| Previous changeset 0:0e37e5b73273 (2018-03-30) |
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Commit message:
Uploaded test-data & added tool help |
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modified:
README.rst clonotype_computation.xml data_filtering.xml exclusive_clonotype_computation.xml gene_comparison.xml gene_computation.xml public_clonotype_computation.xml |
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added:
test-data/README.html test-data/clono_compute_def1_BCR_input1.csv test-data/clono_compute_def1_BCR_output1.csv test-data/clono_compute_def1_BCR_output2.csv test-data/clono_compute_def1_BCR_output3.csv test-data/clono_compute_def1_TCR_input1.csv test-data/clono_compute_def1_TCR_output1.csv test-data/clono_compute_def1_TCR_output2.csv test-data/clono_compute_def1_TCR_output3.csv test-data/clono_compute_def2_BCR_input1.csv test-data/clono_compute_def2_BCR_output1.csv test-data/clono_compute_def2_BCR_output2.csv test-data/clono_compute_def2_BCR_output3.csv test-data/clono_compute_def2_TCR_input1.csv test-data/clono_compute_def2_TCR_output1.csv test-data/clono_compute_def2_TCR_output2.csv test-data/clono_compute_def2_TCR_output3.csv test-data/clono_compute_def3_BCR_input1.csv test-data/clono_compute_def3_BCR_output1.csv test-data/clono_compute_def3_BCR_output2.csv test-data/clono_compute_def3_BCR_output3.csv test-data/clono_compute_def3_TCR_input1.csv test-data/clono_compute_def3_TCR_output1.csv test-data/clono_compute_def3_TCR_output2.csv test-data/clono_compute_def3_TCR_output3.csv test-data/clono_compute_def4_BCR_input1.csv test-data/clono_compute_def4_BCR_output1.csv test-data/clono_compute_def4_BCR_output2.csv test-data/clono_compute_def4_BCR_output3.csv test-data/clono_compute_def4_TCR_input1.csv test-data/clono_compute_def4_TCR_output1.csv test-data/clono_compute_def4_TCR_output2.csv test-data/clono_compute_def4_TCR_output3.csv test-data/clono_compute_def5_BCR_input1.csv test-data/clono_compute_def5_BCR_output1.csv test-data/clono_compute_def5_BCR_output2.csv test-data/clono_compute_def5_BCR_output3.csv test-data/clono_compute_def5_TCR_input1.csv test-data/clono_compute_def5_TCR_output1.csv test-data/clono_compute_def5_TCR_output2.csv test-data/clono_compute_def5_TCR_output3.csv test-data/data_filter_BCR_input1.csv test-data/data_filter_BCR_output1.csv test-data/data_filter_BCR_output2.csv test-data/data_filter_BCR_output3.csv test-data/data_filter_BCR_parameters.txt test-data/data_filter_TCR_input1.csv test-data/data_filter_TCR_output1.csv test-data/data_filter_TCR_output2.csv test-data/data_filter_TCR_output3.csv test-data/data_filter_TCR_parameters.txt test-data/exclusive_clonos_def1_BCR_input1.csv test-data/exclusive_clonos_def1_BCR_input2.csv test-data/exclusive_clonos_def1_BCR_output1.csv test-data/exclusive_clonos_def1_BCR_parameters.txt test-data/exclusive_clonos_def1_TCR_input1.csv test-data/exclusive_clonos_def1_TCR_input2.csv test-data/exclusive_clonos_def1_TCR_output1.csv test-data/exclusive_clonos_def1_TCR_parameters.txt test-data/exclusive_clonos_def2_BCR_input1.csv test-data/exclusive_clonos_def2_BCR_input2.csv test-data/exclusive_clonos_def2_BCR_output1.csv test-data/exclusive_clonos_def2_BCR_parameters.txt test-data/exclusive_clonos_def2_TCR_input1.csv test-data/exclusive_clonos_def2_TCR_input2.csv test-data/exclusive_clonos_def2_TCR_output1.csv test-data/exclusive_clonos_def2_TCR_parameters.txt test-data/exclusive_clonos_def3_BCR_input1.csv test-data/exclusive_clonos_def3_BCR_input2.csv test-data/exclusive_clonos_def3_BCR_output1.csv test-data/exclusive_clonos_def3_BCR_parameters.txt test-data/exclusive_clonos_def3_TCR_input1.csv test-data/exclusive_clonos_def3_TCR_input2.csv test-data/exclusive_clonos_def3_TCR_output1.csv test-data/exclusive_clonos_def3_TCR_parameters.txt test-data/gene_compare_geneJ_BCR_input1.csv test-data/gene_compare_geneJ_BCR_input2.csv test-data/gene_compare_geneJ_BCR_output1.csv test-data/gene_compare_geneJ_TCR_input1.csv test-data/gene_compare_geneJ_TCR_input2.csv test-data/gene_compare_geneJ_TCR_output1.csv test-data/gene_compare_geneV_BCR_input1.csv test-data/gene_compare_geneV_BCR_input2.csv test-data/gene_compare_geneV_BCR_output1.csv test-data/gene_compare_geneV_TCR_input1.csv test-data/gene_compare_geneV_TCR_input2.csv test-data/gene_compare_geneV_TCR_output1.csv test-data/gene_usage_geneJ_BCR_input1.csv test-data/gene_usage_geneJ_BCR_output1.csv test-data/gene_usage_geneJ_BCR_output2.csv test-data/gene_usage_geneJ_BCR_output3.csv test-data/gene_usage_geneJ_TCR_input1.csv test-data/gene_usage_geneJ_TCR_output1.csv test-data/gene_usage_geneJ_TCR_output2.csv test-data/gene_usage_geneJ_TCR_output3.csv test-data/gene_usage_geneV_BCR_input1.csv test-data/gene_usage_geneV_BCR_output1.csv test-data/gene_usage_geneV_BCR_output2.csv test-data/gene_usage_geneV_BCR_output3.csv test-data/gene_usage_geneV_TCR_input1.csv test-data/gene_usage_geneV_TCR_output1.csv test-data/gene_usage_geneV_TCR_output2.csv test-data/gene_usage_geneV_TCR_output3.csv test-data/public_clonos_def1_BCR_input1.csv test-data/public_clonos_def1_BCR_input2.csv test-data/public_clonos_def1_BCR_output1.csv test-data/public_clonos_def1_BCR_parameters.txt test-data/public_clonos_def1_TCR_input1.csv test-data/public_clonos_def1_TCR_input2.csv test-data/public_clonos_def1_TCR_output1.csv test-data/public_clonos_def1_TCR_parameters.txt test-data/public_clonos_def2_BCR_input1.csv test-data/public_clonos_def2_BCR_input2.csv test-data/public_clonos_def2_BCR_output1.csv test-data/public_clonos_def2_BCR_parameters.txt test-data/public_clonos_def2_TCR_input1.csv test-data/public_clonos_def2_TCR_input2.csv test-data/public_clonos_def2_TCR_output1.csv test-data/public_clonos_def2_TCR_parameters.txt test-data/public_clonos_def3_BCR_input1.csv test-data/public_clonos_def3_BCR_input2.csv test-data/public_clonos_def3_BCR_output1.csv test-data/public_clonos_def3_BCR_parameters.txt test-data/public_clonos_def3_TCR_input1.csv test-data/public_clonos_def3_TCR_input2.csv test-data/public_clonos_def3_TCR_output1.csv test-data/public_clonos_def3_TCR_parameters.txt |
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| diff -r 0e37e5b73273 -r acaa8e8a0b88 README.rst --- a/README.rst Fri Mar 30 07:22:29 2018 -0400 +++ b/README.rst Mon Apr 30 04:47:52 2018 -0400 |
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| @@ -1,7 +1,7 @@ About ----- -IRProfiler is a Galaxy toolbox for immunogenetic repertoire profiling. It is made available as supplementary material for the article *IRProfiler - A Software Toolbox for High Throughput Immune Receptor Profiling*, authored by C. Maramis et al. and submitted for possible publication to `BMC Bioinformatics <https://bmcbioinformatics.biomedcentral.com>`_. +IRProfiler is a Galaxy toolbox for immunogenetic repertoire profiling. It is made available as supplementary material for the article *IRProfiler - A Software Toolbox for High Throughput Immune Receptor Profiling*, authored by C. Maramis et al. and published in `BMC Bioinformatics <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2144-z>`_. Tools ----- |
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| diff -r 0e37e5b73273 -r acaa8e8a0b88 clonotype_computation.xml --- a/clonotype_computation.xml Fri Mar 30 07:22:29 2018 -0400 +++ b/clonotype_computation.xml Mon Apr 30 04:47:52 2018 -0400 |
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| @@ -1,8 +1,8 @@ -<tool id="clonoComput" name="Clonotype Diversity & Expression" version="0.9"> +<tool id="clonoComput" name="Clonotype Diversity & Expression" version="1.0"> <description>Compute clonotype diversity and expression from filtered file</description> <requirements> <requirement type="package" version="0.19">pandas</requirement> - </requirements> + </requirements> <command interpreter="python">clonotype_computation.py $input $clonotype $clonos_file $top10_file $summary_file ${input.name}</command> <inputs> <param name="clonotype" type="select" label="Clonotype definition"> @@ -20,6 +20,6 @@ <data name="summary_file" format="tabular" label="${input.name}_clonotypesSummary" /> </outputs> <help> -Coming soon +This tool calculates the clonotype diversity and expression of a filtered-in dataset (1st output file of the Data Filtering tool) according to the 5 supported clonotype definitions. </help> </tool> |
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| diff -r 0e37e5b73273 -r acaa8e8a0b88 data_filtering.xml --- a/data_filtering.xml Fri Mar 30 07:22:29 2018 -0400 +++ b/data_filtering.xml Mon Apr 30 04:47:52 2018 -0400 |
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| @@ -1,8 +1,8 @@ -<tool id="dataFilter" name="Data Filtering" version="0.9"> +<tool id="dataFilter" name="Data Filtering" version="1.0"> <description>Filter IMGT Summary dataset</description> <requirements> <requirement type="package" version="0.19">pandas</requirement> - </requirements> + </requirements> <command interpreter="python">data_filtering.py $input $TCR_or_BCR $Vfun $spChar $prod $delCF $threshold $Vg.Vgid $clen.cdr3len1 $cdp.cdr3part $filterin_file $filterout_file $summary_file $Jg.Jgid $Dg.Dgid $clen.cdr3len2 $process_id </command> <inputs> |
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| diff -r 0e37e5b73273 -r acaa8e8a0b88 exclusive_clonotype_computation.xml --- a/exclusive_clonotype_computation.xml Fri Mar 30 07:22:29 2018 -0400 +++ b/exclusive_clonotype_computation.xml Mon Apr 30 04:47:52 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="exclClonoComput" name="Exclusive Clonotypes" version="0.9"> +<tool id="exclClonoComput" name="Exclusive Clonotypes" version="1.0"> <description>Compute exclusive clonotypes between 2 repertoires</description> <requirements> <requirement type="package" version="0.19">pandas</requirement> @@ -13,13 +13,13 @@ </param> <conditional name="Th"> - <param name="thres_select" type="select" label="Remove CDR3 With Reads Fewer Than Threshold?"> + <param name="thres_select" type="select" label="Remove Clonotypes With Reads Fewer Than Threshold?"> <option value="y">Yes</option> <option value="n" selected="true">No</option> </param> <when value="y"> - <param name="thres" type="integer" size="4" value="1" min="1" label="Keep CDR3 with Number of Reads more than"/> + <param name="thres" type="integer" size="4" value="1" min="1" label="Keep Clonotypes with Number of Reads more than"/> </when> <when value="n"> @@ -35,6 +35,6 @@ <data format="tabular" name="output_file" label="exclusiveClonotypes"/> </outputs> <help> -Coming soon +This tool extracts the exclusive (i.e., found in the 1st dataset but not in the 2nd) clonotypes between 2 clonotype repertoires (1st output of the Clonotype Diversity & Expression tool) according to 3 of the 5 supported clonotype definitions. </help> </tool> |
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| diff -r 0e37e5b73273 -r acaa8e8a0b88 gene_comparison.xml --- a/gene_comparison.xml Fri Mar 30 07:22:29 2018 -0400 +++ b/gene_comparison.xml Mon Apr 30 04:47:52 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="geneCompar" name="Gene Usage Comparison" version="0.9"> +<tool id="geneCompar" name="Gene Usage Comparison" version="1.0"> <description>Compare gene usages from multiple repertoires</description> <requirements> <requirement type="package" version="0.19">pandas</requirement> @@ -18,6 +18,6 @@ <data format="tabular" name="output_file" label="geneUsageComparison"/> </outputs> <help> -Coming soon +This tool compares the usage of each gene of the V or J family in 2 or more clonotype repertoires; uses the 1st output of the Gene Usage tool. </help> </tool> |
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| diff -r 0e37e5b73273 -r acaa8e8a0b88 gene_computation.xml --- a/gene_computation.xml Fri Mar 30 07:22:29 2018 -0400 +++ b/gene_computation.xml Mon Apr 30 04:47:52 2018 -0400 |
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| @@ -1,8 +1,8 @@ -<tool id="geneComput" name="Gene Usage" version="0.9"> +<tool id="geneComput" name="Gene Usage" version="1.0"> <description>Compute gene usage from clonotype file</description> <requirements> <requirement type="package" version="0.19">pandas</requirement> - </requirements> + </requirements> <command interpreter="python">gene_computation.py $input $gene $usage_file $top10_file $summary_file ${input.name}</command> <inputs> <param name="gene" type="select" label="Gene family"> @@ -17,6 +17,6 @@ <data name="summary_file" format="tabular" label="${input.name}_geneUsageSummary" /> </outputs> <help> -Coming soon +This tool caclulates the usage of each gene of the V or J family in a clonotype repertoire (1st output of the Clonotype Diversity & Expression tool). </help> </tool> |
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| diff -r 0e37e5b73273 -r acaa8e8a0b88 public_clonotype_computation.xml --- a/public_clonotype_computation.xml Fri Mar 30 07:22:29 2018 -0400 +++ b/public_clonotype_computation.xml Mon Apr 30 04:47:52 2018 -0400 |
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| @@ -1,8 +1,8 @@ -<tool id="pubClonoComput" name="Public Clonotypes" version="0.9"> +<tool id="pubClonoComput" name="Public Clonotypes" version="1.0"> <description>Compute public clonotypes from multiple repertoires</description> <requirements> <requirement type="package" version="0.19">pandas</requirement> - </requirements> + </requirements> <command interpreter="python">public_clonotype_computation.py "$clonotype" "$output_file" "$Th.thres" #for x in $clono_files "$x.clfile" @@ -35,6 +35,6 @@ <data format="tabular" name="output_file" label="publicClonotypes" /> </outputs> <help> -Coming soon +This tool extracts the public (i.e., shared in at least two datasets) clonotypes between 2 or more clonotype repertoires (1st output of the Clonotype Diversity & Expression tool) according to 3 of the 5 supported clonotype definitions. </help> </tool> |
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| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/README.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/README.html Mon Apr 30 04:47:52 2018 -0400 |
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| @@ -0,0 +1,93 @@ +<!DOCTYPE html> +<html lang="en"> +<head> + <meta charset="utf-8"> + <!--<link rel="stylesheet" href="style/base.css" type="text/css" />--> +</head> +<body style="margin-left: 1cm"> +<div class="jumbotron"> +<div class="container"> +<h3>Test Data Name Conventions</h3> +<p>Concerning the naming of the execution parameters, input and output files, the following convention applies: </p> +<ul> +<li class="container">The name starts with the tool specifier; see Tool Specifiers Table below.</li> +<li class="container">The clonotype definition specifier follows, if needed; see Clonotype Definition Specifiers Table below.</li> +<li class="container">The gene specifier (geneV or geneJ) follows, if needed.</li> +<li class="container">The cell type specifier (BCR or TCR) follows.</li> +<li class="container">The name ends with the file content specifier (input, output or parameters).</li> +</ul> + +<p><i>Tool Specifiers Table</i></p> +<table style="border-spacing: 10px 0px"> +<tr align="left"> +<th>Index</th> +<th>Tool</th> +<th>Specifier</th> +</tr> +<tr> +<td>1</td> +<td>Data Filtering</td> +<td>data_filter</td> +</tr> +<tr> +<td>2</td> +<td>Clonotype Diversity & Expression</td> +<td>clono_compute</td> +</tr> +<tr> +<td>3</td> +<td>Gene Usage</td> +<td>gene_usage</td> +</tr> +<tr> +<td>4</td> +<td>Public Clonotypes</td> +<td>public_clonos</td> +</tr> +<tr> +<td>5</td> +<td>Exclusive Clonotypes</td> +<td>exclusive_clonos</td> +</tr> +<tr> +<td>6</td> +<td>Gene Usage Comparison</td> +<td>gene_compare</td> +</tr> +</table> + +<br> + +<p><i>Clonotype Definition Specifiers Table</i></p> +<table style="border-spacing: 10px 0px"> +<tr align="left"> +<th>Index</th> +<th>Clonotype Definition</th> +<th>Specifier</th> +</tr> +<tr> +<td>1</td> +<td>CDR3</td> +<td>def1</td> +</tr> +<tr> +<td>2</td> +<td>V+CDR3</td> +<td>def2</td> +</tr> +<tr> +<td>3</td> +<td>J+CDR3</td> +<td>def3</td> +</tr> +<tr> +<td>4</td> +<td>V+J+CDR3</td> +<td>def4</td> +</tr> +<tr> +<td>5</td> +<td>V+D+J+CDR3</td> +<td>def5</td> +</tr> +</table> |
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| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def1_BCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def1_BCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
