.0 TGTGCAATGAGAGAGGGTCTCTGGGGGTTACCAGAAAGTTACCTTT 58 GGAACTGGAACAAAGCTCCAAGTCATCCCAA 58 CAMREGLWGYQKVTF GTGTKLQVIP :::::::::60:0:77:::::79:-5:106:137:: 1051 4.0 0.01762114537444934 AATAAACATACAGGAAAAGCACAGCTCCCTGCACATCACAGCCTCCCATCCCAGAGACTCTGCCGTCTACATCTGTGCTGTCGACTCTGGGGCTGGGAGTTACCAACTCACTTTC [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV4100(410) TRAJ2800(90) 351|433|456|0|82||410.0 23|55|86|83|115||160.0 TGTGCTGTCGACTCTGGGGCTGGGAGTTACCAACTCACTTTC 58 CAVDSGAGSYQLTF :::::::::73:-3:82:::::83:-3:115::: 1053 4.0 0.01762114537444934 CTCGGCTGTCTACTTCTGTGCAGCAAGAGGAGGAACGGGCAGGAGAGCACTTACTTTTGGGAGTGGAACAAGACTCCAAGTGCAACCAAATATCCAGAACC [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV13-100(135) TRAJ500(275) TRAC00(565) 408|435|457|0|27||135.0 25|80|80|34|89||275.0 TGTGCAGCAAGAGGAGGAACGGGCAGGAGAGCACTTACTTTT 58 GGGAGTGGAACAAGACTCCAAGTGCAACCAA 58 CAARGGTGRRALTF GSGTRLQVQP_ :::::::::16:-2:27:::::34:-5:58:89:: 1058 4.0 0.01762114537444934 AAAAAACAATGAAACCAATGAAATGGCCTCTCTGATCATCACAGAAGACAGAAAGTCCAGCACCTTGATCCTGCCCCACGCTACGCTGAGAGACACTGCTGTGTACTATTGCATCGTCAGAGTCGTTTCAGATGGCCAGAAGCTGCTCTTTGCAAGGGGG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV26-100(625) TRAJ1600(159) 303|428|448|0|125||625.0 23|58|80|125|160|SA57G|159.0 GAAACCAATGAAATGGCCTCTCTGATCATCACAGAAGACAGAAAGTCCAGCACCTTGATCCTGCCCCACGCTACGCTGAGAGACACTGCTGTGTACTAT 58 TGCATCGTCAGAGTCGTTTCAGATGGCCAGAAGCTGCTCTTT 58 ETNEMASLIITEDRKSSTLILPHATLRDTAVYY CIVRVVSDGQKLLF ::::::::10:109:0:125:::::125:-3:151::: 1065 4.0 0.01762114537444934 CTCTGTGCATTGGAGTGATGCTGCTGAGTACTTCTGTGCTGTGGGACTTTATTCCTACGACAAGGTGATATTTGGGCCAGGGACAAGCTTATCAGTCATTCCAAATATCCAGAACCCTGAC [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV8-300(225),TRAV8-500(205) TRAJ5000(260) TRAC00(85) 393|438|461|0|45||225.0;1504|1511|1538|34|41||35.0 28|80|80|52|104||260.0 TGTGCTGTGGGACTTTATTCCTACGACAAGGTGATATTT 58 GGGCCAGGGACAAGCTTATCAGTCATTCCAA 58 CAVGLYSYDKVIF GPGTSLSVIP_ :::::::::34:-3:45:::::52:-8:73:104:: 1066 4.0 0.01762114537444934 GGGAAGCAACAAAGGTTTTGAAGCCACATACCGTAAAGAAACCACTTCTTTCCACTTGGAGAAAGGCTCAGTTCAAGTGTCAGACTCAGCGGTGTACTTCTGTGCTTTCTGTACCTCAGGAACCTACAAATACATCTTT [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV9-200(530) TRAJ4000(70) 324|430|458|0|106||530.0 22|50|81|111|139||140.0 GGAAGCAACAAAGGTTTTGAAGCCACATACCGTAAAGAAACCACTTCTTTCCACTTGGAGAAAGGCTCAGTTCAAGTGTCAGACTCAGCGGTGTACTTC 58 TGTGCTTTCTGTACCTCAGGAACCTACAAATACATCTTT 58 GSNKGFEATYRKETTSFHLEKGSVQVSDSAVYF CAFCTSGTYKYIF ::::::::1:100:-8:106:::::111:-2:139::: 1068 4.0 0.01762114537444934 AGCAGACACTGCTTCTTACTTCTGTGCTACGGTCTCGGATAGCAACTATCAGTTAATCTGGGGCGCTGGGACCAAGCTAATTATAAAGCCAGATATCCAGAACCCTGACCCTGCCGTGTACCAGCTGA [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV1700(160) TRAJ3300(280) TRAC00(180) 402|434|457|0|32||160.0 21|77|77|36|92||280.0 TGTGCTACGGTCTCGGATAGCAACTATCAGTTAATCTGG 58 GGCGCTGGGACCAAGCTAATTATAAAGCCAG 58 CATVSDSNYQLIW GAGTKLIIKP :::::::::22:-3:32:::::36:-1:61:92:: 1100 4.0 0.01762114537444934 GGAAACCCTCTGTGCATTGGAGTGATGCTGCTGAGTACTTCTGTGCTGTAGGGGACAACTTCAACAAATTTTACTTTGGATCTGGGACCAAACTCAATGTAAAACCAAATATCCAGAACCCTGACCCTGCCGTG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV8-500(246),TRAV8-300(245) TRAJ2100(270) TRAC00(130) 1463|1515|1538|0|52|SG1466ASC1511T|228.0;427|435|461|41|49||40.0 21|75|75|54|108||270.0 TGTGCTGTAGGGGACAACTTCAACAAATTTTACTTT 58 GGATCTGGGACCAAACTCAATGTAAAACCAA 58 CAVGDNFNKFYF GSGTKLNVKP :::::::::41:-3:52:::::54:-1:77:108:: 1188 3.0 0.013215859030837005 CCATTGTGAAATATTCAGTCCAGGTATCAGACTCAGCCGTGTACTACTGTCTTCTGGGAGGTGTACTGGGGGATACGGAGGACACCGATAAACTCATCTTTGGAAAAGGAACCCGTGTGACTGTGG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV4000(305) TRDD300(75) TRDJ100(235) TRDC00(113.3) 356|416|437|0|60||300.0 11|26|39|62|77||75.0 20|65|71|81|126||225.0 TGTCTTCTGGGAGGTGTACTGGGGGATACGGAGGACACCGATAAACTCATCTTT 58 CLLGGVLGDTEDTDKLIF :::::::::47:-1:60:62:2:0:77:81:0:101::: 1222 3.0 0.013215859030837005 GATTAAGAGTCACGCTTGACACTTCCAAGAAAAGCAGTTCCTTGTTGATCACGGCTTCCCGGGCAGCAGACACTGCTTCTTACTTCTGTGCTACGGATTATGGCTCTAGCAACACAGGCAAACTAATCTTTGGGCAAGGG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV1700(485) TRAJ3700(189) 338|435|457|0|97||485.0 19|60|82|99|140|SG27A|189.0 TGTGCTACGGATTATGGCTCTAGCAACACAGGCAAACTAATCTTT 58 CATDYGSSNTGKLIF :::::::::86:-2:97:::::99:1:131::: 1224 3.0 0.013215859030837005 GAAGGTCGCTACTCATTGAATTTCCAGAAGGCAAGAAAATCCGCCAACCTTGTCATCTCCGCTTCACAACTGGGGGACTCAGCAATGTACTTCTGTGCAATGAGAGACGACTTCAGATGGCCAGAAGCTGCTCTTTGCAAGG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV14DV400(519) TRAJ1600(155) 340|447|470|0|107|ST429C|519.0 24|55|80|111|142||155.0 TGTGCAATGAGAGACGACTTCAGATGGCCAGAAGCTGCTCTTT 58 CAMRDDF_DGQKLLF :::::::::93:-3:107:::::111:-4:136::: 1225 3.0 0.013215859030837005 AAAGAAGTCAGGAAGACTAAGTAGCATATTAGATAAGAAAGAACTTTTCAGCATCCTGAACATCACAGCCACCCAGACCGGAGACTCGGCCATCTACCTCTGTGCTGTGGAGGCCCCCCTTGAGGGGTGGGAATGTGCTGCATTGCGG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPP[[ TRAV36DV700(559) TRAJ3500(105) 327|442|460|0|115|SC374T|559.0 29|50|79|127|148||105.0 AAGAAGTCAGGAAGACTAAGTAGCATATTAGATAAGAAAGAACTTTTCAGCATCCTGAACATCACAGCCACCCAGACCGGAGACTCGGCCATCTACCTC 58 TGTGCTGTGGAGGCCCCCCTTGAGGGGTGGGAATGTGCTGCATTGC 47 KKSGRLSSILDKKELFSILNITATQTGDSAIYL CAVEAPLE_GGNVLHC ::::::::1:100:2:115:::::127:-9:146::: 1228 