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| b'@@ -0,0 +1,21 @@\n+\tSequence ID\tFunctionality\tV-GENE\tV-REGION score\tV-REGION identity %\tV-REGION identity nt\tV-REGION identity % (with ins/del events)\tV-REGION identity nt (with ins/del events)\tJ-GENE\tJ-REGION score\tJ-REGION identity %\tJ-REGION identity nt\tD-GENE\tD-REGION reading frame\tCDR1-IMGT length\tCDR2-IMGT length\tCDR3-IMGT length\tCDR-IMGT lengths\tFR-IMGT lengths\tAA JUNCTION\tJUNCTION frame\tOrientation\tFunctionality comment\tV-REGION potential ins/del\tJ-GENE and allele comment\tV-REGION insertions\tV-REGION deletions\tSequence\n+1\tlcl|FLN1FA001B9SVM.1|\tproductive\tIGHV1-69 or IGHV1-69D\t790\t100\t159/159 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD2-15\t2\tX\t8\t16\tX.8.16\t[X.7.38.11]\tCYLGYCSGGSCYPQVGYW\tin-frame\t+\t\t\t\t\t\tgggcttgagtggatgggagggatcatccctatctttggtacagcaaactacgcacagaagttccagggcagagtcacgattaccgcggacgaatccacgagcacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag\n+2\tlcl|FLN1FA001CUVDF.1|\tproductive\tIGHV3-30 or IGHV3-30-3\t786\t99.38\t159/160 nt\t\t\tIGHJ4\t231\t97.92\t47/48 nt\tIGHD2-15\t2\tX\t8\t13\tX.8.13\t[X.7.38.11]\tCVTYCSGGSCYFDYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtggcagttatatcatatgatggaagtaataaatactacgtagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagctgaggacacggctgtgtattactgtgttacatattgtagtggtggtagctgctactttgactactggggccagggaaccctggtcaccgtctcctcag\n+3\tlcl|FLN1FA001DLPHD.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag\n+4\tlcl|FLN1FA002QTWMQ.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+5\tlcl|FLN1FA002Q975Z.1|\tproductive\tIGHV3-53\t771\t99.36\t156/157 nt\t\t\tIGHJ4\t168\t83.33\t40/48 nt\tIGHD2-21\t3\tX\t7\t10\tX.7.10\t[X.7.38.11]\tCVVVTATPHGYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag\n+6\tlcl|FLN1FA001AX4MF.1|\tproductive\tIGHV4-39\t770\t100\t155/155 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t7\t15\tX.7.15\t[X.6.38.11]\tCVVNYYDSSGYYYIDYW\tin-frame\t+\t\t\t\t\t\tggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag\n+7\tlcl|FLN1FA0074PUDE.1|\tproductive\tIGHV4-39\t770\t100\t155/155 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t7\t15\tX.7.15\t[X.6.38.11]\tCVVNYYDSSGYYYIDYW\tin-frame\t+\t\t\t\t\t\tggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag\n+8\tlcl|FLN1FA0013V4SA.1|\tproductive\tIGHV1-3\t790\t100\t159/159 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD2-15\t2\tX\t8\t16\tX.8.16\t[X.7.38.11]\tCYLGYCSGGSCYPQVGYW\tin-frame\t+\t\t\t\t\t\taggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag\n+9\tlcl|FLN1FA00056KW6.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgtta'..b'tgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag\n+11\tlcl|FLN1FA008ANOPH.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+12\tlcl|FLN1FA005T7JJ8.1|\tproductive\tIGHV3-33\t795\t100\t160/160 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t8\t15\tX.8.15\t[X.7.38.11]\tCVTYYYDSSGYPYFDYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag\n+13\tlcl|FLN1FA0018WER7.1|\tproductive\tIGHV4-39\t770\t100\t155/155 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t7\t15\tX.7.15\t[X.6.38.11]\tCVVNYYDSSGYYYIDYW\tin-frame\t+\t\t\t\t\t\tggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag\n+14\tlcl|FLN1FA004BRKX9.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag\n+15\tlcl|FLN1FA00826HO1.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+16\tlcl|FLN1FA0041SQ1V.1|\tproductive\tIGHV3-53\t771\t99.36\t156/157 nt\t\t\tIGHJ4\t168\t83.33\t40/48 nt\tIGHD2-21\t3\tX\t7\t10\tX.7.10\t[X.7.38.11]\tCVVVTATPHGYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag\n+17\tlcl|FLN1FA000BBO91.1|\tproductive\tIGHV3-33\t795\t100\t160/160 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t8\t15\tX.8.15\t[X.7.38.11]\tCVTYYYDSSGYPYFDYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag\n+18\tlcl|FLN1FA008W37HH.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+19\tlcl|FLN1FA0080EWJB.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag\n+20\tlcl|FLN1FA003C09AP.1|\tproductive\tIGHV1-3\t790\t100\t159/159 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD2-15\t2\tX\t8\t16\tX.8.16\t[X.7.38.11]\tCYLGYCSGGSCYPQVGYW\tin-frame\t+\t\t\t\t\t\taggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag\n' |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def1_BCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def1_BCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,8 @@ + AA JUNCTION Reads Reads/Total Frequency % +1 CYISGSYVGYW 4 4/20 20.0000 +2 CYSAVVRGRFDYW 4 4/20 20.0000 +3 CVVNYYDSSGYYYIDYW 3 3/20 15.0000 +4 CVVVTATPHGYW 3 3/20 15.0000 +5 CYLGYCSGGSCYPQVGYW 3 3/20 15.0000 +6 CVTYYYDSSGYPYFDYW 2 2/20 10.0000 +7 CVTYCSGGSCYFDYW 1 1/20 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def1_BCR_output2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def1_BCR_output2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,8 @@ + AA JUNCTION Frequency % +1 CYISGSYVGYW 20.0000 +2 CYSAVVRGRFDYW 20.0000 +3 CVVNYYDSSGYYYIDYW 15.0000 +4 CVVVTATPHGYW 15.0000 +5 CYLGYCSGGSCYPQVGYW 15.0000 +6 CVTYYYDSSGYPYFDYW 10.0000 +7 CVTYCSGGSCYFDYW 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def1_BCR_output3.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def1_BCR_output3.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ + input % +Dominant CDR3 CYISGSYVGYW +Frequency 20.0000 +Number of unique CDR3 7 +Num of unique CDR3 > 1 6 85.7143 +Num of unique CDR3 = 1 1 14.2857 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def1_TCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def1_TCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| [ |
| b'@@ -0,0 +1,21 @@\n+\tSequence ID\tFunctionality\tV-GENE\tV-REGION score\tV-REGION identity %\tV-REGION identity nt\tV-REGION identity % (with ins/del events)\tV-REGION identity nt (with ins/del events)\tJ-GENE\tJ-REGION score\tJ-REGION identity %\tJ-REGION identity nt\tD-GENE\tD-REGION reading frame\tCDR1-IMGT length\tCDR2-IMGT length\tCDR3-IMGT length\tCDR-IMGT lengths\tFR-IMGT lengths\tAA JUNCTION\tJUNCTION frame\tOrientation\tFunctionality comment\tV-REGION potential ins/del\tJ-GENE and allele comment\tV-REGION insertions\tV-REGION deletions\tSequence\n+1\t@SRR060727.12120 SOLEXA7:7:2:351:1247 length=202\tproductive\tTRBV28\t145\t100\t30/30 nt\t\t\tTRBJ2-7\t235\t100\t47/47 nt\tTRBD1\t3\tX\tX\t12\tX.X.12\t[X.X.10.10]\tCAAGGQGNSYEQYF\tin-frame\t+\t\t\t\t\t\tagcaccaaccagacatctatgtacctctgtgccgctggggggcagggaaactcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagtttccctgccccccagcggcacag\n+2\t@SRR060727.14069 SOLEXA7:7:2:622:201 length=202\tproductive\tTRBV30\t95\t100\t20/20 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.6.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtgttctaacgggtgggnacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+3\t@SRR060727.45221 SOLEXA7:7:5:1541:638 length=202\tproductive\tTRBV30\t145\t100\t30/30 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.10.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tcttctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+4\t@SRR060727.49324 SOLEXA7:7:6:384:121 length=202\tproductive\tTRBV10-3\t165\t100\t34/34 nt\t\t\tTRBJ1-1\t240\t100\t48/48 nt\tTRBD1\t2\tX\tX\t11\tX.X.11\t[X.X.11.10]\tCAACEGLNTEAFF\tin-frame\t+\t\t\t\t\t\tcgctaccagctcccagacatctgtgtacttctgtgccgcatgtgaggggctgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcagcccctcacatgcggcacagaag\n+5\t@SRR060727.85642 SOLEXA7:7:10:98:1840 length=202\tproductive\tTRBV30\t115\t100\t24/24 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.8.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagcggacctgaacaagggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+6\t@SRR060727.100243 SOLEXA7:7:11:766:821 length=202\tproductive\tTRBV15\t105\t100\t22/22 nt\t\t\tTRBJ1-1\t222\t95.83\t46/48 nt\tTRBD1\t1\tX\tX\t11\tX.X.11\t[X.X.7.10]\tCAAGGKRYTEAFF\tin-frame\t-\t\t\t\t\t\tggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctggacaaggtacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacaggtacatggctgcgtcccccaggcctggtgagc\n+7\t@SRR060727.114177 SOLEXA7:7:12:1063:980 length=202\tproductive\tTRBV19\t150\t100\t31/31 nt\t\t\tTRBJ1-5\t241\t98\t49/50 nt\tTRBD1\t2\tX\tX\t13\tX.X.13\t[X.X.10.10]\tCAAGEGEVRNQPQHF\tin-frame\t+\t\t\t\t\t\tccaaaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggtgatgggactcgactctccatcctagtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgatttctaacctccccctcacccgcagca\n+8\t@SRR060727.130541 SOLEXA7:7:14:145:1124 length=202\tproductive\tTRBV3-1\t160\t100\t33/33 nt\t\t\tTRBJ1-5\t232\t96\t48/50 nt\tTRBD1\t2\tX\tX\t12\tX.X.12\t[X.X.11.10]\tCAAGQGFGNQPQHF\tin-frame\t+\t\t\t\t\t\tctggagcttggtgactctgctgtgtatttctgtgccgcaggtcagggttttgggaatcagccccagcattttggtgatgggactcgactctccatcctagataacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattcccaaaaccctgacctgcggcacag\n+9\t@SRR060727.175366 SOLEXA7:7:18:291:1226 length=202\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6\t95\t100\t20/20 nt\t\t\tTRBJ1-1\t231\t97.92\t47/48 nt\tTRBD1\t1\tX\tX\t13\tX.X.13\t[X.X.6.10]\tCAAGPRAGTNTEAFF\tin-frame\t+\t\t\t\t\t\tagacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaactaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcgtcc'..b'cccccctgtgcgtccgcggcacag\n+11\t@SRR060727.187683 SOLEXA7:7:19:809:1493 length=202\tproductive\tTRBV19\t135\t100\t28/28 nt\t\t\tTRBJ1-5\t232\t96\t48/50 nt\tTRBD1\t2\tX\tX\t13\tX.X.13\t[X.X.9.10]\tCAAGEGEVRNQPQHF\tin-frame\t+\t\t\t\t\t\taaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggagatgggactcgactctccatcctagaggtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatctccaaaatgctggggctgatttctaacctccccctcacccgcagca\n+12\t@SRR060727.190355 SOLEXA7:7:19:1314:185 length=202\tproductive\tTRBV27\t130\t100\t27/27 nt\t\t\tTRBJ1-5\t223\t94\t47/50 nt\tTRBD1\t3\tX\tX\t9\tX.X.9\t[X.X.9.10]\tCAAGPNQPQHF\tin-frame\t+\t\t\t\t\t\tcccaaccagacctctctgtacttctgtgccgccgggcccaatcagccccagcattttggtgatgggactcgactctccatcctagaggacctgaacaaggttaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattgggcccggcggcacagaagtacaga\n+13\t@SRR060727.196094 SOLEXA7:7:20:579:567 length=202\tproductive\tTRBV12-3 or TRBV12-4\t120\t100\t25/25 nt\t\t\tTRBJ2-5\t195\t89.58\t43/48 nt\tTRBD1\t1\tX\tX\t9\tX.X.9\t[X.X.8.10]\tCAAGTIETQYF\tin-frame\t+\t\t\t\t\t\tcagggactcagctgtgtacttctgtgccgcggggacaattgagacccagtacttcgggccaggcacgcggctcctggtgctcgaggacatgaaaaaagtgttaacgggtgggaacacgtttttcaggtcctcgagcaccaggagccgcgtgcctggcccgaagtactgggtctcaattgtccccgcggcacagaagtacaca\n+14\t@SRR060727.208531_SOLEXA7:7:21:1082:1793_length=20\tproductive\tTRBV25-1\t120\t100\t25/25 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t2\tX\tX\t10\tX.X.10\t[X.X.8.10]\tCAAGGGAPEAFF\tin-frame\t+\t\t\t\t\t\tctcacatacctctcagtacctctgtgcagcgggtggaggggccccagaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttctggggcccctccacccgctgcacagagggaa\n+15\t@SRR060727.236848 SOLEXA7:7:24:1329:676 length=202\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6\t120\t100\t25/25 nt\t\t\tTRBJ2-7\t235\t100\t47/47 nt\tTRBD1\t1\tX\tX\t11\tX.X.11\t[X.X.8.10]\tCAAGTGLSYEQYF\tin-frame\t+\t\t\t\t\t\tctcccagacatctgtgtacttctgtgccgcggggacaggactctcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggacctgaaaataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagagtcctgtccccgcggcacagaag\n+16\t@SRR060727.258473 SOLEXA7:7:27:271:1727 length=202\tproductive\tTRBV30\t100\t100\t21/21 nt\t\t\tTRBJ1-4\t201\t88.24\t45/51 nt\tTRBD1\t2\tX\tX\t10\tX.X.10\t[X.X.7.10]\tCAAGQVGEKLFF\tin-frame\t+\t\t\t\t\t\tgactctggcttctatctctgtgccgcgggacaagtgggtgaaaaactgttttttggcagtggaacccagctctctgtcttggaggacctgaacaacgaggttaacgggtgggaacaccttgttcaggtcctccaagacagagagctgggttccactgccaaaaaacagtttttcacccacttgtcccgcggcacagagatag\n+17\t@SRR060727.274111 SOLEXA7:7:28:1699:290 length=202\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6\t100\t100\t21/21 nt\t\t\tTRBJ1-1\t222\t95.83\t46/48 nt\tTRBD1\t1\tX\tX\t13\tX.X.13\t[X.X.7.10]\tCAAGPRAGTNTEAFF\tin-frame\t+\t\t\t\t\t\tcagacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttgtacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtacaaagaaagcttcagtgttcgtccctgcccttggtccagcggca\n+18\t@SRR060727.275014 SOLEXA7:7:29:152:1739 length=202\tproductive\tTRBV30\t130\t100\t27/27 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.9.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+19\t@SRR060727.281458_SOLEXA7:7:29:1133:1441_length=20\tproductive\tTRBV15\t141\t96.77\t30/31 nt\t\t\tTRBJ1-1\t222\t95.83\t46/48 nt\tTRBD1\t1\tX\tX\t11\tX.X.11\t[X.X.10.10]\tCAAGGKRYTEAFF\tin-frame\t+\t\t\t\t\t\tatgcctgggggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacagg\n+20\t@SRR060727.283135_SOLEXA7:7:29:1539:1405_length=20\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6\t100\t100\t21/21 nt\t\t\tTRBJ2-3\t200\t89.8\t44/49 nt\tTRBD2\t1\tX\tX\t8\tX.X.8\t[X.X.7.10]\tCAAGEDTQYF\tin-frame\t+\t\t\t\t\t\tcagacatctgtgtacttctgtgccgccggggaggatacgcagtattttggcccaggcacccggctgacagtgctcgaggacctgaaaaacgtgttcccacctaacgggtgggaacacgtttttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatcctccccggcggcacagaagtacacagat\n' |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def1_TCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def1_TCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,15 @@ + AA JUNCTION Reads Reads/Total Frequency % +1 CAAEGILAEAFF 4 4/20 20.0000 +2 CAAGEGEVRNQPQHF 2 2/20 10.0000 +3 CAAGGKRYTEAFF 2 2/20 10.0000 +4 CAAGPRAGTNTEAFF 2 2/20 10.0000 +5 CAACEGLNTEAFF 1 1/20 5.0000 +6 CAADAQGGNTEAFF 1 1/20 5.0000 +7 CAAGEDTQYF 1 1/20 5.0000 +8 CAAGGGAPEAFF 1 1/20 5.0000 +9 CAAGGQGNSYEQYF 1 1/20 5.0000 +10 CAAGPNQPQHF 1 1/20 5.0000 +11 CAAGQGFGNQPQHF 1 1/20 5.0000 +12 CAAGQVGEKLFF 1 1/20 5.0000 +13 CAAGTGLSYEQYF 1 1/20 5.0000 +14 CAAGTIETQYF 1 1/20 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def1_TCR_output2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def1_TCR_output2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ + AA JUNCTION Frequency % +1 CAAEGILAEAFF 20.0000 +2 CAAGEGEVRNQPQHF 10.0000 +3 CAAGGKRYTEAFF 10.0000 +4 CAAGPRAGTNTEAFF 10.0000 +5 CAACEGLNTEAFF 5.0000 +6 CAADAQGGNTEAFF 5.0000 +7 CAAGEDTQYF 5.0000 +8 CAAGGGAPEAFF 5.0000 +9 CAAGGQGNSYEQYF 5.0000 +10 CAAGPNQPQHF 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def1_TCR_output3.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def1_TCR_output3.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ + input1.csv % +Dominant CDR3 CAAEGILAEAFF +Frequency 20.0000 +Number of unique CDR3 14 +Num of unique CDR3 > 1 4 28.5714 +Num of unique CDR3 = 1 10 71.4286 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def2_BCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def2_BCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| [ |
| b'@@ -0,0 +1,21 @@\n+\tSequence ID\tFunctionality\tV-GENE\tV-REGION score\tV-REGION identity %\tV-REGION identity nt\tV-REGION identity % (with ins/del events)\tV-REGION identity nt (with ins/del events)\tJ-GENE\tJ-REGION score\tJ-REGION identity %\tJ-REGION identity nt\tD-GENE\tD-REGION reading frame\tCDR1-IMGT length\tCDR2-IMGT length\tCDR3-IMGT length\tCDR-IMGT lengths\tFR-IMGT lengths\tAA JUNCTION\tJUNCTION frame\tOrientation\tFunctionality comment\tV-REGION potential ins/del\tJ-GENE and allele comment\tV-REGION insertions\tV-REGION deletions\tSequence\n+1\tlcl|FLN1FA001B9SVM.1|\tproductive\tIGHV1-69 or IGHV1-69D\t790\t100\t159/159 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD2-15\t2\tX\t8\t16\tX.8.16\t[X.7.38.11]\tCYLGYCSGGSCYPQVGYW\tin-frame\t+\t\t\t\t\t\tgggcttgagtggatgggagggatcatccctatctttggtacagcaaactacgcacagaagttccagggcagagtcacgattaccgcggacgaatccacgagcacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag\n+2\tlcl|FLN1FA001CUVDF.1|\tproductive\tIGHV3-30 or IGHV3-30-3\t786\t99.38\t159/160 nt\t\t\tIGHJ4\t231\t97.92\t47/48 nt\tIGHD2-15\t2\tX\t8\t13\tX.8.13\t[X.7.38.11]\tCVTYCSGGSCYFDYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtggcagttatatcatatgatggaagtaataaatactacgtagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagctgaggacacggctgtgtattactgtgttacatattgtagtggtggtagctgctactttgactactggggccagggaaccctggtcaccgtctcctcag\n+3\tlcl|FLN1FA001DLPHD.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag\n+4\tlcl|FLN1FA002QTWMQ.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+5\tlcl|FLN1FA002Q975Z.1|\tproductive\tIGHV3-53\t771\t99.36\t156/157 nt\t\t\tIGHJ4\t168\t83.33\t40/48 nt\tIGHD2-21\t3\tX\t7\t10\tX.7.10\t[X.7.38.11]\tCVVVTATPHGYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag\n+6\tlcl|FLN1FA001AX4MF.1|\tproductive\tIGHV4-39\t770\t100\t155/155 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t7\t15\tX.7.15\t[X.6.38.11]\tCVVNYYDSSGYYYIDYW\tin-frame\t+\t\t\t\t\t\tggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag\n+7\tlcl|FLN1FA0074PUDE.1|\tproductive\tIGHV4-39\t770\t100\t155/155 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t7\t15\tX.7.15\t[X.6.38.11]\tCVVNYYDSSGYYYIDYW\tin-frame\t+\t\t\t\t\t\tggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag\n+8\tlcl|FLN1FA0013V4SA.1|\tproductive\tIGHV1-3\t790\t100\t159/159 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD2-15\t2\tX\t8\t16\tX.8.16\t[X.7.38.11]\tCYLGYCSGGSCYPQVGYW\tin-frame\t+\t\t\t\t\t\taggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag\n+9\tlcl|FLN1FA00056KW6.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgtta'..b'tgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag\n+11\tlcl|FLN1FA008ANOPH.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+12\tlcl|FLN1FA005T7JJ8.1|\tproductive\tIGHV3-33\t795\t100\t160/160 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t8\t15\tX.8.15\t[X.7.38.11]\tCVTYYYDSSGYPYFDYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag\n+13\tlcl|FLN1FA0018WER7.1|\tproductive\tIGHV4-39\t770\t100\t155/155 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t7\t15\tX.7.15\t[X.6.38.11]\tCVVNYYDSSGYYYIDYW\tin-frame\t+\t\t\t\t\t\tggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag\n+14\tlcl|FLN1FA004BRKX9.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag\n+15\tlcl|FLN1FA00826HO1.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+16\tlcl|FLN1FA0041SQ1V.1|\tproductive\tIGHV3-53\t771\t99.36\t156/157 nt\t\t\tIGHJ4\t168\t83.33\t40/48 nt\tIGHD2-21\t3\tX\t7\t10\tX.7.10\t[X.7.38.11]\tCVVVTATPHGYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag\n+17\tlcl|FLN1FA000BBO91.1|\tproductive\tIGHV3-33\t795\t100\t160/160 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t8\t15\tX.8.15\t[X.7.38.11]\tCVTYYYDSSGYPYFDYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag\n+18\tlcl|FLN1FA008W37HH.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+19\tlcl|FLN1FA0080EWJB.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag\n+20\tlcl|FLN1FA003C09AP.1|\tproductive\tIGHV1-3\t790\t100\t159/159 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD2-15\t2\tX\t8\t16\tX.8.16\t[X.7.38.11]\tCYLGYCSGGSCYPQVGYW\tin-frame\t+\t\t\t\t\t\taggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag\n' |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def2_BCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def2_BCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,9 @@ + V-GENE AA JUNCTION Reads Reads/Total Frequency % +1 IGHV1-3 CYISGSYVGYW 4 4/20 20.0000 +2 IGHV4-39 CYSAVVRGRFDYW 4 4/20 20.0000 +3 IGHV3-53 CVVVTATPHGYW 3 3/20 15.0000 +4 IGHV4-39 CVVNYYDSSGYYYIDYW 3 3/20 15.0000 +5 IGHV1-3 CYLGYCSGGSCYPQVGYW 2 2/20 10.0000 +6 IGHV3-33 CVTYYYDSSGYPYFDYW 2 2/20 10.0000 +7 IGHV1-69 or IGHV1-69D CYLGYCSGGSCYPQVGYW 1 1/20 5.0000 +8 IGHV3-30 or IGHV3-30-3 CVTYCSGGSCYFDYW 1 1/20 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def2_BCR_output2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def2_BCR_output2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,9 @@ + V-GENE AA JUNCTION Frequency % +1 IGHV1-3 CYISGSYVGYW 20.0000 +2 IGHV4-39 CYSAVVRGRFDYW 20.0000 +3 IGHV3-53 CVVVTATPHGYW 15.0000 +4 IGHV4-39 CVVNYYDSSGYYYIDYW 15.0000 +5 IGHV1-3 CYLGYCSGGSCYPQVGYW 10.0000 +6 IGHV3-33 CVTYYYDSSGYPYFDYW 10.0000 +7 IGHV1-69 or IGHV1-69D CYLGYCSGGSCYPQVGYW 5.0000 +8 IGHV3-30 or IGHV3-30-3 CVTYCSGGSCYFDYW 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def2_BCR_output3.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def2_BCR_output3.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ + input % +Dominant Clonotype IGHV1-3,CYISGSYVGYW +Frequency 20.0000 +Number of Clonotypes 8 +Expanding Clonotypes 6 75.0000 +Singletons 2 25.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def2_TCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def2_TCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| [ |
| b'@@ -0,0 +1,21 @@\n+\tSequence ID\tFunctionality\tV-GENE\tV-REGION score\tV-REGION identity %\tV-REGION identity nt\tV-REGION identity % (with ins/del events)\tV-REGION identity nt (with ins/del events)\tJ-GENE\tJ-REGION score\tJ-REGION identity %\tJ-REGION identity nt\tD-GENE\tD-REGION reading frame\tCDR1-IMGT length\tCDR2-IMGT length\tCDR3-IMGT length\tCDR-IMGT lengths\tFR-IMGT lengths\tAA JUNCTION\tJUNCTION frame\tOrientation\tFunctionality comment\tV-REGION potential ins/del\tJ-GENE and allele comment\tV-REGION insertions\tV-REGION deletions\tSequence\n+1\t@SRR060727.12120 SOLEXA7:7:2:351:1247 length=202\tproductive\tTRBV28\t145\t100\t30/30 nt\t\t\tTRBJ2-7\t235\t100\t47/47 nt\tTRBD1\t3\tX\tX\t12\tX.X.12\t[X.X.10.10]\tCAAGGQGNSYEQYF\tin-frame\t+\t\t\t\t\t\tagcaccaaccagacatctatgtacctctgtgccgctggggggcagggaaactcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagtttccctgccccccagcggcacag\n+2\t@SRR060727.14069 SOLEXA7:7:2:622:201 length=202\tproductive\tTRBV30\t95\t100\t20/20 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.6.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtgttctaacgggtgggnacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+3\t@SRR060727.45221 SOLEXA7:7:5:1541:638 length=202\tproductive\tTRBV30\t145\t100\t30/30 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.10.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tcttctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+4\t@SRR060727.49324 SOLEXA7:7:6:384:121 length=202\tproductive\tTRBV10-3\t165\t100\t34/34 nt\t\t\tTRBJ1-1\t240\t100\t48/48 nt\tTRBD1\t2\tX\tX\t11\tX.X.11\t[X.X.11.10]\tCAACEGLNTEAFF\tin-frame\t+\t\t\t\t\t\tcgctaccagctcccagacatctgtgtacttctgtgccgcatgtgaggggctgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcagcccctcacatgcggcacagaag\n+5\t@SRR060727.85642 SOLEXA7:7:10:98:1840 length=202\tproductive\tTRBV30\t115\t100\t24/24 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.8.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagcggacctgaacaagggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+6\t@SRR060727.100243 SOLEXA7:7:11:766:821 length=202\tproductive\tTRBV15\t105\t100\t22/22 nt\t\t\tTRBJ1-1\t222\t95.83\t46/48 nt\tTRBD1\t1\tX\tX\t11\tX.X.11\t[X.X.7.10]\tCAAGGKRYTEAFF\tin-frame\t-\t\t\t\t\t\tggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctggacaaggtacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacaggtacatggctgcgtcccccaggcctggtgagc\n+7\t@SRR060727.114177 SOLEXA7:7:12:1063:980 length=202\tproductive\tTRBV19\t150\t100\t31/31 nt\t\t\tTRBJ1-5\t241\t98\t49/50 nt\tTRBD1\t2\tX\tX\t13\tX.X.13\t[X.X.10.10]\tCAAGEGEVRNQPQHF\tin-frame\t+\t\t\t\t\t\tccaaaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggtgatgggactcgactctccatcctagtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgatttctaacctccccctcacccgcagca\n+8\t@SRR060727.130541 SOLEXA7:7:14:145:1124 length=202\tproductive\tTRBV3-1\t160\t100\t33/33 nt\t\t\tTRBJ1-5\t232\t96\t48/50 nt\tTRBD1\t2\tX\tX\t12\tX.X.12\t[X.X.11.10]\tCAAGQGFGNQPQHF\tin-frame\t+\t\t\t\t\t\tctggagcttggtgactctgctgtgtatttctgtgccgcaggtcagggttttgggaatcagccccagcattttggtgatgggactcgactctccatcctagataacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattcccaaaaccctgacctgcggcacag\n+9\t@SRR060727.175366 SOLEXA7:7:18:291:1226 length=202\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6\t95\t100\t20/20 nt\t\t\tTRBJ1-1\t231\t97.92\t47/48 nt\tTRBD1\t1\tX\tX\t13\tX.X.13\t[X.X.6.10]\tCAAGPRAGTNTEAFF\tin-frame\t+\t\t\t\t\t\tagacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaactaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcgtcc'..b'cccccctgtgcgtccgcggcacag\n+11\t@SRR060727.187683 SOLEXA7:7:19:809:1493 length=202\tproductive\tTRBV19\t135\t100\t28/28 nt\t\t\tTRBJ1-5\t232\t96\t48/50 nt\tTRBD1\t2\tX\tX\t13\tX.X.13\t[X.X.9.10]\tCAAGEGEVRNQPQHF\tin-frame\t+\t\t\t\t\t\taaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggagatgggactcgactctccatcctagaggtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatctccaaaatgctggggctgatttctaacctccccctcacccgcagca\n+12\t@SRR060727.190355 SOLEXA7:7:19:1314:185 length=202\tproductive\tTRBV27\t130\t100\t27/27 nt\t\t\tTRBJ1-5\t223\t94\t47/50 nt\tTRBD1\t3\tX\tX\t9\tX.X.9\t[X.X.9.10]\tCAAGPNQPQHF\tin-frame\t+\t\t\t\t\t\tcccaaccagacctctctgtacttctgtgccgccgggcccaatcagccccagcattttggtgatgggactcgactctccatcctagaggacctgaacaaggttaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattgggcccggcggcacagaagtacaga\n+13\t@SRR060727.196094 SOLEXA7:7:20:579:567 length=202\tproductive\tTRBV12-3 or TRBV12-4\t120\t100\t25/25 nt\t\t\tTRBJ2-5\t195\t89.58\t43/48 nt\tTRBD1\t1\tX\tX\t9\tX.X.9\t[X.X.8.10]\tCAAGTIETQYF\tin-frame\t+\t\t\t\t\t\tcagggactcagctgtgtacttctgtgccgcggggacaattgagacccagtacttcgggccaggcacgcggctcctggtgctcgaggacatgaaaaaagtgttaacgggtgggaacacgtttttcaggtcctcgagcaccaggagccgcgtgcctggcccgaagtactgggtctcaattgtccccgcggcacagaagtacaca\n+14\t@SRR060727.208531_SOLEXA7:7:21:1082:1793_length=20\tproductive\tTRBV25-1\t120\t100\t25/25 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t2\tX\tX\t10\tX.X.10\t[X.X.8.10]\tCAAGGGAPEAFF\tin-frame\t+\t\t\t\t\t\tctcacatacctctcagtacctctgtgcagcgggtggaggggccccagaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttctggggcccctccacccgctgcacagagggaa\n+15\t@SRR060727.236848 SOLEXA7:7:24:1329:676 length=202\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6\t120\t100\t25/25 nt\t\t\tTRBJ2-7\t235\t100\t47/47 nt\tTRBD1\t1\tX\tX\t11\tX.X.11\t[X.X.8.10]\tCAAGTGLSYEQYF\tin-frame\t+\t\t\t\t\t\tctcccagacatctgtgtacttctgtgccgcggggacaggactctcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggacctgaaaataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagagtcctgtccccgcggcacagaag\n+16\t@SRR060727.258473 SOLEXA7:7:27:271:1727 length=202\tproductive\tTRBV30\t100\t100\t21/21 nt\t\t\tTRBJ1-4\t201\t88.24\t45/51 nt\tTRBD1\t2\tX\tX\t10\tX.X.10\t[X.X.7.10]\tCAAGQVGEKLFF\tin-frame\t+\t\t\t\t\t\tgactctggcttctatctctgtgccgcgggacaagtgggtgaaaaactgttttttggcagtggaacccagctctctgtcttggaggacctgaacaacgaggttaacgggtgggaacaccttgttcaggtcctccaagacagagagctgggttccactgccaaaaaacagtttttcacccacttgtcccgcggcacagagatag\n+17\t@SRR060727.274111 SOLEXA7:7:28:1699:290 length=202\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6\t100\t100\t21/21 nt\t\t\tTRBJ1-1\t222\t95.83\t46/48 nt\tTRBD1\t1\tX\tX\t13\tX.X.13\t[X.X.7.10]\tCAAGPRAGTNTEAFF\tin-frame\t+\t\t\t\t\t\tcagacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttgtacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtacaaagaaagcttcagtgttcgtccctgcccttggtccagcggca\n+18\t@SRR060727.275014 SOLEXA7:7:29:152:1739 length=202\tproductive\tTRBV30\t130\t100\t27/27 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.9.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+19\t@SRR060727.281458_SOLEXA7:7:29:1133:1441_length=20\tproductive\tTRBV15\t141\t96.77\t30/31 nt\t\t\tTRBJ1-1\t222\t95.83\t46/48 nt\tTRBD1\t1\tX\tX\t11\tX.X.11\t[X.X.10.10]\tCAAGGKRYTEAFF\tin-frame\t+\t\t\t\t\t\tatgcctgggggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacagg\n+20\t@SRR060727.283135_SOLEXA7:7:29:1539:1405_length=20\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6\t100\t100\t21/21 nt\t\t\tTRBJ2-3\t200\t89.8\t44/49 nt\tTRBD2\t1\tX\tX\t8\tX.X.8\t[X.X.7.10]\tCAAGEDTQYF\tin-frame\t+\t\t\t\t\t\tcagacatctgtgtacttctgtgccgccggggaggatacgcagtattttggcccaggcacccggctgacagtgctcgaggacctgaaaaacgtgttcccacctaacgggtgggaacacgtttttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatcctccccggcggcacagaagtacacagat\n' |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def2_TCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def2_TCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,15 @@ + V-GENE AA JUNCTION Reads Reads/Total Frequency % +1 TRBV30 CAAEGILAEAFF 4 4/20 20.0000 +2 TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6 CAAGPRAGTNTEAFF 2 2/20 10.0000 +3 TRBV15 CAAGGKRYTEAFF 2 2/20 10.0000 +4 TRBV19 CAAGEGEVRNQPQHF 2 2/20 10.0000 +5 TRBV10-3 CAACEGLNTEAFF 1 1/20 5.0000 +6 TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6 CAAGEDTQYF 1 1/20 5.0000 +7 TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6 CAAGTGLSYEQYF 1 1/20 5.0000 +8 TRBV12-3 or TRBV12-4 CAAGTIETQYF 1 1/20 5.0000 +9 TRBV25-1 CAAGGGAPEAFF 1 1/20 5.0000 +10 TRBV27 CAAGPNQPQHF 1 1/20 5.0000 +11 TRBV28 CAAGGQGNSYEQYF 1 1/20 5.0000 +12 TRBV3-1 CAAGQGFGNQPQHF 1 1/20 5.0000 +13 TRBV30 CAAGQVGEKLFF 1 1/20 5.0000 +14 TRBV6-1 or TRBV6-5 or TRBV6-6 CAADAQGGNTEAFF 1 1/20 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def2_TCR_output2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def2_TCR_output2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ + V-GENE AA JUNCTION Frequency % +1 TRBV30 CAAEGILAEAFF 20.0000 +2 TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6 CAAGPRAGTNTEAFF 10.0000 +3 TRBV15 CAAGGKRYTEAFF 10.0000 +4 TRBV19 CAAGEGEVRNQPQHF 10.0000 +5 TRBV10-3 CAACEGLNTEAFF 5.0000 +6 TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6 CAAGEDTQYF 5.0000 +7 TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6 CAAGTGLSYEQYF 5.0000 +8 TRBV12-3 or TRBV12-4 CAAGTIETQYF 5.0000 +9 TRBV25-1 CAAGGGAPEAFF 5.0000 +10 TRBV27 CAAGPNQPQHF 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def2_TCR_output3.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def2_TCR_output3.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ + input1.csv % +Dominant Clonotype TRBV30,CAAEGILAEAFF +Frequency 20.0000 +Number of Clonotypes 14 +Expanding Clonotypes 4 28.5714 +Singletons 10 71.4286 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def3_BCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def3_BCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| [ |
| b'@@ -0,0 +1,21 @@\n+\tSequence ID\tFunctionality\tV-GENE\tV-REGION score\tV-REGION identity %\tV-REGION identity nt\tV-REGION identity % (with ins/del events)\tV-REGION identity nt (with ins/del events)\tJ-GENE\tJ-REGION score\tJ-REGION identity %\tJ-REGION identity nt\tD-GENE\tD-REGION reading frame\tCDR1-IMGT length\tCDR2-IMGT length\tCDR3-IMGT length\tCDR-IMGT lengths\tFR-IMGT lengths\tAA JUNCTION\tJUNCTION frame\tOrientation\tFunctionality comment\tV-REGION potential ins/del\tJ-GENE and allele comment\tV-REGION insertions\tV-REGION deletions\tSequence\n+1\tlcl|FLN1FA001B9SVM.1|\tproductive\tIGHV1-69 or IGHV1-69D\t790\t100\t159/159 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD2-15\t2\tX\t8\t16\tX.8.16\t[X.7.38.11]\tCYLGYCSGGSCYPQVGYW\tin-frame\t+\t\t\t\t\t\tgggcttgagtggatgggagggatcatccctatctttggtacagcaaactacgcacagaagttccagggcagagtcacgattaccgcggacgaatccacgagcacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag\n+2\tlcl|FLN1FA001CUVDF.1|\tproductive\tIGHV3-30 or IGHV3-30-3\t786\t99.38\t159/160 nt\t\t\tIGHJ4\t231\t97.92\t47/48 nt\tIGHD2-15\t2\tX\t8\t13\tX.8.13\t[X.7.38.11]\tCVTYCSGGSCYFDYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtggcagttatatcatatgatggaagtaataaatactacgtagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagctgaggacacggctgtgtattactgtgttacatattgtagtggtggtagctgctactttgactactggggccagggaaccctggtcaccgtctcctcag\n+3\tlcl|FLN1FA001DLPHD.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag\n+4\tlcl|FLN1FA002QTWMQ.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+5\tlcl|FLN1FA002Q975Z.1|\tproductive\tIGHV3-53\t771\t99.36\t156/157 nt\t\t\tIGHJ4\t168\t83.33\t40/48 nt\tIGHD2-21\t3\tX\t7\t10\tX.7.10\t[X.7.38.11]\tCVVVTATPHGYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag\n+6\tlcl|FLN1FA001AX4MF.1|\tproductive\tIGHV4-39\t770\t100\t155/155 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t7\t15\tX.7.15\t[X.6.38.11]\tCVVNYYDSSGYYYIDYW\tin-frame\t+\t\t\t\t\t\tggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag\n+7\tlcl|FLN1FA0074PUDE.1|\tproductive\tIGHV4-39\t770\t100\t155/155 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t7\t15\tX.7.15\t[X.6.38.11]\tCVVNYYDSSGYYYIDYW\tin-frame\t+\t\t\t\t\t\tggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag\n+8\tlcl|FLN1FA0013V4SA.1|\tproductive\tIGHV1-3\t790\t100\t159/159 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD2-15\t2\tX\t8\t16\tX.8.16\t[X.7.38.11]\tCYLGYCSGGSCYPQVGYW\tin-frame\t+\t\t\t\t\t\taggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag\n+9\tlcl|FLN1FA00056KW6.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgtta'..b'tgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag\n+11\tlcl|FLN1FA008ANOPH.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+12\tlcl|FLN1FA005T7JJ8.1|\tproductive\tIGHV3-33\t795\t100\t160/160 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t8\t15\tX.8.15\t[X.7.38.11]\tCVTYYYDSSGYPYFDYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag\n+13\tlcl|FLN1FA0018WER7.1|\tproductive\tIGHV4-39\t770\t100\t155/155 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t7\t15\tX.7.15\t[X.6.38.11]\tCVVNYYDSSGYYYIDYW\tin-frame\t+\t\t\t\t\t\tggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag\n+14\tlcl|FLN1FA004BRKX9.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag\n+15\tlcl|FLN1FA00826HO1.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+16\tlcl|FLN1FA0041SQ1V.1|\tproductive\tIGHV3-53\t771\t99.36\t156/157 nt\t\t\tIGHJ4\t168\t83.33\t40/48 nt\tIGHD2-21\t3\tX\t7\t10\tX.7.10\t[X.7.38.11]\tCVVVTATPHGYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag\n+17\tlcl|FLN1FA000BBO91.1|\tproductive\tIGHV3-33\t795\t100\t160/160 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t8\t15\tX.8.15\t[X.7.38.11]\tCVTYYYDSSGYPYFDYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag\n+18\tlcl|FLN1FA008W37HH.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+19\tlcl|FLN1FA0080EWJB.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag\n+20\tlcl|FLN1FA003C09AP.1|\tproductive\tIGHV1-3\t790\t100\t159/159 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD2-15\t2\tX\t8\t16\tX.8.16\t[X.7.38.11]\tCYLGYCSGGSCYPQVGYW\tin-frame\t+\t\t\t\t\t\taggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag\n' |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def3_BCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def3_BCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,8 @@ + J-GENE AA JUNCTION Reads Reads/Total Frequency % +1 IGHJ4 CYISGSYVGYW 4 4/20 20.0000 +2 IGHJ4 CYSAVVRGRFDYW 4 4/20 20.0000 +3 IGHJ4 CVVNYYDSSGYYYIDYW 3 3/20 15.0000 +4 IGHJ4 CVVVTATPHGYW 3 3/20 15.0000 +5 IGHJ4 CYLGYCSGGSCYPQVGYW 3 3/20 15.0000 +6 IGHJ4 CVTYYYDSSGYPYFDYW 2 2/20 10.0000 +7 IGHJ4 CVTYCSGGSCYFDYW 1 1/20 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def3_BCR_output2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def3_BCR_output2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,8 @@ + J-GENE AA JUNCTION Frequency % +1 IGHJ4 CYISGSYVGYW 20.0000 +2 IGHJ4 CYSAVVRGRFDYW 20.0000 +3 IGHJ4 CVVNYYDSSGYYYIDYW 15.0000 +4 IGHJ4 CVVVTATPHGYW 15.0000 +5 IGHJ4 CYLGYCSGGSCYPQVGYW 15.0000 +6 IGHJ4 CVTYYYDSSGYPYFDYW 10.0000 +7 IGHJ4 CVTYCSGGSCYFDYW 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def3_BCR_output3.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def3_BCR_output3.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ + input % +Dominant Clonotype(J-CDR3) IGHJ4,CYISGSYVGYW +Frequency 20.0000 +Number of Clonotypes(J-CDR3) 7 +Expanding Clonotypes(J-CDR3) 6 85.7143 +Singletons 1 14.2857 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def3_TCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def3_TCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| [ |