3.0 0.013215859030837005 GAAGACTCGGCTGTCTACTTCTGTGCAGCAAGTATCGTCAGGAGGAAGCTACATACCTACATTTGGAAGAGGAACCAGCCTTATTGTTCATCCGTGTAAGTATTATAGAAATGATCAAGGGAAATTTTGCAGACAGATTATATTATGG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV13-100(175) TRAJ600(290) 403|438|457|0|35||175.0 24|82|82|37|95||290.0 TGTGCAGCAAGTATCGTCAGGAGGAAGCTACATACCTACATTT 58 GGAAGAGGAACCAGCCTTATTGTTCATCCGT 58 CAASIVRGSYIPTF GRGTSLIVHP :::::::::21:1:35:::::37:-4:64:95:: 1229 3.0 0.013215859030837005 GTGATTCAGCCACCTACCTCTGTGCAATGAAGTACCCTCAGGGAGCCCAGAAGCTGGTATTTGGCCAAGGAACCAGGCTGACTATCAACCCAAGTAAGTATGACAGGGTGAAGCTACATGCA [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV12-300(150) TRAJ5400(280) 410|440|463|0|30||150.0 24|80|80|37|93||280.0 TGTGCAATGAAGTACCCTCAGGGAGCCCAGAAGCTGGTATTT 58 GGCCAAGGAACCAGGCTGACTATCAACCCAA 58 CAMKYPQGAQKLVF GQGTRLTINP :::::::::20:-3:30:::::37:-4:62:93:: 1270 3.0 0.013215859030837005 GCAGGAAAGAACCTAAGTTGCTGATGTCCGTATACTCCAGTGGTAATGAAGATGGAAGGTTTACAGCACAGCTCAATAGAGCCAGCCAGTATATTTCCCTG,CACCTACCTCTGTGTGGTCCTTGGGGGCAGGAGAGCACTTACTTTTGGGAGTGGAACAAGACTCCAAGTGCAACCAAATATCCAGAACCCTGACCCTGCCG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[)[[[[[[[[[[,[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV12-100(589.7) TRAJ500(265) TRAC*00(120) 281|382|457|0|101||505.0,414|432|457|0|18||90.0 ,27|80|80|24|77||265.0 , GTATACTCCAGTGGT 58 TGTGTGGTCCTTGGGGGCAGGAGAGCACTTACTTTT 58 GGGAGTGGAACAAGACTCCAAGTGCAACCAA 58 VYSSG CVVLGGRRALTF GSGTRLQVQP :::::::29:44:::::::::::::,:::::::::10:-5:18:::::24:-7:46:77:: 1406 2.0 0.00881057268722467 TCTCTGCTGTGTACTACTGCCTCGTGGGTGACATAGAACACCGGTAACCAGTTCTATTTTGGGACAGGGACAAGTTTGACGGTCATTCCAAGTAAGTCAAAAGA [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV400(138) TRAJ4900(280) 395|429|448|0|34|SA395TSA397T|138.0 20|76|76|35|91||280.0 TGCCTCGTGGGTGACATAGAACACCGGTAACCAGTTCTATTTT 58 GGGACAGGGACAAGTTTGACGGTCATTCCAA 58 CLVGDIETGNQFYF GTGTSLTVIP :::::::::17:1:34:::::35:0:60:91:: 1409 2.0 0.00881057268722467 ACCTGACGAAACCCTCAGCCCATATGAGCGACGCGGCTGAGTACTTCTGTGTTGTGAGTGACGCCCCAGGAACCTACAAATACATCTTTGGAACAGGCACCAGGCTGAAGGTTTTAGCAA [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV8-400(306),TRAV8-200(305) TRAJ4000(270) 380|441|461|0|61|SC431T|289.0;427|441|461|47|61||70.0 27|81|81|66|120||270.0 TGTGTTGTGAGTGACGCCCCAGGAACCTACAAATACATCTTT 58 GGAACAGGCACCAGGCTGAAGGTTTTAGCAA 58 CVVSDAPGTYKYIF GTGTRLKVLA_ :::::::::47:0:61:::::66:-7:89:120:: 1412 2.0 0.00881057268722467 TGAAACAAGACCAAAGACTCACTGTTCTATTGAATAAAAAGGATAAACATCTGTCTCTGCGCATTGCAGACACCCAGACTGGGGACTCAGCTATCTACTTCTGTGCAGAGAACTCAACTGACAGCTGGGGGGAATTGCAGTTT [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX TRAV500(555) TRAJ2400(74) 326|437|460|0|111||555.0 23|52|83|114|143|SA40G|129.0 AAACAAGACCAAAGACTCACTGTTCTATTGAATAAAAAGGATAAACATCTGTCTCTGCGCATTGCAGACACCCAGACTGGGGACTCAGCTATCTACTTC 58 TGTGCAGAGAACTCAACTGACAGCTGGGGGGAATTGCAGTTT 55 KQDQRLTVLLNKKDKHLSLRIADTQTGDSAIYF CAENSTDSWGELQF ::::::::2:101:-3:111:::::114:-3:143::: 1449 2.0 0.00881057268722467 AGCACCTCTCTCTGCACATTGTGCCCTCCCAGCCTGGAGACTCTGCAGTGTACTTCTGTGCAGCAAGCGATCCCCACCGACAAGCTCATCTTTGGGACTGGGACCAGATTACAAGTCTTTCCAAG [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV29DV500(345) TRAJ3400(250) 389|458|478|0|69||345.0 28|78|78|74|124||250.0 TGTGCAGCAAGCGATCCCCACCGACAAGCTCATCTTT 58 GGGACTGGGACCAGATTACAAGTCTTTCCAA 58 CAASDPTDKLIF GTGTRLQVFP :::::::::56:0:69:::::74:-8:93:124:: 1462 2.0 0.00881057268722467 TCTACTTCTGTGCAGCAAATCGGTGCTTCCAAGATAATCTTTGGATCAGGGACCAGACTCAGCATCCGGCCAA [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRAV13-100(137.5) TRAJ300(255) TRAC00(57.5) 416|434|457|0|18||90.0 31|82|82|22|73||255.0 TGTGCAGCAAATCGGTGCTTCCAAGATAATCTTT 58 GGATCAGGGACCAGACTCAGCATCCGGCCAA 58 CAANRCSKIIF GSGTRLSIRP :::::::::8:-3:18:::::22:-11:42:73:: 1585 1.0 0.004405286343612335 TGTGCTGTGAGAGATGCTCGCGGTGGCTACAATAAGCTGATTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF TRAV1-200(355) TRAJ400(275) TRAC00(195) 412|427|446|0|15||75.0 28|52|83|21|45||120.0 TGTGCTGTGAGAGATGCTCGCGGTGGCTACAATAAGCTGATTTTT 37 CAVRDARGGYNKLIF :::::::::0:1:15:::::21:-8:45::: 1586 1.0 0.004405286343612335 TGTGCTACGGGGGGGATCTAACTTTGGAAATGAGAAATTAACCTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF TRAV1700(375) TRAJ4800(260) 424|434|457|0|10||50.0 21|52|83|15|46||155.0 TGTGCTACGGGGGGGATCTAACTTTGGAAATGAGAAATTAACCTTT 37 CATGGIL_GNEKLTF :::::::::0:-3:10:::::15:-1:46::: 1605 1.0 0.004405286343612335 TGTGCAATGACTCCCTCAAATTCCGGGTATGCACTCAACTTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF TRAV14DV400(434) TRAJ4100(245) 433|443|470|0|10||50.0 23|51|82|14|42||140.0 TGTGCAATGACTCCCTCAAATTCCGGGTATGCACTCAACTTC 37 CAMTPSNSGYALNF :::::::::0:-7:10:::::14:-3:42::: 1608 1.0 0.004405286343612335 TGTGCAGAGAGTATGGGGAAGAATGCAGGCAAATCAACCTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF TRAV500(245) TRAJ2700(260) TRAC00(195) 427|441|460|0|14||70.0 27|48|79|21|42||105.0 TGTGCAGAGAGTATGGGGAAGAATGCAGGCAAATCAACCTTT 37 CAESMGKNAGKSTF :::::::::0:1:14:::::21:-7:42::: 1615 1.0 0.004405286343612335 TGTGCTCTGAGTGGCTCAGCAGTGCTTCCAAGATAATCTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF TRAV9-200(295) TRAJ3*00(280) 424|437|458|0|13||65.0 26|51|82|16|41||125.0 TGTGCTCTGAGTGGCTCAGCAGTGCTTCCAAGATAATCTTT 37 CALSGSA_ASKIIF :::::::::0:-1:13:::::16:-6:41:::