| b'@@ -0,0 +1,21 @@\n+\tSequence ID\tFunctionality\tV-GENE\tV-REGION score\tV-REGION identity %\tV-REGION identity nt\tV-REGION identity % (with ins/del events)\tV-REGION identity nt (with ins/del events)\tJ-GENE\tJ-REGION score\tJ-REGION identity %\tJ-REGION identity nt\tD-GENE\tD-REGION reading frame\tCDR1-IMGT length\tCDR2-IMGT length\tCDR3-IMGT length\tCDR-IMGT lengths\tFR-IMGT lengths\tAA JUNCTION\tJUNCTION frame\tOrientation\tFunctionality comment\tV-REGION potential ins/del\tJ-GENE and allele comment\tV-REGION insertions\tV-REGION deletions\tSequence\n+1\t@SRR060727.12120 SOLEXA7:7:2:351:1247 length=202\tproductive\tTRBV28\t145\t100\t30/30 nt\t\t\tTRBJ2-7\t235\t100\t47/47 nt\tTRBD1\t3\tX\tX\t12\tX.X.12\t[X.X.10.10]\tCAAGGQGNSYEQYF\tin-frame\t+\t\t\t\t\t\tagcaccaaccagacatctatgtacctctgtgccgctggggggcagggaaactcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagtttccctgccccccagcggcacag\n+2\t@SRR060727.14069 SOLEXA7:7:2:622:201 length=202\tproductive\tTRBV30\t95\t100\t20/20 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.6.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtgttctaacgggtgggnacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+3\t@SRR060727.45221 SOLEXA7:7:5:1541:638 length=202\tproductive\tTRBV30\t145\t100\t30/30 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.10.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tcttctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+4\t@SRR060727.49324 SOLEXA7:7:6:384:121 length=202\tproductive\tTRBV10-3\t165\t100\t34/34 nt\t\t\tTRBJ1-1\t240\t100\t48/48 nt\tTRBD1\t2\tX\tX\t11\tX.X.11\t[X.X.11.10]\tCAACEGLNTEAFF\tin-frame\t+\t\t\t\t\t\tcgctaccagctcccagacatctgtgtacttctgtgccgcatgtgaggggctgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcagcccctcacatgcggcacagaag\n+5\t@SRR060727.85642 SOLEXA7:7:10:98:1840 length=202\tproductive\tTRBV30\t115\t100\t24/24 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.8.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagcggacctgaacaagggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+6\t@SRR060727.100243 SOLEXA7:7:11:766:821 length=202\tproductive\tTRBV15\t105\t100\t22/22 nt\t\t\tTRBJ1-1\t222\t95.83\t46/48 nt\tTRBD1\t1\tX\tX\t11\tX.X.11\t[X.X.7.10]\tCAAGGKRYTEAFF\tin-frame\t-\t\t\t\t\t\tggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctggacaaggtacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacaggtacatggctgcgtcccccaggcctggtgagc\n+7\t@SRR060727.114177 SOLEXA7:7:12:1063:980 length=202\tproductive\tTRBV19\t150\t100\t31/31 nt\t\t\tTRBJ1-5\t241\t98\t49/50 nt\tTRBD1\t2\tX\tX\t13\tX.X.13\t[X.X.10.10]\tCAAGEGEVRNQPQHF\tin-frame\t+\t\t\t\t\t\tccaaaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggtgatgggactcgactctccatcctagtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgatttctaacctccccctcacccgcagca\n+8\t@SRR060727.130541 SOLEXA7:7:14:145:1124 length=202\tproductive\tTRBV3-1\t160\t100\t33/33 nt\t\t\tTRBJ1-5\t232\t96\t48/50 nt\tTRBD1\t2\tX\tX\t12\tX.X.12\t[X.X.11.10]\tCAAGQGFGNQPQHF\tin-frame\t+\t\t\t\t\t\tctggagcttggtgactctgctgtgtatttctgtgccgcaggtcagggttttgggaatcagccccagcattttggtgatgggactcgactctccatcctagataacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattcccaaaaccctgacctgcggcacag\n+9\t@SRR060727.175366 SOLEXA7:7:18:291:1226 length=202\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6\t95\t100\t20/20 nt\t\t\tTRBJ1-1\t231\t97.92\t47/48 nt\tTRBD1\t1\tX\tX\t13\tX.X.13\t[X.X.6.10]\tCAAGPRAGTNTEAFF\tin-frame\t+\t\t\t\t\t\tagacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaactaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcgtcc'..b'cccccctgtgcgtccgcggcacag\n+11\t@SRR060727.187683 SOLEXA7:7:19:809:1493 length=202\tproductive\tTRBV19\t135\t100\t28/28 nt\t\t\tTRBJ1-5\t232\t96\t48/50 nt\tTRBD1\t2\tX\tX\t13\tX.X.13\t[X.X.9.10]\tCAAGEGEVRNQPQHF\tin-frame\t+\t\t\t\t\t\taaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggagatgggactcgactctccatcctagaggtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatctccaaaatgctggggctgatttctaacctccccctcacccgcagca\n+12\t@SRR060727.190355 SOLEXA7:7:19:1314:185 length=202\tproductive\tTRBV27\t130\t100\t27/27 nt\t\t\tTRBJ1-5\t223\t94\t47/50 nt\tTRBD1\t3\tX\tX\t9\tX.X.9\t[X.X.9.10]\tCAAGPNQPQHF\tin-frame\t+\t\t\t\t\t\tcccaaccagacctctctgtacttctgtgccgccgggcccaatcagccccagcattttggtgatgggactcgactctccatcctagaggacctgaacaaggttaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattgggcccggcggcacagaagtacaga\n+13\t@SRR060727.196094 SOLEXA7:7:20:579:567 length=202\tproductive\tTRBV12-3 or TRBV12-4\t120\t100\t25/25 nt\t\t\tTRBJ2-5\t195\t89.58\t43/48 nt\tTRBD1\t1\tX\tX\t9\tX.X.9\t[X.X.8.10]\tCAAGTIETQYF\tin-frame\t+\t\t\t\t\t\tcagggactcagctgtgtacttctgtgccgcggggacaattgagacccagtacttcgggccaggcacgcggctcctggtgctcgaggacatgaaaaaagtgttaacgggtgggaacacgtttttcaggtcctcgagcaccaggagccgcgtgcctggcccgaagtactgggtctcaattgtccccgcggcacagaagtacaca\n+14\t@SRR060727.208531_SOLEXA7:7:21:1082:1793_length=20\tproductive\tTRBV25-1\t120\t100\t25/25 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t2\tX\tX\t10\tX.X.10\t[X.X.8.10]\tCAAGGGAPEAFF\tin-frame\t+\t\t\t\t\t\tctcacatacctctcagtacctctgtgcagcgggtggaggggccccagaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttctggggcccctccacccgctgcacagagggaa\n+15\t@SRR060727.236848 SOLEXA7:7:24:1329:676 length=202\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6\t120\t100\t25/25 nt\t\t\tTRBJ2-7\t235\t100\t47/47 nt\tTRBD1\t1\tX\tX\t11\tX.X.11\t[X.X.8.10]\tCAAGTGLSYEQYF\tin-frame\t+\t\t\t\t\t\tctcccagacatctgtgtacttctgtgccgcggggacaggactctcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggacctgaaaataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagagtcctgtccccgcggcacagaag\n+16\t@SRR060727.258473 SOLEXA7:7:27:271:1727 length=202\tproductive\tTRBV30\t100\t100\t21/21 nt\t\t\tTRBJ1-4\t201\t88.24\t45/51 nt\tTRBD1\t2\tX\tX\t10\tX.X.10\t[X.X.7.10]\tCAAGQVGEKLFF\tin-frame\t+\t\t\t\t\t\tgactctggcttctatctctgtgccgcgggacaagtgggtgaaaaactgttttttggcagtggaacccagctctctgtcttggaggacctgaacaacgaggttaacgggtgggaacaccttgttcaggtcctccaagacagagagctgggttccactgccaaaaaacagtttttcacccacttgtcccgcggcacagagatag\n+17\t@SRR060727.274111 SOLEXA7:7:28:1699:290 length=202\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6\t100\t100\t21/21 nt\t\t\tTRBJ1-1\t222\t95.83\t46/48 nt\tTRBD1\t1\tX\tX\t13\tX.X.13\t[X.X.7.10]\tCAAGPRAGTNTEAFF\tin-frame\t+\t\t\t\t\t\tcagacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttgtacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtacaaagaaagcttcagtgttcgtccctgcccttggtccagcggca\n+18\t@SRR060727.275014 SOLEXA7:7:29:152:1739 length=202\tproductive\tTRBV30\t130\t100\t27/27 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.9.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+19\t@SRR060727.281458_SOLEXA7:7:29:1133:1441_length=20\tproductive\tTRBV15\t141\t96.77\t30/31 nt\t\t\tTRBJ1-1\t222\t95.83\t46/48 nt\tTRBD1\t1\tX\tX\t11\tX.X.11\t[X.X.10.10]\tCAAGGKRYTEAFF\tin-frame\t+\t\t\t\t\t\tatgcctgggggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacagg\n+20\t@SRR060727.283135_SOLEXA7:7:29:1539:1405_length=20\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6\t100\t100\t21/21 nt\t\t\tTRBJ2-3\t200\t89.8\t44/49 nt\tTRBD2\t1\tX\tX\t8\tX.X.8\t[X.X.7.10]\tCAAGEDTQYF\tin-frame\t+\t\t\t\t\t\tcagacatctgtgtacttctgtgccgccggggaggatacgcagtattttggcccaggcacccggctgacagtgctcgaggacctgaaaaacgtgttcccacctaacgggtgggaacacgtttttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatcctccccggcggcacagaagtacacagat\n' |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def3_TCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def3_TCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,15 @@ + J-GENE AA JUNCTION Reads Reads/Total Frequency % +1 TRBJ1-1 CAAEGILAEAFF 4 4/20 20.0000 +2 TRBJ1-1 CAAGGKRYTEAFF 2 2/20 10.0000 +3 TRBJ1-1 CAAGPRAGTNTEAFF 2 2/20 10.0000 +4 TRBJ1-5 CAAGEGEVRNQPQHF 2 2/20 10.0000 +5 TRBJ1-1 CAACEGLNTEAFF 1 1/20 5.0000 +6 TRBJ1-1 CAADAQGGNTEAFF 1 1/20 5.0000 +7 TRBJ1-1 CAAGGGAPEAFF 1 1/20 5.0000 +8 TRBJ1-4 CAAGQVGEKLFF 1 1/20 5.0000 +9 TRBJ1-5 CAAGPNQPQHF 1 1/20 5.0000 +10 TRBJ1-5 CAAGQGFGNQPQHF 1 1/20 5.0000 +11 TRBJ2-3 CAAGEDTQYF 1 1/20 5.0000 +12 TRBJ2-5 CAAGTIETQYF 1 1/20 5.0000 +13 TRBJ2-7 CAAGGQGNSYEQYF 1 1/20 5.0000 +14 TRBJ2-7 CAAGTGLSYEQYF 1 1/20 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def3_TCR_output2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def3_TCR_output2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ + J-GENE AA JUNCTION Frequency % +1 TRBJ1-1 CAAEGILAEAFF 20.0000 +2 TRBJ1-1 CAAGGKRYTEAFF 10.0000 +3 TRBJ1-1 CAAGPRAGTNTEAFF 10.0000 +4 TRBJ1-5 CAAGEGEVRNQPQHF 10.0000 +5 TRBJ1-1 CAACEGLNTEAFF 5.0000 +6 TRBJ1-1 CAADAQGGNTEAFF 5.0000 +7 TRBJ1-1 CAAGGGAPEAFF 5.0000 +8 TRBJ1-4 CAAGQVGEKLFF 5.0000 +9 TRBJ1-5 CAAGPNQPQHF 5.0000 +10 TRBJ1-5 CAAGQGFGNQPQHF 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def3_TCR_output3.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def3_TCR_output3.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ + input1.csv % +Dominant Clonotype(J-CDR3) TRBJ1-1,CAAEGILAEAFF +Frequency 20.0000 +Number of Clonotypes(J-CDR3) 14 +Expanding Clonotypes(J-CDR3) 4 28.5714 +Singletons 10 71.4286 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def4_BCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def4_BCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| [ |
| b'@@ -0,0 +1,21 @@\n+\tSequence ID\tFunctionality\tV-GENE\tV-REGION score\tV-REGION identity %\tV-REGION identity nt\tV-REGION identity % (with ins/del events)\tV-REGION identity nt (with ins/del events)\tJ-GENE\tJ-REGION score\tJ-REGION identity %\tJ-REGION identity nt\tD-GENE\tD-REGION reading frame\tCDR1-IMGT length\tCDR2-IMGT length\tCDR3-IMGT length\tCDR-IMGT lengths\tFR-IMGT lengths\tAA JUNCTION\tJUNCTION frame\tOrientation\tFunctionality comment\tV-REGION potential ins/del\tJ-GENE and allele comment\tV-REGION insertions\tV-REGION deletions\tSequence\n+1\tlcl|FLN1FA001B9SVM.1|\tproductive\tIGHV1-69 or IGHV1-69D\t790\t100\t159/159 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD2-15\t2\tX\t8\t16\tX.8.16\t[X.7.38.11]\tCYLGYCSGGSCYPQVGYW\tin-frame\t+\t\t\t\t\t\tgggcttgagtggatgggagggatcatccctatctttggtacagcaaactacgcacagaagttccagggcagagtcacgattaccgcggacgaatccacgagcacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag\n+2\tlcl|FLN1FA001CUVDF.1|\tproductive\tIGHV3-30 or IGHV3-30-3\t786\t99.38\t159/160 nt\t\t\tIGHJ4\t231\t97.92\t47/48 nt\tIGHD2-15\t2\tX\t8\t13\tX.8.13\t[X.7.38.11]\tCVTYCSGGSCYFDYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtggcagttatatcatatgatggaagtaataaatactacgtagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagctgaggacacggctgtgtattactgtgttacatattgtagtggtggtagctgctactttgactactggggccagggaaccctggtcaccgtctcctcag\n+3\tlcl|FLN1FA001DLPHD.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag\n+4\tlcl|FLN1FA002QTWMQ.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+5\tlcl|FLN1FA002Q975Z.1|\tproductive\tIGHV3-53\t771\t99.36\t156/157 nt\t\t\tIGHJ4\t168\t83.33\t40/48 nt\tIGHD2-21\t3\tX\t7\t10\tX.7.10\t[X.7.38.11]\tCVVVTATPHGYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag\n+6\tlcl|FLN1FA001AX4MF.1|\tproductive\tIGHV4-39\t770\t100\t155/155 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t7\t15\tX.7.15\t[X.6.38.11]\tCVVNYYDSSGYYYIDYW\tin-frame\t+\t\t\t\t\t\tggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag\n+7\tlcl|FLN1FA0074PUDE.1|\tproductive\tIGHV4-39\t770\t100\t155/155 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t7\t15\tX.7.15\t[X.6.38.11]\tCVVNYYDSSGYYYIDYW\tin-frame\t+\t\t\t\t\t\tggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag\n+8\tlcl|FLN1FA0013V4SA.1|\tproductive\tIGHV1-3\t790\t100\t159/159 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD2-15\t2\tX\t8\t16\tX.8.16\t[X.7.38.11]\tCYLGYCSGGSCYPQVGYW\tin-frame\t+\t\t\t\t\t\taggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag\n+9\tlcl|FLN1FA00056KW6.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgtta'..b'tgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag\n+11\tlcl|FLN1FA008ANOPH.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+12\tlcl|FLN1FA005T7JJ8.1|\tproductive\tIGHV3-33\t795\t100\t160/160 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t8\t15\tX.8.15\t[X.7.38.11]\tCVTYYYDSSGYPYFDYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag\n+13\tlcl|FLN1FA0018WER7.1|\tproductive\tIGHV4-39\t770\t100\t155/155 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t7\t15\tX.7.15\t[X.6.38.11]\tCVVNYYDSSGYYYIDYW\tin-frame\t+\t\t\t\t\t\tggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag\n+14\tlcl|FLN1FA004BRKX9.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag\n+15\tlcl|FLN1FA00826HO1.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+16\tlcl|FLN1FA0041SQ1V.1|\tproductive\tIGHV3-53\t771\t99.36\t156/157 nt\t\t\tIGHJ4\t168\t83.33\t40/48 nt\tIGHD2-21\t3\tX\t7\t10\tX.7.10\t[X.7.38.11]\tCVVVTATPHGYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag\n+17\tlcl|FLN1FA000BBO91.1|\tproductive\tIGHV3-33\t795\t100\t160/160 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t8\t15\tX.8.15\t[X.7.38.11]\tCVTYYYDSSGYPYFDYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag\n+18\tlcl|FLN1FA008W37HH.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+19\tlcl|FLN1FA0080EWJB.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag\n+20\tlcl|FLN1FA003C09AP.1|\tproductive\tIGHV1-3\t790\t100\t159/159 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD2-15\t2\tX\t8\t16\tX.8.16\t[X.7.38.11]\tCYLGYCSGGSCYPQVGYW\tin-frame\t+\t\t\t\t\t\taggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag\n' |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def4_BCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def4_BCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,9 @@ + V-GENE J-GENE AA JUNCTION Reads Reads/Total Frequency % +1 IGHV1-3 IGHJ4 CYISGSYVGYW 4 4/20 20.0000 +2 IGHV4-39 IGHJ4 CYSAVVRGRFDYW 4 4/20 20.0000 +3 IGHV3-53 IGHJ4 CVVVTATPHGYW 3 3/20 15.0000 +4 IGHV4-39 IGHJ4 CVVNYYDSSGYYYIDYW 3 3/20 15.0000 +5 IGHV1-3 IGHJ4 CYLGYCSGGSCYPQVGYW 2 2/20 10.0000 +6 IGHV3-33 IGHJ4 CVTYYYDSSGYPYFDYW 2 2/20 10.0000 +7 IGHV1-69 or IGHV1-69D IGHJ4 CYLGYCSGGSCYPQVGYW 1 1/20 5.0000 +8 IGHV3-30 or IGHV3-30-3 IGHJ4 CVTYCSGGSCYFDYW 1 1/20 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def4_BCR_output2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def4_BCR_output2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,9 @@ + V-GENE J-GENE AA JUNCTION Frequency % +1 IGHV1-3 IGHJ4 CYISGSYVGYW 20.0000 +2 IGHV4-39 IGHJ4 CYSAVVRGRFDYW 20.0000 +3 IGHV3-53 IGHJ4 CVVVTATPHGYW 15.0000 +4 IGHV4-39 IGHJ4 CVVNYYDSSGYYYIDYW 15.0000 +5 IGHV1-3 IGHJ4 CYLGYCSGGSCYPQVGYW 10.0000 +6 IGHV3-33 IGHJ4 CVTYYYDSSGYPYFDYW 10.0000 +7 IGHV1-69 or IGHV1-69D IGHJ4 CYLGYCSGGSCYPQVGYW 5.0000 +8 IGHV3-30 or IGHV3-30-3 IGHJ4 CVTYCSGGSCYFDYW 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def4_BCR_output3.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def4_BCR_output3.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ + input % +Dominant Clonotype(V-J-CDR3) IGHV1-3,IGHJ4,CYISGSYVGYW +Frequency 20.0000 +Number of Clonotypes(V-J-CDR3) 8 +Expanding Clonotypes(V-J-CDR3) 6 75.0000 +Singletons 2 25.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def4_TCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def4_TCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| [ |
| b'@@ -0,0 +1,21 @@\n+\tSequence ID\tFunctionality\tV-GENE\tV-REGION score\tV-REGION identity %\tV-REGION identity nt\tV-REGION identity % (with ins/del events)\tV-REGION identity nt (with ins/del events)\tJ-GENE\tJ-REGION score\tJ-REGION identity %\tJ-REGION identity nt\tD-GENE\tD-REGION reading frame\tCDR1-IMGT length\tCDR2-IMGT length\tCDR3-IMGT length\tCDR-IMGT lengths\tFR-IMGT lengths\tAA JUNCTION\tJUNCTION frame\tOrientation\tFunctionality comment\tV-REGION potential ins/del\tJ-GENE and allele comment\tV-REGION insertions\tV-REGION deletions\tSequence\n+1\t@SRR060727.12120 SOLEXA7:7:2:351:1247 length=202\tproductive\tTRBV28\t145\t100\t30/30 nt\t\t\tTRBJ2-7\t235\t100\t47/47 nt\tTRBD1\t3\tX\tX\t12\tX.X.12\t[X.X.10.10]\tCAAGGQGNSYEQYF\tin-frame\t+\t\t\t\t\t\tagcaccaaccagacatctatgtacctctgtgccgctggggggcagggaaactcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagtttccctgccccccagcggcacag\n+2\t@SRR060727.14069 SOLEXA7:7:2:622:201 length=202\tproductive\tTRBV30\t95\t100\t20/20 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.6.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtgttctaacgggtgggnacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+3\t@SRR060727.45221 SOLEXA7:7:5:1541:638 length=202\tproductive\tTRBV30\t145\t100\t30/30 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.10.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tcttctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+4\t@SRR060727.49324 SOLEXA7:7:6:384:121 length=202\tproductive\tTRBV10-3\t165\t100\t34/34 nt\t\t\tTRBJ1-1\t240\t100\t48/48 nt\tTRBD1\t2\tX\tX\t11\tX.X.11\t[X.X.11.10]\tCAACEGLNTEAFF\tin-frame\t+\t\t\t\t\t\tcgctaccagctcccagacatctgtgtacttctgtgccgcatgtgaggggctgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcagcccctcacatgcggcacagaag\n+5\t@SRR060727.85642 SOLEXA7:7:10:98:1840 length=202\tproductive\tTRBV30\t115\t100\t24/24 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.8.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagcggacctgaacaagggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+6\t@SRR060727.100243 SOLEXA7:7:11:766:821 length=202\tproductive\tTRBV15\t105\t100\t22/22 nt\t\t\tTRBJ1-1\t222\t95.83\t46/48 nt\tTRBD1\t1\tX\tX\t11\tX.X.11\t[X.X.7.10]\tCAAGGKRYTEAFF\tin-frame\t-\t\t\t\t\t\tggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctggacaaggtacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacaggtacatggctgcgtcccccaggcctggtgagc\n+7\t@SRR060727.114177 SOLEXA7:7:12:1063:980 length=202\tproductive\tTRBV19\t150\t100\t31/31 nt\t\t\tTRBJ1-5\t241\t98\t49/50 nt\tTRBD1\t2\tX\tX\t13\tX.X.13\t[X.X.10.10]\tCAAGEGEVRNQPQHF\tin-frame\t+\t\t\t\t\t\tccaaaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggtgatgggactcgactctccatcctagtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgatttctaacctccccctcacccgcagca\n+8\t@SRR060727.130541 SOLEXA7:7:14:145:1124 length=202\tproductive\tTRBV3-1\t160\t100\t33/33 nt\t\t\tTRBJ1-5\t232\t96\t48/50 nt\tTRBD1\t2\tX\tX\t12\tX.X.12\t[X.X.11.10]\tCAAGQGFGNQPQHF\tin-frame\t+\t\t\t\t\t\tctggagcttggtgactctgctgtgtatttctgtgccgcaggtcagggttttgggaatcagccccagcattttggtgatgggactcgactctccatcctagataacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattcccaaaaccctgacctgcggcacag\n+9\t@SRR060727.175366 SOLEXA7:7:18:291:1226 length=202\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6\t95\t100\t20/20 nt\t\t\tTRBJ1-1\t231\t97.92\t47/48 nt\tTRBD1\t1\tX\tX\t13\tX.X.13\t[X.X.6.10]\tCAAGPRAGTNTEAFF\tin-frame\t+\t\t\t\t\t\tagacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaactaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcgtcc'..b'cccccctgtgcgtccgcggcacag\n+11\t@SRR060727.187683 SOLEXA7:7:19:809:1493 length=202\tproductive\tTRBV19\t135\t100\t28/28 nt\t\t\tTRBJ1-5\t232\t96\t48/50 nt\tTRBD1\t2\tX\tX\t13\tX.X.13\t[X.X.9.10]\tCAAGEGEVRNQPQHF\tin-frame\t+\t\t\t\t\t\taaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggagatgggactcgactctccatcctagaggtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatctccaaaatgctggggctgatttctaacctccccctcacccgcagca\n+12\t@SRR060727.190355 SOLEXA7:7:19:1314:185 length=202\tproductive\tTRBV27\t130\t100\t27/27 nt\t\t\tTRBJ1-5\t223\t94\t47/50 nt\tTRBD1\t3\tX\tX\t9\tX.X.9\t[X.X.9.10]\tCAAGPNQPQHF\tin-frame\t+\t\t\t\t\t\tcccaaccagacctctctgtacttctgtgccgccgggcccaatcagccccagcattttggtgatgggactcgactctccatcctagaggacctgaacaaggttaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattgggcccggcggcacagaagtacaga\n+13\t@SRR060727.196094 SOLEXA7:7:20:579:567 length=202\tproductive\tTRBV12-3 or TRBV12-4\t120\t100\t25/25 nt\t\t\tTRBJ2-5\t195\t89.58\t43/48 nt\tTRBD1\t1\tX\tX\t9\tX.X.9\t[X.X.8.10]\tCAAGTIETQYF\tin-frame\t+\t\t\t\t\t\tcagggactcagctgtgtacttctgtgccgcggggacaattgagacccagtacttcgggccaggcacgcggctcctggtgctcgaggacatgaaaaaagtgttaacgggtgggaacacgtttttcaggtcctcgagcaccaggagccgcgtgcctggcccgaagtactgggtctcaattgtccccgcggcacagaagtacaca\n+14\t@SRR060727.208531_SOLEXA7:7:21:1082:1793_length=20\tproductive\tTRBV25-1\t120\t100\t25/25 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t2\tX\tX\t10\tX.X.10\t[X.X.8.10]\tCAAGGGAPEAFF\tin-frame\t+\t\t\t\t\t\tctcacatacctctcagtacctctgtgcagcgggtggaggggccccagaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttctggggcccctccacccgctgcacagagggaa\n+15\t@SRR060727.236848 SOLEXA7:7:24:1329:676 length=202\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6\t120\t100\t25/25 nt\t\t\tTRBJ2-7\t235\t100\t47/47 nt\tTRBD1\t1\tX\tX\t11\tX.X.11\t[X.X.8.10]\tCAAGTGLSYEQYF\tin-frame\t+\t\t\t\t\t\tctcccagacatctgtgtacttctgtgccgcggggacaggactctcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggacctgaaaataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagagtcctgtccccgcggcacagaag\n+16\t@SRR060727.258473 SOLEXA7:7:27:271:1727 length=202\tproductive\tTRBV30\t100\t100\t21/21 nt\t\t\tTRBJ1-4\t201\t88.24\t45/51 nt\tTRBD1\t2\tX\tX\t10\tX.X.10\t[X.X.7.10]\tCAAGQVGEKLFF\tin-frame\t+\t\t\t\t\t\tgactctggcttctatctctgtgccgcgggacaagtgggtgaaaaactgttttttggcagtggaacccagctctctgtcttggaggacctgaacaacgaggttaacgggtgggaacaccttgttcaggtcctccaagacagagagctgggttccactgccaaaaaacagtttttcacccacttgtcccgcggcacagagatag\n+17\t@SRR060727.274111 SOLEXA7:7:28:1699:290 length=202\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6\t100\t100\t21/21 nt\t\t\tTRBJ1-1\t222\t95.83\t46/48 nt\tTRBD1\t1\tX\tX\t13\tX.X.13\t[X.X.7.10]\tCAAGPRAGTNTEAFF\tin-frame\t+\t\t\t\t\t\tcagacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttgtacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtacaaagaaagcttcagtgttcgtccctgcccttggtccagcggca\n+18\t@SRR060727.275014 SOLEXA7:7:29:152:1739 length=202\tproductive\tTRBV30\t130\t100\t27/27 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.9.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+19\t@SRR060727.281458_SOLEXA7:7:29:1133:1441_length=20\tproductive\tTRBV15\t141\t96.77\t30/31 nt\t\t\tTRBJ1-1\t222\t95.83\t46/48 nt\tTRBD1\t1\tX\tX\t11\tX.X.11\t[X.X.10.10]\tCAAGGKRYTEAFF\tin-frame\t+\t\t\t\t\t\tatgcctgggggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacagg\n+20\t@SRR060727.283135_SOLEXA7:7:29:1539:1405_length=20\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6\t100\t100\t21/21 nt\t\t\tTRBJ2-3\t200\t89.8\t44/49 nt\tTRBD2\t1\tX\tX\t8\tX.X.8\t[X.X.7.10]\tCAAGEDTQYF\tin-frame\t+\t\t\t\t\t\tcagacatctgtgtacttctgtgccgccggggaggatacgcagtattttggcccaggcacccggctgacagtgctcgaggacctgaaaaacgtgttcccacctaacgggtgggaacacgtttttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatcctccccggcggcacagaagtacacagat\n' |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def4_TCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def4_TCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,15 @@ + V-GENE J-GENE AA JUNCTION Reads Reads/Total Frequency % +1 TRBV30 TRBJ1-1 CAAEGILAEAFF 4 4/20 20.0000 +2 TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6 TRBJ1-1 CAAGPRAGTNTEAFF 2 2/20 10.0000 +3 TRBV15 TRBJ1-1 CAAGGKRYTEAFF 2 2/20 10.0000 +4 TRBV19 TRBJ1-5 CAAGEGEVRNQPQHF 2 2/20 10.0000 +5 TRBV10-3 TRBJ1-1 CAACEGLNTEAFF 1 1/20 5.0000 +6 TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6 TRBJ2-3 CAAGEDTQYF 1 1/20 5.0000 +7 TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6 TRBJ2-7 CAAGTGLSYEQYF 1 1/20 5.0000 +8 TRBV12-3 or TRBV12-4 TRBJ2-5 CAAGTIETQYF 1 1/20 5.0000 +9 TRBV25-1 TRBJ1-1 CAAGGGAPEAFF 1 1/20 5.0000 +10 TRBV27 TRBJ1-5 CAAGPNQPQHF 1 1/20 5.0000 +11 TRBV28 TRBJ2-7 CAAGGQGNSYEQYF 1 1/20 5.0000 +12 TRBV3-1 TRBJ1-5 CAAGQGFGNQPQHF 1 1/20 5.0000 +13 TRBV30 TRBJ1-4 CAAGQVGEKLFF 1 1/20 5.0000 +14 TRBV6-1 or TRBV6-5 or TRBV6-6 TRBJ1-1 CAADAQGGNTEAFF 1 1/20 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def4_TCR_output2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def4_TCR_output2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ + V-GENE J-GENE AA JUNCTION Frequency % +1 TRBV30 TRBJ1-1 CAAEGILAEAFF 20.0000 +2 TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6 TRBJ1-1 CAAGPRAGTNTEAFF 10.0000 +3 TRBV15 TRBJ1-1 CAAGGKRYTEAFF 10.0000 +4 TRBV19 TRBJ1-5 CAAGEGEVRNQPQHF 10.0000 +5 TRBV10-3 TRBJ1-1 CAACEGLNTEAFF 5.0000 +6 TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6 TRBJ2-3 CAAGEDTQYF 5.0000 +7 TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6 TRBJ2-7 CAAGTGLSYEQYF 5.0000 +8 TRBV12-3 or TRBV12-4 TRBJ2-5 CAAGTIETQYF 5.0000 +9 TRBV25-1 TRBJ1-1 CAAGGGAPEAFF 5.0000 +10 TRBV27 TRBJ1-5 CAAGPNQPQHF 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def4_TCR_output3.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def4_TCR_output3.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ + input1.csv % +Dominant Clonotype(V-J-CDR3) TRBV30,TRBJ1-1,CAAEGILAEAFF +Frequency 20.0000 +Number of Clonotypes(V-J-CDR3) 14 +Expanding Clonotypes(V-J-CDR3) 4 28.5714 +Singletons 10 71.4286 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def5_BCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def5_BCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| [ |
| b'@@ -0,0 +1,21 @@\n+\tSequence ID\tFunctionality\tV-GENE\tV-REGION score\tV-REGION identity %\tV-REGION identity nt\tV-REGION identity % (with ins/del events)\tV-REGION identity nt (with ins/del events)\tJ-GENE\tJ-REGION score\tJ-REGION identity %\tJ-REGION identity nt\tD-GENE\tD-REGION reading frame\tCDR1-IMGT length\tCDR2-IMGT length\tCDR3-IMGT length\tCDR-IMGT lengths\tFR-IMGT lengths\tAA JUNCTION\tJUNCTION frame\tOrientation\tFunctionality comment\tV-REGION potential ins/del\tJ-GENE and allele comment\tV-REGION insertions\tV-REGION deletions\tSequence\n+1\tlcl|FLN1FA001B9SVM.1|\tproductive\tIGHV1-69 or IGHV1-69D\t790\t100\t159/159 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD2-15\t2\tX\t8\t16\tX.8.16\t[X.7.38.11]\tCYLGYCSGGSCYPQVGYW\tin-frame\t+\t\t\t\t\t\tgggcttgagtggatgggagggatcatccctatctttggtacagcaaactacgcacagaagttccagggcagagtcacgattaccgcggacgaatccacgagcacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag\n+2\tlcl|FLN1FA001CUVDF.1|\tproductive\tIGHV3-30 or IGHV3-30-3\t786\t99.38\t159/160 nt\t\t\tIGHJ4\t231\t97.92\t47/48 nt\tIGHD2-15\t2\tX\t8\t13\tX.8.13\t[X.7.38.11]\tCVTYCSGGSCYFDYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtggcagttatatcatatgatggaagtaataaatactacgtagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagctgaggacacggctgtgtattactgtgttacatattgtagtggtggtagctgctactttgactactggggccagggaaccctggtcaccgtctcctcag\n+3\tlcl|FLN1FA001DLPHD.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag\n+4\tlcl|FLN1FA002QTWMQ.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+5\tlcl|FLN1FA002Q975Z.1|\tproductive\tIGHV3-53\t771\t99.36\t156/157 nt\t\t\tIGHJ4\t168\t83.33\t40/48 nt\tIGHD2-21\t3\tX\t7\t10\tX.7.10\t[X.7.38.11]\tCVVVTATPHGYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag\n+6\tlcl|FLN1FA001AX4MF.1|\tproductive\tIGHV4-39\t770\t100\t155/155 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t7\t15\tX.7.15\t[X.6.38.11]\tCVVNYYDSSGYYYIDYW\tin-frame\t+\t\t\t\t\t\tggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag\n+7\tlcl|FLN1FA0074PUDE.1|\tproductive\tIGHV4-39\t770\t100\t155/155 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t7\t15\tX.7.15\t[X.6.38.11]\tCVVNYYDSSGYYYIDYW\tin-frame\t+\t\t\t\t\t\tggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag\n+8\tlcl|FLN1FA0013V4SA.1|\tproductive\tIGHV1-3\t790\t100\t159/159 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD2-15\t2\tX\t8\t16\tX.8.16\t[X.7.38.11]\tCYLGYCSGGSCYPQVGYW\tin-frame\t+\t\t\t\t\t\taggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag\n+9\tlcl|FLN1FA00056KW6.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgtta'..b'tgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag\n+11\tlcl|FLN1FA008ANOPH.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+12\tlcl|FLN1FA005T7JJ8.1|\tproductive\tIGHV3-33\t795\t100\t160/160 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t8\t15\tX.8.15\t[X.7.38.11]\tCVTYYYDSSGYPYFDYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag\n+13\tlcl|FLN1FA0018WER7.1|\tproductive\tIGHV4-39\t770\t100\t155/155 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t7\t15\tX.7.15\t[X.6.38.11]\tCVVNYYDSSGYYYIDYW\tin-frame\t+\t\t\t\t\t\tggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag\n+14\tlcl|FLN1FA004BRKX9.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag\n+15\tlcl|FLN1FA00826HO1.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+16\tlcl|FLN1FA0041SQ1V.1|\tproductive\tIGHV3-53\t771\t99.36\t156/157 nt\t\t\tIGHJ4\t168\t83.33\t40/48 nt\tIGHD2-21\t3\tX\t7\t10\tX.7.10\t[X.7.38.11]\tCVVVTATPHGYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag\n+17\tlcl|FLN1FA000BBO91.1|\tproductive\tIGHV3-33\t795\t100\t160/160 nt\t\t\tIGHJ4\t222\t95.83\t46/48 nt\tIGHD3-22\t2\tX\t8\t15\tX.8.15\t[X.7.38.11]\tCVTYYYDSSGYPYFDYW\tin-frame\t+\t\t\t\t\t\tggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag\n+18\tlcl|FLN1FA008W37HH.1|\tproductive\tIGHV4-39\t775\t100\t156/156 nt\t\t\tIGHJ4\t195\t89.58\t43/48 nt\tIGHD3-10\t3\tX\t7\t11\tX.7.11\t[X.7.38.11]\tCYSAVVRGRFDYW\tin-frame\t+\t\t\t\t\t\tgggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag\n+19\tlcl|FLN1FA0080EWJB.1|\tproductive\tIGHV1-3\t775\t100\t156/156 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD3-16\t2\tX\t8\t9\tX.8.9\t[X.6.38.11]\tCYISGSYVGYW\tin-frame\t+\t\t\t\t\t\tcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag\n+20\tlcl|FLN1FA003C09AP.1|\tproductive\tIGHV1-3\t790\t100\t159/159 nt\t\t\tIGHJ4\t186\t87.5\t42/48 nt\tIGHD2-15\t2\tX\t8\t16\tX.8.16\t[X.7.38.11]\tCYLGYCSGGSCYPQVGYW\tin-frame\t+\t\t\t\t\t\taggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag\n' |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def5_BCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def5_BCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,9 @@ + V-GENE D-GENE J-GENE AA JUNCTION Reads Reads/Total Frequency % +1 IGHV1-3 IGHD3-16 IGHJ4 CYISGSYVGYW 4 4/20 20.0000 +2 IGHV4-39 IGHD3-10 IGHJ4 CYSAVVRGRFDYW 4 4/20 20.0000 +3 IGHV3-53 IGHD2-21 IGHJ4 CVVVTATPHGYW 3 3/20 15.0000 +4 IGHV4-39 IGHD3-22 IGHJ4 CVVNYYDSSGYYYIDYW 3 3/20 15.0000 +5 IGHV1-3 IGHD2-15 IGHJ4 CYLGYCSGGSCYPQVGYW 2 2/20 10.0000 +6 IGHV3-33 IGHD3-22 IGHJ4 CVTYYYDSSGYPYFDYW 2 2/20 10.0000 +7 IGHV1-69 or IGHV1-69D IGHD2-15 IGHJ4 CYLGYCSGGSCYPQVGYW 1 1/20 5.0000 +8 IGHV3-30 or IGHV3-30-3 IGHD2-15 IGHJ4 CVTYCSGGSCYFDYW 1 1/20 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def5_BCR_output2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def5_BCR_output2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,9 @@ + V-GENE D-GENE J-GENE AA JUNCTION Frequency % +1 IGHV1-3 IGHD3-16 IGHJ4 CYISGSYVGYW 20.0000 +2 IGHV4-39 IGHD3-10 IGHJ4 CYSAVVRGRFDYW 20.0000 +3 IGHV3-53 IGHD2-21 IGHJ4 CVVVTATPHGYW 15.0000 +4 IGHV4-39 IGHD3-22 IGHJ4 CVVNYYDSSGYYYIDYW 15.0000 +5 IGHV1-3 IGHD2-15 IGHJ4 CYLGYCSGGSCYPQVGYW 10.0000 +6 IGHV3-33 IGHD3-22 IGHJ4 CVTYYYDSSGYPYFDYW 10.0000 +7 IGHV1-69 or IGHV1-69D IGHD2-15 IGHJ4 CYLGYCSGGSCYPQVGYW 5.0000 +8 IGHV3-30 or IGHV3-30-3 IGHD2-15 IGHJ4 CVTYCSGGSCYFDYW 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def5_BCR_output3.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def5_BCR_output3.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ + input % +Dominant Clonotype(V-D-J-CDR3) IGHV1-3,IGHD3-16,IGHJ4,CYISGSYVGYW +Frequency 20.0000 +Number of Clonotypes(V-D-J-CDR3) 8 +Expanding Clonotypes(V-D-J-CDR3) 6 75.0000 +Singletons 2 25.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def5_TCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def5_TCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| [ |