Alexander230 commented 3 years ago

Thank you for providing example data! I will work on the support of columns 'nseqCDR1' and 'nseqCDR2' in Immunarch.

Best regards, Aleksandr Popov

fabio-t commented 2 years ago

Hi, it seems like, maybe, the above change has broken my ability to use the mixcr format. I have some weird requirements, and until recently (I was using 0.6.4 I think) I could load a clonal file like this into immunarch without problems:

cloneCount  nSeqCDR3    aaSeqCDR3   bestVHit    bestJHit    bestDHit    CDR3Length  cloneSize   cloneDiversity  cloneEvenness   cloneId cloneFraction
46  TGTGCAAGAGGGGGTCCCTACCCTGGACTTGACTACTGG CARGGPYPGLDYW   IGHV1-54    IGHJ2   NA  39  6   2.90659340659341    0.484432234432234   471.1   0.0518602029312289
41  TGTGCAAGATCGGGAAACTWTGACCACGGGGGAAACTACTTTGACTACTGG CARSGNXDHGGNYFDYW   IGHV1-19    IGHJ2   NA  51  8   5.17230769230769    0.646538461538462   60.1    0.0462232243517475
38  TGTGCAAGTGGTAAGGGGGGCTTTGACTACTGG   CASGKGGFDYW IGHV4-1 IGHJ2   NA  33  5   1.2448275862069 0.248965517241379   1582.1  0.0428410372040586
33  TGTGCAATACTGGACGGTAGGGGGGCTTACTGG   CAILDGRGAYW IGHV1-74    IGHJ3   NA  33  6   2.42538975501114    0.404231625835189   906.1   0.0372040586245772
29  TGTRCAACGAGTAGAGACTGGTACTTCGATGTCTGG    CXTSRDWYFDVW    IGHV1-64    IGHJ1   NA  36  3   1.71283095723014    0.570943652410047   634.1   0.0326944757609921
28  TGTGCAAGRTCTCAACTGGGCCCTGACTACTGG   CARSQLGPDYW IGHV1-53    IGHJ2   NA  33  2   1.07397260273973    0.536986301369863   377.1   0.0315670800450958
27  TGCACMGAKGATGGTTACCCSTTTGCTTACTGG   CTXDGYPFAYW IGHV6-3 IGHJ3   NA  33  3   1.25473321858864    0.418244406196213   1854.1  0.0304396843291995
24  TGTGCAAGGCAGGTGCGGGACGTCTGGTACTTCGATGTCTGG  CARQVRDVWYFDVW  IGHV1-52    IGHJ1   NA  42  2   1.6 0.8 323.1   0.0270574971815107
23  TGTGCAAGACGGGAACACTACTTTGACYACTGG   CARREHYFDXW IGHV1-22    IGHJ2   NA  33  5   3.36942675159236    0.673885350318471   91.1    0.0259301014656144