| b'@@ -0,0 +1,21 @@\n+\tSequence ID\tFunctionality\tV-GENE\tV-REGION score\tV-REGION identity %\tV-REGION identity nt\tV-REGION identity % (with ins/del events)\tV-REGION identity nt (with ins/del events)\tJ-GENE\tJ-REGION score\tJ-REGION identity %\tJ-REGION identity nt\tD-GENE\tD-REGION reading frame\tCDR1-IMGT length\tCDR2-IMGT length\tCDR3-IMGT length\tCDR-IMGT lengths\tFR-IMGT lengths\tAA JUNCTION\tJUNCTION frame\tOrientation\tFunctionality comment\tV-REGION potential ins/del\tJ-GENE and allele comment\tV-REGION insertions\tV-REGION deletions\tSequence\n+1\t@SRR060727.12120 SOLEXA7:7:2:351:1247 length=202\tproductive\tTRBV28\t145\t100\t30/30 nt\t\t\tTRBJ2-7\t235\t100\t47/47 nt\tTRBD1\t3\tX\tX\t12\tX.X.12\t[X.X.10.10]\tCAAGGQGNSYEQYF\tin-frame\t+\t\t\t\t\t\tagcaccaaccagacatctatgtacctctgtgccgctggggggcagggaaactcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagtttccctgccccccagcggcacag\n+2\t@SRR060727.14069 SOLEXA7:7:2:622:201 length=202\tproductive\tTRBV30\t95\t100\t20/20 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.6.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtgttctaacgggtgggnacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+3\t@SRR060727.45221 SOLEXA7:7:5:1541:638 length=202\tproductive\tTRBV30\t145\t100\t30/30 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.10.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tcttctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+4\t@SRR060727.49324 SOLEXA7:7:6:384:121 length=202\tproductive\tTRBV10-3\t165\t100\t34/34 nt\t\t\tTRBJ1-1\t240\t100\t48/48 nt\tTRBD1\t2\tX\tX\t11\tX.X.11\t[X.X.11.10]\tCAACEGLNTEAFF\tin-frame\t+\t\t\t\t\t\tcgctaccagctcccagacatctgtgtacttctgtgccgcatgtgaggggctgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcagcccctcacatgcggcacagaag\n+5\t@SRR060727.85642 SOLEXA7:7:10:98:1840 length=202\tproductive\tTRBV30\t115\t100\t24/24 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.8.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagcggacctgaacaagggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+6\t@SRR060727.100243 SOLEXA7:7:11:766:821 length=202\tproductive\tTRBV15\t105\t100\t22/22 nt\t\t\tTRBJ1-1\t222\t95.83\t46/48 nt\tTRBD1\t1\tX\tX\t11\tX.X.11\t[X.X.7.10]\tCAAGGKRYTEAFF\tin-frame\t-\t\t\t\t\t\tggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctggacaaggtacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacaggtacatggctgcgtcccccaggcctggtgagc\n+7\t@SRR060727.114177 SOLEXA7:7:12:1063:980 length=202\tproductive\tTRBV19\t150\t100\t31/31 nt\t\t\tTRBJ1-5\t241\t98\t49/50 nt\tTRBD1\t2\tX\tX\t13\tX.X.13\t[X.X.10.10]\tCAAGEGEVRNQPQHF\tin-frame\t+\t\t\t\t\t\tccaaaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggtgatgggactcgactctccatcctagtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgatttctaacctccccctcacccgcagca\n+8\t@SRR060727.130541 SOLEXA7:7:14:145:1124 length=202\tproductive\tTRBV3-1\t160\t100\t33/33 nt\t\t\tTRBJ1-5\t232\t96\t48/50 nt\tTRBD1\t2\tX\tX\t12\tX.X.12\t[X.X.11.10]\tCAAGQGFGNQPQHF\tin-frame\t+\t\t\t\t\t\tctggagcttggtgactctgctgtgtatttctgtgccgcaggtcagggttttgggaatcagccccagcattttggtgatgggactcgactctccatcctagataacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattcccaaaaccctgacctgcggcacag\n+9\t@SRR060727.175366 SOLEXA7:7:18:291:1226 length=202\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6\t95\t100\t20/20 nt\t\t\tTRBJ1-1\t231\t97.92\t47/48 nt\tTRBD1\t1\tX\tX\t13\tX.X.13\t[X.X.6.10]\tCAAGPRAGTNTEAFF\tin-frame\t+\t\t\t\t\t\tagacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaactaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcgtcc'..b'cccccctgtgcgtccgcggcacag\n+11\t@SRR060727.187683 SOLEXA7:7:19:809:1493 length=202\tproductive\tTRBV19\t135\t100\t28/28 nt\t\t\tTRBJ1-5\t232\t96\t48/50 nt\tTRBD1\t2\tX\tX\t13\tX.X.13\t[X.X.9.10]\tCAAGEGEVRNQPQHF\tin-frame\t+\t\t\t\t\t\taaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggagatgggactcgactctccatcctagaggtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatctccaaaatgctggggctgatttctaacctccccctcacccgcagca\n+12\t@SRR060727.190355 SOLEXA7:7:19:1314:185 length=202\tproductive\tTRBV27\t130\t100\t27/27 nt\t\t\tTRBJ1-5\t223\t94\t47/50 nt\tTRBD1\t3\tX\tX\t9\tX.X.9\t[X.X.9.10]\tCAAGPNQPQHF\tin-frame\t+\t\t\t\t\t\tcccaaccagacctctctgtacttctgtgccgccgggcccaatcagccccagcattttggtgatgggactcgactctccatcctagaggacctgaacaaggttaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattgggcccggcggcacagaagtacaga\n+13\t@SRR060727.196094 SOLEXA7:7:20:579:567 length=202\tproductive\tTRBV12-3 or TRBV12-4\t120\t100\t25/25 nt\t\t\tTRBJ2-5\t195\t89.58\t43/48 nt\tTRBD1\t1\tX\tX\t9\tX.X.9\t[X.X.8.10]\tCAAGTIETQYF\tin-frame\t+\t\t\t\t\t\tcagggactcagctgtgtacttctgtgccgcggggacaattgagacccagtacttcgggccaggcacgcggctcctggtgctcgaggacatgaaaaaagtgttaacgggtgggaacacgtttttcaggtcctcgagcaccaggagccgcgtgcctggcccgaagtactgggtctcaattgtccccgcggcacagaagtacaca\n+14\t@SRR060727.208531_SOLEXA7:7:21:1082:1793_length=20\tproductive\tTRBV25-1\t120\t100\t25/25 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t2\tX\tX\t10\tX.X.10\t[X.X.8.10]\tCAAGGGAPEAFF\tin-frame\t+\t\t\t\t\t\tctcacatacctctcagtacctctgtgcagcgggtggaggggccccagaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttctggggcccctccacccgctgcacagagggaa\n+15\t@SRR060727.236848 SOLEXA7:7:24:1329:676 length=202\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6\t120\t100\t25/25 nt\t\t\tTRBJ2-7\t235\t100\t47/47 nt\tTRBD1\t1\tX\tX\t11\tX.X.11\t[X.X.8.10]\tCAAGTGLSYEQYF\tin-frame\t+\t\t\t\t\t\tctcccagacatctgtgtacttctgtgccgcggggacaggactctcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggacctgaaaataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagagtcctgtccccgcggcacagaag\n+16\t@SRR060727.258473 SOLEXA7:7:27:271:1727 length=202\tproductive\tTRBV30\t100\t100\t21/21 nt\t\t\tTRBJ1-4\t201\t88.24\t45/51 nt\tTRBD1\t2\tX\tX\t10\tX.X.10\t[X.X.7.10]\tCAAGQVGEKLFF\tin-frame\t+\t\t\t\t\t\tgactctggcttctatctctgtgccgcgggacaagtgggtgaaaaactgttttttggcagtggaacccagctctctgtcttggaggacctgaacaacgaggttaacgggtgggaacaccttgttcaggtcctccaagacagagagctgggttccactgccaaaaaacagtttttcacccacttgtcccgcggcacagagatag\n+17\t@SRR060727.274111 SOLEXA7:7:28:1699:290 length=202\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6\t100\t100\t21/21 nt\t\t\tTRBJ1-1\t222\t95.83\t46/48 nt\tTRBD1\t1\tX\tX\t13\tX.X.13\t[X.X.7.10]\tCAAGPRAGTNTEAFF\tin-frame\t+\t\t\t\t\t\tcagacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttgtacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtacaaagaaagcttcagtgttcgtccctgcccttggtccagcggca\n+18\t@SRR060727.275014 SOLEXA7:7:29:152:1739 length=202\tproductive\tTRBV30\t130\t100\t27/27 nt\t\t\tTRBJ1-1\t195\t89.58\t43/48 nt\tTRBD2\t3\tX\tX\t10\tX.X.10\t[X.X.9.10]\tCAAEGILAEAFF\tin-frame\t+\t\t\t\t\t\tctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag\n+19\t@SRR060727.281458_SOLEXA7:7:29:1133:1441_length=20\tproductive\tTRBV15\t141\t96.77\t30/31 nt\t\t\tTRBJ1-1\t222\t95.83\t46/48 nt\tTRBD1\t1\tX\tX\t11\tX.X.11\t[X.X.10.10]\tCAAGGKRYTEAFF\tin-frame\t+\t\t\t\t\t\tatgcctgggggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacagg\n+20\t@SRR060727.283135_SOLEXA7:7:29:1539:1405_length=20\tproductive\tTRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6\t100\t100\t21/21 nt\t\t\tTRBJ2-3\t200\t89.8\t44/49 nt\tTRBD2\t1\tX\tX\t8\tX.X.8\t[X.X.7.10]\tCAAGEDTQYF\tin-frame\t+\t\t\t\t\t\tcagacatctgtgtacttctgtgccgccggggaggatacgcagtattttggcccaggcacccggctgacagtgctcgaggacctgaaaaacgtgttcccacctaacgggtgggaacacgtttttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatcctccccggcggcacagaagtacacagat\n' |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def5_TCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def5_TCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,15 @@ + V-GENE D-GENE J-GENE AA JUNCTION Reads Reads/Total Frequency % +1 TRBV30 TRBD2 TRBJ1-1 CAAEGILAEAFF 4 4/20 20.0000 +2 TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6 TRBD1 TRBJ1-1 CAAGPRAGTNTEAFF 2 2/20 10.0000 +3 TRBV15 TRBD1 TRBJ1-1 CAAGGKRYTEAFF 2 2/20 10.0000 +4 TRBV19 TRBD1 TRBJ1-5 CAAGEGEVRNQPQHF 2 2/20 10.0000 +5 TRBV10-3 TRBD1 TRBJ1-1 CAACEGLNTEAFF 1 1/20 5.0000 +6 TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6 TRBD2 TRBJ2-3 CAAGEDTQYF 1 1/20 5.0000 +7 TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6 TRBD1 TRBJ2-7 CAAGTGLSYEQYF 1 1/20 5.0000 +8 TRBV12-3 or TRBV12-4 TRBD1 TRBJ2-5 CAAGTIETQYF 1 1/20 5.0000 +9 TRBV25-1 TRBD2 TRBJ1-1 CAAGGGAPEAFF 1 1/20 5.0000 +10 TRBV27 TRBD1 TRBJ1-5 CAAGPNQPQHF 1 1/20 5.0000 +11 TRBV28 TRBD1 TRBJ2-7 CAAGGQGNSYEQYF 1 1/20 5.0000 +12 TRBV3-1 TRBD1 TRBJ1-5 CAAGQGFGNQPQHF 1 1/20 5.0000 +13 TRBV30 TRBD1 TRBJ1-4 CAAGQVGEKLFF 1 1/20 5.0000 +14 TRBV6-1 or TRBV6-5 or TRBV6-6 TRBD1 TRBJ1-1 CAADAQGGNTEAFF 1 1/20 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def5_TCR_output2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def5_TCR_output2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ + V-GENE D-GENE J-GENE AA JUNCTION Frequency % +1 TRBV30 TRBD2 TRBJ1-1 CAAEGILAEAFF 20.0000 +2 TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6 TRBD1 TRBJ1-1 CAAGPRAGTNTEAFF 10.0000 +3 TRBV15 TRBD1 TRBJ1-1 CAAGGKRYTEAFF 10.0000 +4 TRBV19 TRBD1 TRBJ1-5 CAAGEGEVRNQPQHF 10.0000 +5 TRBV10-3 TRBD1 TRBJ1-1 CAACEGLNTEAFF 5.0000 +6 TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6 TRBD2 TRBJ2-3 CAAGEDTQYF 5.0000 +7 TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6 TRBD1 TRBJ2-7 CAAGTGLSYEQYF 5.0000 +8 TRBV12-3 or TRBV12-4 TRBD1 TRBJ2-5 CAAGTIETQYF 5.0000 +9 TRBV25-1 TRBD2 TRBJ1-1 CAAGGGAPEAFF 5.0000 +10 TRBV27 TRBD1 TRBJ1-5 CAAGPNQPQHF 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/clono_compute_def5_TCR_output3.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clono_compute_def5_TCR_output3.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ + input1.csv % +Dominant Clonotype(V-D-J-CDR3) TRBV30,TRBD2,TRBJ1-1,CAAEGILAEAFF +Frequency 20.0000 +Number of Clonotypes(V-D-J-CDR3) 14 +Expanding Clonotypes(V-D-J-CDR3) 4 28.5714 +Singletons 10 71.4286 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/data_filter_BCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data_filter_BCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| [ |
| @@ -0,0 +1,11 @@ +Sequence number Sequence ID Functionality V-GENE and allele V-REGION score V-REGION identity % V-REGION identity nt V-REGION identity % (with ins/del events) V-REGION identity nt (with ins/del events) J-GENE and allele J-REGION score J-REGION identity % J-REGION identity nt D-GENE and allele D-REGION reading frame CDR1-IMGT length CDR2-IMGT length CDR3-IMGT length CDR-IMGT lengths FR-IMGT lengths AA JUNCTION JUNCTION frame Orientation Functionality comment V-REGION potential ins/del J-GENE and allele comment V-REGION insertions V-REGION deletions Sequence Unnamed: 29 +1 lcl|FLN1FA002RWEZA.1| productive Homsap IGHV3-48*01 F 740 96.84 153/158 nt Homsap IGHJ4*02 F 177 85.42 41/48 nt Homsap IGHD3-22*01 F 2 X 8 17 X.8.17 [X.6.38.11] CARAIPRYYYDTSGPNDYW in-frame + ggctggagtgggtttcatacattagtagtaatagtggtgccatatactacgcagactctgtgaagggccgattcaccatctccagaaacaatgccaaggactcactgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgcgagagcgatcccccggtattactatgatactagtggcccaaacgactactggggccagggaaccctggtcaccgtctcctcag +2 lcl|FLN1FA001BLION.1| unproductive Homsap IGHV1-3*01 F 790 100 159/159 nt Homsap IGHJ3*02 F 160 80 40/50 nt Homsap IGHD6-13*01 F 2 X 8 X X.8.X [X.7.38.11] CARVGSSWSDAFD#IW out-of-frame + aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgtgcgagagtgggcagcagctggtctgatgcttttgattatctggggccaagggacaatggtcaccgtctcctcag +3 lcl|FLN1FA002SGU3N.1| unproductive Homsap IGHV3-9*01 F, or Homsap IGHV3-9*02 F 777 98.75 158/160 nt Homsap IGHJ4*02 F 177 85.42 41/48 nt Homsap IGHD3-16*02 F 3 X 8 X X.8.X [X.7.38.11] CAKDKIGYYDYVWGSYRLG#YW out-of-frame + gggcctggagtgggtctcaggtattagttggaatagtggtagaataggctatgcggactctgtgaacggccgattcaccatctccagagacaacgccaagaactccctgtatctgcaaatgaacagtctgagagctgaggacacggccttgtattactgtgcaaaagataaaattgggtattatgattacgtttgggggagttatcgtttgggtctactggggccagggaaccctggtcaccgtctcctcag +4 lcl|FLN1FA001D9GHY.1| productive Homsap IGHV3-33*01 F, or Homsap IGHV3-33*06 F 785 100 158/158 nt Homsap IGHJ4*02 F 213 93.75 45/48 nt Homsap IGHD3-22*01 F 2 X 8 18 X.8.18 [X.6.38.11] CAREMYYYDSSGYYYAFDYW in-frame + ggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgcgagagagatgtattactatgatagtagtggttattactacgcatttgactactggggccagggaaccctggtcaccgtctcctcag +5 lcl|FLN1FA001A1B0O.1| productive Homsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F 776 99.37 157/158 nt Homsap IGHJ4*02 F 168 83.33 40/48 nt Homsap IGHD5-12*01 F 3 X 8 13 X.8.13 [X.6.38.11] CARDMKGYDWSWVYW in-frame + ggctggagtgggtctcagctattagtggtagtggtggtagcacatactacgcagactccgtgaagggccggttcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgcgagagatatgaagggctacgattggagttgggtctactggggccagggaaccctggtcaccgtctcctcag +6 lcl|FLN1FA001DNXA5.1| productive Homsap IGHV4-39*03 F, or Homsap IGHV4-39*07 F 752 98.7 152/154 nt Homsap IGHJ5*02 F 237 96.08 49/51 nt Homsap IGHD3-10*01 F 2 X 7 25 X.7.25 [X.6.38.11] CARDRPAAMKGYYGSGSYLMGNWFDPW in-frame + ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgctgcggacacggccgtgtattactgtgcgagagataggccagctgctatgaagggctactatggttcggggagttacctaatggggaactggttcgacccctggggccagggaaccctggtcaccgtctcctcag +7 lcl|FLN1FA002TLD0B.1| productive Homsap IGHV7-4-1*02 F 790 100 159/159 nt Homsap IGHJ4*02 F 204 91.67 44/48 nt Homsap IGHD3-10*01 F 2 X 8 26 X.8.26 [X.7.38.11] CARGSRWLEVNYYGSGSYSSEKGPFDYW in-frame + gggcttgagtggatgggatggatcaacaccaacactgggaacccaacgtatgcccagggcttcacaggacggtttgtcttctccttggacacctctgtcagcacggcatatctgcagatcagcagcctaaaggctgaggacactgccgtgtattactgtgcgagagggagtaggtggttggaggtaaattactatggttcggggagttatagctcagaaaaaggtccctttgactactggggccagggaaccctggtcaccgtctcctcag +8 lcl|FLN1FA001DMRRX.1| productive Homsap IGHV4-59*08 F 761 99.35 154/155 nt Homsap IGHJ4*02 F 168 83.33 40/48 nt Homsap IGHD5-18*01 F 2 X 7 9 X.7.9 [X.6.38.11] CARALWFGEFW in-frame + gactggagtggattgggtatatctattacagtgggagcaccaactacaacccctccctcaagagtcgagtcaccatatcagtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgcgagagcgctatggttcggggagttctggggccagggaaccctggtcaccgtctcctcag +9 lcl|FLN1FA001DN3RX.1| unproductive (see comment) Homsap IGHV3-72*01 F 825 100 166/166 nt Homsap IGHJ4*02 F 213 93.75 45/48 nt Homsap IGHD3-9*01 F 3 X 10 X X.10.X [X.7.38.11] CARDRLGRSRVYDILTFYL##DYW out-of-frame + stop codons ggggctggagtgggttggccgtactagaaacaaagctaacagttacaccacagaatacgccgcgtctgtgaaaggcagattcaccatctcaagagatgattcaaagaactcactgtatctgcaaatgaacagcctgaaaaccgaggacacggccgtgtattactgtgctagagatcgtttgggtcgttcccgtgtttacgatattttgaccttctacctaaattgactactggggccagggaaccctggtcaccgtctcctcag +10 lcl|FLN1FA001AOHI5.1| productive Homsap IGHV4-31*02 F, or Homsap IGHV4-31*03 F or Homsap IGHV4-31*04 F or Homsap IGHV4-31*06 F or Homsap IGHV4-31*07 F or Homsap IGHV4-59*06 F 667 92.31 144/156 nt Homsap IGHJ4*02 F 195 89.58 43/48 nt Homsap IGHD3-3*01 F 2 X 7 14 X.7.14 [X.7.38.11] CARTSGYRLAPHSDYW in-frame + ggcctggagtggattggatacatccattacagggggaacacctactccaatccgtccctcaagagtcgtgttaccatttcagtagacacgtctaagaaccaggtctccctgaagctgagctctgtgacggccgcggacacggccgtctatttctgtgcgagaacgagtggttatagattagcgccccattcggactactggggccagggaaccctggtcaccgtctcctcag |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/data_filter_BCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data_filter_BCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| [ |
| @@ -0,0 +1,8 @@ + Sequence ID Functionality V-GENE V-REGION score V-REGION identity % V-REGION identity nt V-REGION identity % (with ins/del events) V-REGION identity nt (with ins/del events) J-GENE J-REGION score J-REGION identity % J-REGION identity nt D-GENE D-REGION reading frame CDR1-IMGT length CDR2-IMGT length CDR3-IMGT length CDR-IMGT lengths FR-IMGT lengths AA JUNCTION JUNCTION frame Orientation Functionality comment V-REGION potential ins/del J-GENE and allele comment V-REGION insertions V-REGION deletions Sequence +1 lcl|FLN1FA002RWEZA.1| productive IGHV3-48 740 96.84 153/158 nt IGHJ4 177 85.42 41/48 nt IGHD3-22 2 X 8 17 X.8.17 [X.6.38.11] CARAIPRYYYDTSGPNDYW in-frame + ggctggagtgggtttcatacattagtagtaatagtggtgccatatactacgcagactctgtgaagggccgattcaccatctccagaaacaatgccaaggactcactgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgcgagagcgatcccccggtattactatgatactagtggcccaaacgactactggggccagggaaccctggtcaccgtctcctcag +2 lcl|FLN1FA001D9GHY.1| productive IGHV3-33 785 100.0 158/158 nt IGHJ4 213 93.75 45/48 nt IGHD3-22 2 X 8 18 X.8.18 [X.6.38.11] CAREMYYYDSSGYYYAFDYW in-frame + ggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgcgagagagatgtattactatgatagtagtggttattactacgcatttgactactggggccagggaaccctggtcaccgtctcctcag +3 lcl|FLN1FA001A1B0O.1| productive IGHV3-23 or IGHV3-23D 776 99.37 157/158 nt IGHJ4 168 83.33 40/48 nt IGHD5-12 3 X 8 13 X.8.13 [X.6.38.11] CARDMKGYDWSWVYW in-frame + ggctggagtgggtctcagctattagtggtagtggtggtagcacatactacgcagactccgtgaagggccggttcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgcgagagatatgaagggctacgattggagttgggtctactggggccagggaaccctggtcaccgtctcctcag +4 lcl|FLN1FA001DNXA5.1| productive IGHV4-39 752 98.7 152/154 nt IGHJ5 237 96.08 49/51 nt IGHD3-10 2 X 7 25 X.7.25 [X.6.38.11] CARDRPAAMKGYYGSGSYLMGNWFDPW in-frame + ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgctgcggacacggccgtgtattactgtgcgagagataggccagctgctatgaagggctactatggttcggggagttacctaatggggaactggttcgacccctggggccagggaaccctggtcaccgtctcctcag +5 lcl|FLN1FA002TLD0B.1| productive IGHV7-4-1 790 100.0 159/159 nt IGHJ4 204 91.67 44/48 nt IGHD3-10 2 X 8 26 X.8.26 [X.7.38.11] CARGSRWLEVNYYGSGSYSSEKGPFDYW in-frame + gggcttgagtggatgggatggatcaacaccaacactgggaacccaacgtatgcccagggcttcacaggacggtttgtcttctccttggacacctctgtcagcacggcatatctgcagatcagcagcctaaaggctgaggacactgccgtgtattactgtgcgagagggagtaggtggttggaggtaaattactatggttcggggagttatagctcagaaaaaggtccctttgactactggggccagggaaccctggtcaccgtctcctcag +6 lcl|FLN1FA001DMRRX.1| productive IGHV4-59 761 99.35 154/155 nt IGHJ4 168 83.33 40/48 nt IGHD5-18 2 X 7 9 X.7.9 [X.6.38.11] CARALWFGEFW in-frame + gactggagtggattgggtatatctattacagtgggagcaccaactacaacccctccctcaagagtcgagtcaccatatcagtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgcgagagcgctatggttcggggagttctggggccagggaaccctggtcaccgtctcctcag +7 lcl|FLN1FA001AOHI5.1| productive IGHV4-31 or IGHV4-59 667 92.31 144/156 nt IGHJ4 195 89.58 43/48 nt IGHD3-3 2 X 7 14 X.7.14 [X.7.38.11] CARTSGYRLAPHSDYW in-frame + ggcctggagtggattggatacatccattacagggggaacacctactccaatccgtccctcaagagtcgtgttaccatttcagtagacacgtctaagaaccaggtctccctgaagctgagctctgtgacggccgcggacacggccgtctatttctgtgcgagaacgagtggttatagattagcgccccattcggactactggggccagggaaccctggtcaccgtctcctcag |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/data_filter_BCR_output2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data_filter_BCR_output2.csv Mon Apr 30 04:47:52 2018 -0400 |
| [ |
| @@ -0,0 +1,4 @@ + Sequence ID Functionality V-GENE and allele V-REGION score V-REGION identity % V-REGION identity nt V-REGION identity % (with ins/del events) V-REGION identity nt (with ins/del events) J-GENE and allele J-REGION score J-REGION identity % J-REGION identity nt D-GENE and allele D-REGION reading frame CDR1-IMGT length CDR2-IMGT length CDR3-IMGT length CDR-IMGT lengths FR-IMGT lengths AA JUNCTION JUNCTION frame Orientation Functionality comment V-REGION potential ins/del J-GENE and allele comment V-REGION insertions V-REGION deletions Sequence Reason +2 lcl|FLN1FA001BLION.1| unproductive IGHV1-3 790 100.0 159/159 nt Homsap IGHJ3*02 F 160 80.0 40/50 nt Homsap IGHD6-13*01 F 2 X 8 X X.8.X [X.7.38.11] CARVGSSWSDAFD#IW out-of-frame + aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgtgcgagagtgggcagcagctggtctgatgcttttgattatctggggccaagggacaatggtcaccgtctcctcag X,#,* +3 lcl|FLN1FA002SGU3N.1| unproductive IGHV3-9 777 98.75 158/160 nt Homsap IGHJ4*02 F 177 85.42 41/48 nt Homsap IGHD3-16*02 F 3 X 8 X X.8.X [X.7.38.11] CAKDKIGYYDYVWGSYRLG#YW out-of-frame + gggcctggagtgggtctcaggtattagttggaatagtggtagaataggctatgcggactctgtgaacggccgattcaccatctccagagacaacgccaagaactccctgtatctgcaaatgaacagtctgagagctgaggacacggccttgtattactgtgcaaaagataaaattgggtattatgattacgtttgggggagttatcgtttgggtctactggggccagggaaccctggtcaccgtctcctcag X,#,* +9 lcl|FLN1FA001DN3RX.1| unproductive (see comment) IGHV3-72 825 100.0 166/166 nt Homsap IGHJ4*02 F 213 93.75 45/48 nt Homsap IGHD3-9*01 F 3 X 10 X X.10.X [X.7.38.11] CARDRLGRSRVYDILTFYL##DYW out-of-frame + stop codons ggggctggagtgggttggccgtactagaaacaaagctaacagttacaccacagaatacgccgcgtctgtgaaaggcagattcaccatctcaagagatgattcaaagaactcactgtatctgcaaatgaacagcctgaaaaccgaggacacggccgtgtattactgtgctagagatcgtttgggtcgttcccgtgtttacgatattttgaccttctacctaaattgactactggggccagggaaccctggtcaccgtctcctcag X,#,* |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/data_filter_BCR_output3.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data_filter_BCR_output3.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,18 @@ + sample % +Total reads of raw data 10 100.0000 +Not Null CDR3/V 10 100.0000 +filter out 0 0.0000 +Functional TRBV 10 100.0000 +filter out 0 0.0000 +Not Containing X,#,* 7 70.0000 +filter out 3 30.0000 +Productive 7 70.0000 +filter out 0 0.0000 +CDR3 landmarks C-W 7 70.0000 +filter out 0 0.0000 +Identity >= 70.0% 7 70.0000 +filter out 0 0.0000 +Total filter out A 3 30.0000 +Total filter in A 7 70.0000 +Total filter out 3 30.0000 +Total filter in 7 70.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/data_filter_BCR_parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data_filter_BCR_parameters.txt Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,14 @@ +Process ID: sample, +T-cell or B-cell option: B-cell, +Only Take Into Account Fuctional V-GENE?: Yes, +Only Take Into Account CDR3 with no Special Characters (X,*,#)?: Yes, +Only Take Into Account Productive Sequences?: Yes, +Only Take Into Account CDR3 with valid start/end landmarks?: Yes, +V-REGION identity %: 70, +Select Specific V gene?: No, +Select Specific J gene?: No, +Select Specific D gene?: No, +Select CDR3 length range?: No, +Only select CDR3 containing specific amino-acid sequence?: No + + |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/data_filter_TCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data_filter_TCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| [ |
| @@ -0,0 +1,21 @@ +Sequence number Sequence ID Functionality V-GENE and allele V-REGION score V-REGION identity % V-REGION identity nt V-REGION identity % (with ins/del events) V-REGION identity nt (with ins/del events) J-GENE and allele J-REGION score J-REGION identity % J-REGION identity nt D-GENE and allele D-REGION reading frame CDR1-IMGT length CDR2-IMGT length CDR3-IMGT length CDR-IMGT lengths FR-IMGT lengths AA JUNCTION JUNCTION frame Orientation Functionality comment V-REGION potential ins/del J-GENE and allele comment V-REGION insertions V-REGION deletions Sequence +1 @SRR060727.1 SOLEXA7:7:1:6:706 length=202 productive Homsap TRBV20-1*01 F, or Homsap TRBV20-1*02 F or Homsap TRBV20-1*03 (F) or Homsap TRBV20-1*04 (F) or Homsap TRBV20-1*05 (F) or Homsap TRBV20-1*06 (F) or Homsap TRBV20-1*07 (F) 175 100 36/36 nt Homsap TRBJ1-3*01 F 169 82 41/50 nt Homsap TRBD1*01 F 3 X X 9 X.X.9 [X.X.12.10] CSARRLGTIYF in-frame + agtgcccatcctgaagacagcagcttctacatctgcagtgcccgaaggcttggcaccatatattttggagagggaagttggctcactgttgtagaggaccttaacgggtgggaacaccttgttcaggtcctctacaacagtgagccaacttccctctccaaaatatatggtgccaagccttcgggcactgcagatgtagaag +2 @SRR060727.2 SOLEXA7:7:1:6:556 length=202 productive Homsap TRBV10-3*01 F, or Homsap TRBV10-3*02 F or Homsap TRBV10-3*03 [F] or Homsap TRBV10-3*04 [F] or Homsap TRBV6-1*01 F or Homsap TRBV6-4*01 F or Homsap TRBV6-4*02 F or Homsap TRBV6-5*01 F or Homsap TRBV6-6*01 F or Homsap TRBV6-6*02 F or Homsap TRBV6-6*03 (F) or Homsap TRBV6-6*04 (F) or Homsap TRBV6-6*05 (F) 95 100 20/20 nt Homsap TRBJ1-1*01 F 222 95.83 46/48 nt Homsap TRBD2*01 F 2 X X 11 X.X.11 [X.X.6.10] CASSSGGYTEAFF in-frame + agacatctgtgtacttctgtgccagcagttcgggggggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtgtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtacccccccgaactgctggcaccgaag +3 @SRR060727.3 SOLEXA7:7:1:9:1224 length=202 No results +4 @SRR060727.4 SOLEXA7:7:1:9:193 length=202 productive Homsap TRBV2*01 F, or Homsap TRBV2*02 (F) or Homsap TRBV2*03 (F) 100 100 21/21 nt Homsap TRBJ2-3*01 F 245 100 49/49 nt X X 9 X.X.9 [X.X.7.10] CASSSTDTQYF in-frame + gactcagccatgtacttctgtgccagctcaagcacagatacgcagtattttggcccaggcacccggctgacagtgctcgaggacctgaaaatcgtgttccctaacgggtgggaacacgattttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatctgtgcttgagctggcacagaagtacatg +5 @SRR060727.5 SOLEXA7:7:1:9:1328 length=202 No results +6 @SRR060727.6 SOLEXA7:7:1:11:979 length=202 No results +7 @SRR060727.7 SOLEXA7:7:1:11:499 length=202 No results +8 @SRR060727.8 SOLEXA7:7:1:15:1714 length=202 productive Homsap TRBV20-1*01 F, or Homsap TRBV20-1*02 F or Homsap TRBV20-1*03 (F) or Homsap TRBV20-1*04 (F) or Homsap TRBV20-1*05 (F) or Homsap TRBV20-1*06 (F) or Homsap TRBV20-1*07 (F) 180 100 37/37 nt Homsap TRBJ2-3*01 F 227 95.92 47/49 nt Homsap TRBD2*01 F 3 X X 11 X.X.11 [X.X.12.10] CSVKLRPTDTQYF in-frame + cagtgcccatcctgaagacagcagcttctacatctgcagtgttaagctccgccccacagatacgcagtattttggcccaggcacccggctgacagtgctcgtaacgggtgggaacacgtttttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatctgtggggcggagcttaacactgcagatg +9 @SRR060727.9 SOLEXA7:7:1:16:1132 length=202 No results +10 @SRR060727.10 SOLEXA7:7:1:16:803 length=202 No results +11 @SRR060727.11 SOLEXA7:7:1:17:1854 length=202 No results +12 @SRR060727.12 SOLEXA7:7:1:17:955 length=202 No results +13 @SRR060727.13 SOLEXA7:7:1:19:1481 length=202 No results +14 @SRR060727.14 SOLEXA7:7:1:19:1339 length=202 productive Homsap TRBV2*01 F, or Homsap TRBV2*02 (F) or Homsap TRBV2*03 (F) 120 100 25/25 nt Homsap TRBJ2-3*01 F 245 100 49/49 nt X X 9 X.X.9 [X.X.8.10] CASSSTDTQYF in-frame + ggaggactcagccatgtacttctgtgccagctcaagcacagatacgcagtattttggcccaggcacccggctgacagtgctcgaggccctgacaaacgtgttaacgggtgggaacacgtttttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatctgtgcttgagctggcacagaagtacatg +15 @SRR060727.15 SOLEXA7:7:1:19:820 length=202 No results +16 @SRR060727.16 SOLEXA7:7:1:20:1001 length=202 No results +17 @SRR060727.17 SOLEXA7:7:1:20:734 length=202 No results +18 @SRR060727.18 SOLEXA7:7:1:20:560 length=202 No results +19 @SRR060727.19 SOLEXA7:7:1:20:1343 length=202 productive Homsap TRBV29-1*01 F, or Homsap TRBV29-1*02 (F) or Homsap TRBV29-1*03 (F) 110 100 23/23 nt Homsap TRBJ2-1*01 F 223 94 47/50 nt Homsap TRBD1*01 F 3 X X 10 X.X.10 [X.X.7.10] CSVADRYNEQFF in-frame + aagacagcagcatatatctctgcagcgtagcggacaggtacaatgagcagttcttcgggccagggacacggctcaccgtgctagaggacctgaaaaacgtgtaacgggtgggaacacgtttttcaggtcctctagcacggtgagccgtgtccctggcccgaagaactgctcattgtacctgtccgctacgctgcagagatat +20 @SRR060727.20 SOLEXA7:7:1:20:838 length=202 productive Homsap TRBV20-1*01 F, or Homsap TRBV20-1*02 F or Homsap TRBV20-1*03 (F) or Homsap TRBV20-1*04 (F) or Homsap TRBV20-1*05 (F) or Homsap TRBV20-1*06 (F) or Homsap TRBV20-1*07 (F) 125 100 26/26 nt Homsap TRBJ1-1*01 F 213 93.75 45/48 nt Homsap TRBD1*01 F 2 X X 10 X.X.10 [X.X.8.10] CSAKGVSPEAFF in-frame + ctgaagacagcagcttctacatctgcagtgccaagggggtcagccctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaagtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagggctgacccccttggcactgcagatgtag |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/data_filter_TCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data_filter_TCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| [ |
| @@ -0,0 +1,8 @@ + Sequence ID Functionality V-GENE V-REGION score V-REGION identity % V-REGION identity nt V-REGION identity % (with ins/del events) V-REGION identity nt (with ins/del events) J-GENE J-REGION score J-REGION identity % J-REGION identity nt D-GENE D-REGION reading frame CDR1-IMGT length CDR2-IMGT length CDR3-IMGT length CDR-IMGT lengths FR-IMGT lengths AA JUNCTION JUNCTION frame Orientation Functionality comment V-REGION potential ins/del J-GENE and allele comment V-REGION insertions V-REGION deletions Sequence +1 @SRR060727.1 SOLEXA7:7:1:6:706 length=202 productive TRBV20-1 175.0 100.0 36/36 nt TRBJ1-3 169.0 82.0 41/50 nt TRBD1 3.0 X X 9.0 X.X.9 [X.X.12.10] CSARRLGTIYF in-frame + agtgcccatcctgaagacagcagcttctacatctgcagtgcccgaaggcttggcaccatatattttggagagggaagttggctcactgttgtagaggaccttaacgggtgggaacaccttgttcaggtcctctacaacagtgagccaacttccctctccaaaatatatggtgccaagccttcgggcactgcagatgtagaag +2 @SRR060727.2 SOLEXA7:7:1:6:556 length=202 productive TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6 95.0 100.0 20/20 nt TRBJ1-1 222.0 95.83 46/48 nt TRBD2 2.0 X X 11.0 X.X.11 [X.X.6.10] CASSSGGYTEAFF in-frame + agacatctgtgtacttctgtgccagcagttcgggggggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtgtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtacccccccgaactgctggcaccgaag +3 @SRR060727.4 SOLEXA7:7:1:9:193 length=202 productive TRBV2 100.0 100.0 21/21 nt TRBJ2-3 245.0 100.0 49/49 nt none X X 9.0 X.X.9 [X.X.7.10] CASSSTDTQYF in-frame + gactcagccatgtacttctgtgccagctcaagcacagatacgcagtattttggcccaggcacccggctgacagtgctcgaggacctgaaaatcgtgttccctaacgggtgggaacacgattttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatctgtgcttgagctggcacagaagtacatg +4 @SRR060727.8 SOLEXA7:7:1:15:1714 length=202 productive TRBV20-1 180.0 100.0 37/37 nt TRBJ2-3 227.0 95.92 47/49 nt TRBD2 3.0 X X 11.0 X.X.11 [X.X.12.10] CSVKLRPTDTQYF in-frame + cagtgcccatcctgaagacagcagcttctacatctgcagtgttaagctccgccccacagatacgcagtattttggcccaggcacccggctgacagtgctcgtaacgggtgggaacacgtttttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatctgtggggcggagcttaacactgcagatg +5 @SRR060727.14 SOLEXA7:7:1:19:1339 length=202 productive TRBV2 120.0 100.0 25/25 nt TRBJ2-3 245.0 100.0 49/49 nt none X X 9.0 X.X.9 [X.X.8.10] CASSSTDTQYF in-frame + ggaggactcagccatgtacttctgtgccagctcaagcacagatacgcagtattttggcccaggcacccggctgacagtgctcgaggccctgacaaacgtgttaacgggtgggaacacgtttttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatctgtgcttgagctggcacagaagtacatg +6 @SRR060727.19 SOLEXA7:7:1:20:1343 length=202 productive TRBV29-1 110.0 100.0 23/23 nt TRBJ2-1 223.0 94.0 47/50 nt TRBD1 3.0 X X 10.0 X.X.10 [X.X.7.10] CSVADRYNEQFF in-frame + aagacagcagcatatatctctgcagcgtagcggacaggtacaatgagcagttcttcgggccagggacacggctcaccgtgctagaggacctgaaaaacgtgtaacgggtgggaacacgtttttcaggtcctctagcacggtgagccgtgtccctggcccgaagaactgctcattgtacctgtccgctacgctgcagagatat +7 @SRR060727.20 SOLEXA7:7:1:20:838 length=202 productive TRBV20-1 125.0 100.0 26/26 nt TRBJ1-1 213.0 93.75 45/48 nt TRBD1 2.0 X X 10.0 X.X.10 [X.X.8.10] CSAKGVSPEAFF in-frame + ctgaagacagcagcttctacatctgcagtgccaagggggtcagccctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaagtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagggctgacccccttggcactgcagatgtag |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/data_filter_TCR_output2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data_filter_TCR_output2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,14 @@ + Sequence ID Functionality V-GENE and allele V-REGION score V-REGION identity % V-REGION identity nt V-REGION identity % (with ins/del events) V-REGION identity nt (with ins/del events) J-GENE and allele J-REGION score J-REGION identity % J-REGION identity nt D-GENE and allele D-REGION reading frame CDR1-IMGT length CDR2-IMGT length CDR3-IMGT length CDR-IMGT lengths FR-IMGT lengths AA JUNCTION JUNCTION frame Orientation Functionality comment V-REGION potential ins/del J-GENE and allele comment V-REGION insertions V-REGION deletions Sequence Reason +3 @SRR060727.3 SOLEXA7:7:1:9:1224 length=202 No results NoResults +5 @SRR060727.5 SOLEXA7:7:1:9:1328 length=202 No results NoResults +6 @SRR060727.6 SOLEXA7:7:1:11:979 length=202 No results NoResults +7 @SRR060727.7 SOLEXA7:7:1:11:499 length=202 No results NoResults +9 @SRR060727.9 SOLEXA7:7:1:16:1132 length=202 No results NoResults +10 @SRR060727.10 SOLEXA7:7:1:16:803 length=202 No results NoResults +11 @SRR060727.11 SOLEXA7:7:1:17:1854 length=202 No results NoResults +12 @SRR060727.12 SOLEXA7:7:1:17:955 length=202 No results NoResults +13 @SRR060727.13 SOLEXA7:7:1:19:1481 length=202 No results NoResults +15 @SRR060727.15 SOLEXA7:7:1:19:820 length=202 No results NoResults +16 @SRR060727.16 SOLEXA7:7:1:20:1001 length=202 No results NoResults +17 @SRR060727.17 SOLEXA7:7:1:20:734 length=202 No results NoResults +18 @SRR060727.18 SOLEXA7:7:1:20:560 length=202 No results NoResults |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/data_filter_TCR_output3.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data_filter_TCR_output3.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,18 @@ + sample % +Total reads of raw data 20 100.0000 +Not Null CDR3/V 7 35.0000 +filter out 13 65.0000 +Functional TRBV 7 35.0000 +filter out 0 0.0000 +Not Containing X,#,* 7 35.0000 +filter out 0 0.0000 +Productive 7 35.0000 +filter out 0 0.0000 +CDR3 landmarks C-F 7 35.0000 +filter out 0 0.0000 +Identity >= 70.0% 7 35.0000 +filter out 0 0.0000 +Total filter out A 13 65.0000 +Total filter in A 7 35.0000 +Total filter out 13 65.0000 +Total filter in 7 35.