Now I get the following error:

Processing "<initial>" ...
  -- [1/12] Parsing "mid1_clones.csv" -- mixcr
Error: Assigned data `bunch_translate(df[[nuc_headers[[i]]]])` must be compatible with existing data.
✖ Existing data has 196 rows.
✖ Assigned data has 0 rows.
ℹ Only vectors of size 1 are recycled.
Backtrace:
     â–ˆ
  1. ├─global::immload(which = "not full")
  2. │ └─immunarch::repLoad(...)
  3. │   └─immunarch:::.process_batch(...)
  4. │     └─immunarch:::.read_repertoire(.filepath, .format, .mode, .coding)
  5. │       └─immunarch:::parse_fun(.path, .mode)
  6. │         ├─base::`[[<-`(`*tmp*`, aa_headers[[i]], value = list())
  7. │         └─tibble:::`[[<-.tbl_df`(`*tmp*`, aa_headers[[i]], value = list())
  8. │           └─tibble:::tbl_subassign(...)
  9. │             └─tibble:::vectbl_recycle_rhs_rows(...)
 10. │               ├─base::withCallingHandlers(...)
 11. │               └─vctrs::vec_recycle(value[[j]], nrow)
 12. ├─vctrs:::stop_recycle_incompatible_size(...)
 13. │ └─vctrs:::stop_vctrs(...)
 14. │   └─rlang::abort(message, class = c(class, "vctrs_error"), ...)
 15. │     └─rlang:::signal_abort(cnd)
 16. │       └─base::signalCondition(cnd)
 17. └─(function (cnd) ...
Execution halted

and I think this is due to CDR1 and CDR2 being expected? I'm not sure. Could the kind of "modified mixcr format" I use be brought back? It used to work fine (ignoring the extra columns and using only V/J gene, CDR3 and count/fraction).

Alexander230 commented 2 years ago

Hi, Fabio!

Thank you for providing the example data! It was a bug in the new parser for MiXCR format; I've added a fix to dev branch of Immunarch. Please try this data with the development version, it must work now. To install the development version, you can use these commands:

install.packages(c("devtools", "pkgload"))
devtools::install_github("immunomind/immunarch", ref="dev")
devtools::reload(pkgload::inst("immunarch"))

Best regards, Aleksandr

fabio-t commented 2 years ago

Thanks @Alexander230 - it works like a charm, will let you know is any other issue arises ;)

Alexander230 commented 2 years ago

Thank you! :-)

By the way, @parkjaeming, the feature with CDR1 and CDR2 is now implemented, you are welcome to use it!

vadimnazarov commented 10 months ago

Closing this issue for now. It will be implemented in the next version of Immunarch.

More details on the next version of Immunarch are here: https://b-t.cr/t/immunarch-will-significantly-evolve-but-it-will-break-things-and-we-need-your-help/1123