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/data_filter_TCR_parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data_filter_TCR_parameters.txt Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,14 @@ +Process ID: sample, +T-cell or B-cell option: T-cell, +Only Take Into Account Fuctional V-GENE?: Yes, +Only Take Into Account CDR3 with no Special Characters (X,*,#)?: Yes, +Only Take Into Account Productive Sequences?: Yes, +Only Take Into Account CDR3 with valid start/end landmarks?: Yes, +V-REGION identity %: 70, +Select Specific V gene?: No, +Select Specific J gene?: No, +Select Specific D gene?: No, +Select CDR3 length range?: No, +Only select CDR3 containing specific amino-acid sequence?: No + + |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def1_BCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def1_BCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + AA JUNCTION Reads Reads/Total Frequency % +1 CTREEQYSSWYFDFW 191 191/240554 0.0794 +2 CARGMVRGVNYYYYYGMDVW 119 119/240554 0.0495 +3 CARGTWYNDGWPHFDYW 107 107/240554 0.0445 +4 CARDLGVLGYCSGGSCYSHVW 102 102/240554 0.0424 +5 CARVLGDSFDYW 97 97/240554 0.0403 +6 CATITMAYYFDYW 95 95/240554 0.0395 +7 CARGGGSYPYYYYGMDVW 93 93/240554 0.0387 +8 CARDGGQLGIYFDYW 89 89/240554 0.037 +9 CARGLPRPYSGSYSGFDYW 88 88/240554 0.0366 +10 CARVRELDAFDIW 88 88/240554 0.0366 +11 CARVQYVWDSPGAFDIW 86 86/240554 0.0358 +12 CARGQGTVTTEIDYW 86 86/240554 0.0358 +13 CARDRANYGSGSPIDYW 85 85/240554 0.0353 +14 CARLGRLERSPYYYMDVW 85 85/240554 0.0353 +15 CARGPFYCSGGSCNLHYYYGMDVW 84 84/240554 0.0349 +16 CARDDSTGGNWDAFDIW 84 84/240554 0.0349 +17 CARYKRGGIAVAGTLSSSFDYW 84 84/240554 0.0349 +18 CARINYYDSSGYYHKGMYYFDYW 83 83/240554 0.0345 +19 CARVGSYSGIRAFDIW 83 83/240554 0.0345 +20 CARGPRHYDSSGYCVKLDYW 82 82/240554 0.0341 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def1_BCR_input2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def1_BCR_input2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + AA JUNCTION Reads Reads/Total Frequency % +1 CARGYYDSSGYYGVGQYYYYYMDVW 133 133/198331 0.0671 +2 CARGMVRGVNYYYYYGMDVW 122 122/198331 0.0615 +3 CARDRDLKDHHIAAAGSGYYYGMDVW 115 115/198331 0.058 +4 CARSYYYGSGSYLAYAFDIW 104 104/198331 0.0524 +5 CARDLGVLGYCSGGSCYSHVW 101 101/198331 0.0509 +6 CASFPEQQLKWYGMDVW 101 101/198331 0.0509 +7 CASTESGGYYFDAFDIW 97 97/198331 0.0489 +8 CARDPRSGYDFDYW 95 95/198331 0.0479 +9 CARDHSTAEDAFDIW 92 92/198331 0.0464 +10 CARDGYDSSGYYVGGALRLGVLQSYYGMDVW 88 88/198331 0.0444 +11 CATDPARITDTDYW 88 88/198331 0.0444 +12 CARAGRVTMIVVVIKPLDYW 87 87/198331 0.0439 +13 CARGEGYGDCW 86 86/198331 0.0434 +14 CARAGDYGSGTNAFDIW 85 85/198331 0.0429 +15 CARLGRLERSPYYYMDVW 84 84/198331 0.0424 +16 CARDGIAAATSGLDVW 84 84/198331 0.0424 +17 CARDVEYYYDSSGQYFDYW 84 84/198331 0.0424 +18 CARDRHCSGGSCRGLW 83 83/198331 0.0418 +19 CARVGSYSGIRAFDIW 82 82/198331 0.0413 +20 CARGDLVVVRGVINQGKLDYW 81 81/198331 0.0408 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def1_BCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def1_BCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,17 @@ + AA JUNCTION Reads Reads/Total Frequency % +1 CTREEQYSSWYFDFW 191 191/240554 0.0794 +2 CARGTWYNDGWPHFDYW 107 107/240554 0.0445 +3 CARVLGDSFDYW 97 97/240554 0.0403 +4 CATITMAYYFDYW 95 95/240554 0.0395 +5 CARGGGSYPYYYYGMDVW 93 93/240554 0.0387 +6 CARDGGQLGIYFDYW 89 89/240554 0.037 +7 CARGLPRPYSGSYSGFDYW 88 88/240554 0.0366 +8 CARVRELDAFDIW 88 88/240554 0.0366 +9 CARVQYVWDSPGAFDIW 86 86/240554 0.0358 +10 CARGQGTVTTEIDYW 86 86/240554 0.0358 +11 CARDRANYGSGSPIDYW 85 85/240554 0.0353 +12 CARGPFYCSGGSCNLHYYYGMDVW 84 84/240554 0.0349 +13 CARDDSTGGNWDAFDIW 84 84/240554 0.0349 +14 CARYKRGGIAVAGTLSSSFDYW 84 84/240554 0.0349 +15 CARINYYDSSGYYHKGMYYFDYW 83 83/240554 0.0345 +16 CARGPRHYDSSGYCVKLDYW 82 82/240554 0.0341 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def1_BCR_parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def1_BCR_parameters.txt Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Remove Clonotypes With Reads Fewer Than Threshold?: Yes, +Keep Clonotypes with Number of Reads more than: 3 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def1_TCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def1_TCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + AA JUNCTION Reads Reads/Total Frequency % +1 CASSSTDTQYF 3569 3569/56731 6.2911 +2 CASSLSGNTEAFF 673 673/56731 1.1863 +3 CASSEGGWTEAFF 399 399/56731 0.7033 +4 CASSEIGQGANEQFF 203 203/56731 0.3578 +5 CASSYMSSGSEQYF 105 105/56731 0.1851 +6 CASSRTETQYF 95 95/56731 0.1675 +7 CASSSRDPLNTEAFF 85 85/56731 0.1498 +8 CASMGGLNIYNSPLHF 78 78/56731 0.1375 +9 CSASRGEEAFF 69 69/56731 0.1216 +10 CASSKSGGAFNEQFF 63 63/56731 0.1111 +11 CASSLIPGQYQYF 59 59/56731 0.104 +12 CASSEMGNEQFF 52 52/56731 0.0917 +13 CASSPEVEGQPQHF 48 48/56731 0.0846 +14 CAITGTAGNTEAFF 47 47/56731 0.0828 +15 CSANRGEEAFF 45 45/56731 0.0793 +16 CAWSVGAEAFF 44 44/56731 0.0776 +17 CASSPGTAEAFF 42 42/56731 0.074 +18 CASSASGYEQYF 40 40/56731 0.0705 +19 CASSRGLNGADTQYF 40 40/56731 0.0705 +20 CASSRQIEAEAFF 39 39/56731 0.0687 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def1_TCR_input2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def1_TCR_input2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + AA JUNCTION Reads Reads/Total Frequency % +1 CASRLVPDTQYF 2898 2898/54828 5.2856 +2 CASSSFDEQFF 544 544/54828 0.9922 +3 CASSPGSTDTQYF 332 332/54828 0.6055 +4 CASSVLGVMNTEAFF 182 182/54828 0.3319 +5 CSAFLGGTQFF 104 104/54828 0.1897 +6 CASSSRDPLNTEAFF 81 81/54828 0.1477 +7 CASSEHGRAAEAFF 73 73/54828 0.1331 +8 CASSVRRYSNQPQHF 69 69/54828 0.1258 +9 CASSKSGGAFNEQFF 62 62/54828 0.1131 +10 CASSSPYANNEQFF 61 61/54828 0.1113 +11 CASSFRTGFTDTQYF 55 55/54828 0.1003 +12 CASSVTGYEQFF 49 49/54828 0.0894 +13 CATATSGSTDTQYF 47 47/54828 0.0857 +14 CAITGTAGNTEAFF 47 47/54828 0.0857 +15 CASSFRAPNTDTQYF 46 46/54828 0.0839 +16 CSVGSGEGYEQYF 44 44/54828 0.0803 +17 CSGIAGSTDTQYF 43 43/54828 0.0784 +18 CSARRLGTIYF 41 41/54828 0.0748 +19 CASGGNTQYF 40 40/54828 0.073 +20 CASLSSNEQYF 39 39/54828 0.0711 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def1_TCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def1_TCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,18 @@ + AA JUNCTION Reads Reads/Total Frequency % +1 CASSSTDTQYF 3569 3569/56731 6.2911 +2 CASSLSGNTEAFF 673 673/56731 1.1863 +3 CASSEGGWTEAFF 399 399/56731 0.7033 +4 CASSEIGQGANEQFF 203 203/56731 0.3578 +5 CASSYMSSGSEQYF 105 105/56731 0.1851 +6 CASSRTETQYF 95 95/56731 0.1675 +7 CASMGGLNIYNSPLHF 78 78/56731 0.1375 +8 CSASRGEEAFF 69 69/56731 0.1216 +9 CASSLIPGQYQYF 59 59/56731 0.104 +10 CASSEMGNEQFF 52 52/56731 0.0917 +11 CASSPEVEGQPQHF 48 48/56731 0.0846 +12 CSANRGEEAFF 45 45/56731 0.0793 +13 CAWSVGAEAFF 44 44/56731 0.0776 +14 CASSPGTAEAFF 42 42/56731 0.074 +15 CASSASGYEQYF 40 40/56731 0.0705 +16 CASSRGLNGADTQYF 40 40/56731 0.0705 +17 CASSRQIEAEAFF 39 39/56731 0.0687 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def1_TCR_parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def1_TCR_parameters.txt Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Remove Clonotypes With Reads Fewer Than Threshold?: Yes, +Keep Clonotypes with Number of Reads more than: 2 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def2_BCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def2_BCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + V-GENE AA JUNCTION Reads Reads/Total Frequency % +1 IGHV3-23 or IGHV3-23D CTREEQYSSWYFDFW 84 84/240554 0.0349 +2 IGHV1-69 CASRMVRGVILPPYYYYYMDVW 74 74/240554 0.0308 +3 IGHV7-4-1 CARASSHHYCSGGSCYSYYYYYYYMDVW 72 72/240554 0.0299 +4 IGHV1-18 CARELYVWGSRHEVFDIW 71 71/240554 0.0295 +5 IGHV3-33 CAKGGGSYYGVYYFDYW 69 69/240554 0.0287 +6 IGHV4-59 or IGHV4-61 CARDLGYSGSYLGRAFDIW 66 66/240554 0.0274 +7 IGHV3-33 CARDLHPRARGVIVIPGYW 65 65/240554 0.027 +8 IGHV1-69 CARLGRLERSPYYYMDVW 64 64/240554 0.0266 +9 IGHV1-69 CARDSSGGTDYYYYYMDVW 62 62/240554 0.0258 +10 IGHV3-49 CTRPRGIVISAGIYFDYW 61 61/240554 0.0254 +11 IGHV1-69 CARDPVLYCGGDCSSSDAFDIW 60 60/240554 0.0249 +12 IGHV7-4-1 CARDTLYPPNYYGSGSYEGMDVW 60 60/240554 0.0249 +13 IGHV4-39 CAGRASPFGPSYYFNSW 60 60/240554 0.0249 +14 IGHV3-9 CAKDISLRDEGDSSVGYDYW 59 59/240554 0.0245 +15 IGHV4-39 CARLMLGTMVKTPDAFDIW 59 59/240554 0.0245 +16 IGHV1-3 CARALPPRYCSGGSCYYPSNWGQGTLVGYYPSNW 59 59/240554 0.0245 +17 IGHV3-30 or IGHV3-30-3 CARDQFGVVTVKGGYFQHW 58 58/240554 0.0241 +18 IGHV1-3 CARERYYNRGAFDIW 57 57/240554 0.0237 +19 IGHV3-9 CAIGRGVISTFFDYW 57 57/240554 0.0237 +20 IGHV3-23 or IGHV3-23D CAKERALGFGEPHYW 56 56/240554 0.0233 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def2_BCR_input2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def2_BCR_input2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + V-GENE AA JUNCTION Reads Reads/Total Frequency % +1 IGHV3-11 CARGMVRGVNYYYYYGMDVW 78 78/251182 0.0311 +2 IGHV1-46 CARDRDLKDHHIAAAGSGYYYGMDVW 74 74/251182 0.0295 +3 IGHV4-59 or IGHV4-61 CARGTWYNDGWPHFDYW 71 71/251182 0.0283 +4 IGHV1-46 CASAGGVYTSGWHGTFYW 70 70/251182 0.0279 +5 IGHV3-33 CAKGGGSYYGVYYFDYW 68 68/251182 0.0271 +6 IGHV1-24 CATGDYDVLTGNYRAFW 67 67/251182 0.0267 +7 IGHV3-33 CARDLHPRARGVIVIPGYW 65 65/251182 0.0259 +8 IGHV4-34 CARVYPYDSSSWQAPYYYGMDVW 64 64/251182 0.0255 +9 IGHV3-49 CTRDRGERQYDAFDIW 61 61/251182 0.0243 +10 IGHV1-69 CARDPVLYCGGDCSSSDAFDIW 60 60/251182 0.0239 +11 IGHV1-69 CARPRIAAAVYWYFDLW 60 60/251182 0.0239 +12 IGHV3-21 CARDHFVWGSPSPMDIW 60 60/251182 0.0239 +13 IGHV3-23 or IGHV3-23D CARVGSYSGIRAFDIW 59 59/251182 0.0235 +14 IGHV4-39 CARLMLGTMVKTPDAFDIW 59 59/251182 0.0235 +15 IGHV4-59 or IGHV4-61 CARHDGIAAAGHFDYW 59 59/251182 0.0235 +16 IGHV1-69 CAREEKFGELLERSYYYYYYMDVW 59 59/251182 0.0235 +17 IGHV1-69 CARGYYDSSGYYGVGQYYYYYMDVW 58 58/251182 0.0231 +18 IGHV3-33 CAKGPRMVRGVLDYW 57 57/251182 0.0227 +19 IGHV3-9 CAIGRGVISTFFDYW 57 57/251182 0.0227 +20 IGHV3-64 CATEHIAAAGEASAFDIW 57 57/251182 0.0227 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def2_BCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def2_BCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,16 @@ + V-GENE AA JUNCTION Reads Reads/Total Frequency % +1 IGHV3-23 or IGHV3-23D CTREEQYSSWYFDFW 84 84/240554 0.0349 +2 IGHV1-69 CASRMVRGVILPPYYYYYMDVW 74 74/240554 0.0308 +3 IGHV7-4-1 CARASSHHYCSGGSCYSYYYYYYYMDVW 72 72/240554 0.0299 +4 IGHV1-18 CARELYVWGSRHEVFDIW 71 71/240554 0.0295 +5 IGHV4-59 or IGHV4-61 CARDLGYSGSYLGRAFDIW 66 66/240554 0.0274 +6 IGHV1-69 CARLGRLERSPYYYMDVW 64 64/240554 0.0266 +7 IGHV1-69 CARDSSGGTDYYYYYMDVW 62 62/240554 0.0258 +8 IGHV3-49 CTRPRGIVISAGIYFDYW 61 61/240554 0.0254 +9 IGHV7-4-1 CARDTLYPPNYYGSGSYEGMDVW 60 60/240554 0.0249 +10 IGHV4-39 CAGRASPFGPSYYFNSW 60 60/240554 0.0249 +11 IGHV3-9 CAKDISLRDEGDSSVGYDYW 59 59/240554 0.0245 +12 IGHV1-3 CARALPPRYCSGGSCYYPSNWGQGTLVGYYPSNW 59 59/240554 0.0245 +13 IGHV3-30 or IGHV3-30-3 CARDQFGVVTVKGGYFQHW 58 58/240554 0.0241 +14 IGHV1-3 CARERYYNRGAFDIW 57 57/240554 0.0237 +15 IGHV3-23 or IGHV3-23D CAKERALGFGEPHYW 56 56/240554 0.0233 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def2_BCR_parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def2_BCR_parameters.txt Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Remove Clonotypes With Reads Fewer Than Threshold?: Yes, +Keep Clonotypes with Number of Reads more than: 3 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def2_TCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def2_TCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + V-GENE AA JUNCTION Reads Reads/Total Frequency % +1 TRBV2 CASSSTDTQYF 3545 3545/56731 6.2488 +2 TRBV2 CASRLVPDTQYF 2893 2893/56731 5.0995 +3 TRBV13 CASSLSGNTEAFF 670 670/56731 1.181 +4 TRBV2 CASSEGGWTEAFF 398 398/56731 0.7016 +5 TRBV5-1 CASSPGSTDTQYF 329 329/56731 0.5799 +6 TRBV2 CASSEIGQGANEQFF 201 201/56731 0.3543 +7 TRBV20-1 CSAFLGGTQFF 104 104/56731 0.1833 +8 TRBV12-3 or TRBV12-4 CASSSRDPLNTEAFF 84 84/56731 0.1481 +9 TRBV25-1 CASSEHGRAAEAFF 72 72/56731 0.1269 +10 TRBV20-1 CSASRGEEAFF 69 69/56731 0.1216 +11 TRBV27 CASSLIPGQYQYF 59 59/56731 0.104 +12 TRBV10-2 CASSEMGNEQFF 52 52/56731 0.0917 +13 TRBV3-1 CASSPEVEGQPQHF 48 48/56731 0.0846 +14 TRBV7-8 CASSFRAPNTDTQYF 46 46/56731 0.0811 +15 TRBV30 CAWSVGAEAFF 44 44/56731 0.0776 +16 TRBV29-1 CSGIAGSTDTQYF 43 43/56731 0.0758 +17 TRBV20-1 CSARRLGTIYF 41 41/56731 0.0723 +18 TRBV2 CASGGNTQYF 40 40/56731 0.0705 +19 TRBV2 CASLSSNEQYF 39 39/56731 0.0687 +20 TRBV25-1 CASTSGTGSDTQYF 37 37/56731 0.0652 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def2_TCR_input2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def2_TCR_input2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + V-GENE AA JUNCTION Reads Reads/Total Frequency % +1 TRBV2 CASRLVPDTQYF 2931 2931/57218 5.1225 +2 TRBV13 CASSLSGNTEAFF 753 753/57218 1.316 +3 TRBV27 CASSSFDEQFF 544 544/57218 0.9507 +4 TRBV5-1 CASSPGSTDTQYF 322 322/57218 0.5628 +5 TRBV10-2 CASSVLGVMNTEAFF 181 181/57218 0.3163 +6 TRBV20-1 CSAFLGGTQFF 107 107/57218 0.187 +7 TRBV12-3 or TRBV12-4 CASSRTETQYF 94 94/57218 0.1643 +8 TRBV2 CASMGGLNIYNSPLHF 77 77/57218 0.1346 +9 TRBV25-1 CASSEHGRAAEAFF 74 74/57218 0.1293 +10 TRBV9 CASSVRRYSNQPQHF 69 69/57218 0.1206 +11 TRBV2 CASSKSGGAFNEQFF 62 62/57218 0.1084 +12 TRBV7-8 CASSFRTGFTDTQYF 55 55/57218 0.0961 +13 TRBV25-1 CASSVTGYEQFF 49 49/57218 0.0856 +14 TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6 CASSYMSSGSEQYF 47 47/57218 0.0821 +15 TRBV20-1 CSANRGEEAFF 45 45/57218 0.0786 +16 TRBV29-1 CSVGSGEGYEQYF 44 44/57218 0.0769 +17 TRBV12-3 or TRBV12-4 CASSPGTAEAFF 42 42/57218 0.0734 +18 TRBV7-9 CASSSPYANNEQFF 41 41/57218 0.0717 +19 TRBV25-1 CASSASGYEQYF 40 40/57218 0.0699 +20 TRBV12-3 or TRBV12-4 CASSRQIEAEAFF 38 38/57218 0.0664 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def2_TCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def2_TCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,16 @@ + V-GENE AA JUNCTION Reads Reads/Total Frequency % +1 TRBV2 CASSSTDTQYF 3545 3545/56731 6.2488 +2 TRBV2 CASSEGGWTEAFF 398 398/56731 0.7016 +3 TRBV2 CASSEIGQGANEQFF 201 201/56731 0.3543 +4 TRBV12-3 or TRBV12-4 CASSSRDPLNTEAFF 84 84/56731 0.1481 +5 TRBV20-1 CSASRGEEAFF 69 69/56731 0.1216 +6 TRBV27 CASSLIPGQYQYF 59 59/56731 0.104 +7 TRBV10-2 CASSEMGNEQFF 52 52/56731 0.0917 +8 TRBV3-1 CASSPEVEGQPQHF 48 48/56731 0.0846 +9 TRBV7-8 CASSFRAPNTDTQYF 46 46/56731 0.0811 +10 TRBV30 CAWSVGAEAFF 44 44/56731 0.0776 +11 TRBV29-1 CSGIAGSTDTQYF 43 43/56731 0.0758 +12 TRBV20-1 CSARRLGTIYF 41 41/56731 0.0723 +13 TRBV2 CASGGNTQYF 40 40/56731 0.0705 +14 TRBV2 CASLSSNEQYF 39 39/56731 0.0687 +15 TRBV25-1 CASTSGTGSDTQYF 37 37/56731 0.0652 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def2_TCR_parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def2_TCR_parameters.txt Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Remove Clonotypes With Reads Fewer Than Threshold?: Yes, +Keep Clonotypes with Number of Reads more than: 2 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def3_BCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def3_BCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + J-GENE AA JUNCTION Reads Reads/Total Frequency % +1 IGHJ4 CTREEQYSSWYFDFW 191 191/240554 0.0794 +2 IGHJ6 CARGMVRGVNYYYYYGMDVW 119 119/240554 0.0495 +3 IGHJ4 CARGTWYNDGWPHFDYW 107 107/240554 0.0445 +4 IGHJ4 CARDLGVLGYCSGGSCYSHVW 102 102/240554 0.0424 +5 IGHJ3 CASTESGGYYFDAFDIW 97 97/240554 0.0403 +6 IGHJ4 CATITMAYYFDYW 95 95/240554 0.0395 +7 IGHJ6 CARGGGSYPYYYYGMDVW 93 93/240554 0.0387 +8 IGHJ4 CARDGGQLGIYFDYW 89 89/240554 0.037 +9 IGHJ6 CARDGYDSSGYYVGGALRLGVLQSYYGMDVW 88 88/240554 0.0366 +10 IGHJ4 CATDPARITDTDYW 88 88/240554 0.0366 +11 IGHJ4 CARGLPRPYSGSYSGFDYW 88 88/240554 0.0366 +12 IGHJ4 CARGEGYGDCW 86 86/240554 0.0358 +13 IGHJ4 CARGQGTVTTEIDYW 86 86/240554 0.0358 +14 IGHJ3 CARAGDYGSGTNAFDIW 85 85/240554 0.0353 +15 IGHJ4 CARYKRGGIAVAGTLSSSFDYW 84 84/240554 0.0349 +16 IGHJ4 CARDVEYYYDSSGQYFDYW 84 84/240554 0.0349 +17 IGHJ6 CARDGIAAATSGLDVW 84 84/240554 0.0349 +18 IGHJ4 CARINYYDSSGYYHKGMYYFDYW 83 83/240554 0.0345 +19 IGHJ4 CARGPRHYDSSGYCVKLDYW 82 82/240554 0.0341 +20 IGHJ6 CARGVSGYYNFFYMDVW 81 81/240554 0.0337 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def3_BCR_input2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def3_BCR_input2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + J-GENE AA JUNCTION Reads Reads/Total Frequency % +1 IGHJ6 CARGYYDSSGYYGVGQYYYYYMDVW 133 133/229003 0.0581 +2 IGHJ6 CARGMVRGVNYYYYYGMDVW 124 124/229003 0.0541 +3 IGHJ6 CARDRDLKDHHIAAAGSGYYYGMDVW 115 115/229003 0.0502 +4 IGHJ3 CARSYYYGSGSYLAYAFDIW 104 104/229003 0.0454 +5 IGHJ6 CASFPEQQLKWYGMDVW 101 101/229003 0.0441 +6 IGHJ4 CARVLGDSFDYW 97 97/229003 0.0424 +7 IGHJ4 CARDPRSGYDFDYW 95 95/229003 0.0415 +8 IGHJ3 CARDHSTAEDAFDIW 92 92/229003 0.0402 +9 IGHJ6 CARDGYDSSGYYVGGALRLGVLQSYYGMDVW 88 88/229003 0.0384 +10 IGHJ3 CARVRELDAFDIW 88 88/229003 0.0384 +11 IGHJ4 CARAGRVTMIVVVIKPLDYW 87 87/229003 0.038 +12 IGHJ3 CARVQYVWDSPGAFDIW 86 86/229003 0.0376 +13 IGHJ6 CARLGRLERSPYYYMDVW 85 85/229003 0.0371 +14 IGHJ4 CARDRANYGSGSPIDYW 85 85/229003 0.0371 +15 IGHJ6 CARGPFYCSGGSCNLHYYYGMDVW 84 84/229003 0.0367 +16 IGHJ3 CARDDSTGGNWDAFDIW 84 84/229003 0.0367 +17 IGHJ6 CARDGIAAATSGLDVW 83 83/229003 0.0362 +18 IGHJ5 CARDRHCSGGSCRGLW 83 83/229003 0.0362 +19 IGHJ3 CARVGSYSGIRAFDIW 83 83/229003 0.0362 +20 IGHJ4 CARGDLVVVRGVINQGKLDYW 81 81/229003 0.0354 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def3_BCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def3_BCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,18 @@ + J-GENE AA JUNCTION Reads Reads/Total Frequency % +1 IGHJ4 CTREEQYSSWYFDFW 191 191/240554 0.0794 +2 IGHJ4 CARGTWYNDGWPHFDYW 107 107/240554 0.0445 +3 IGHJ4 CARDLGVLGYCSGGSCYSHVW 102 102/240554 0.0424 +4 IGHJ3 CASTESGGYYFDAFDIW 97 97/240554 0.0403 +5 IGHJ4 CATITMAYYFDYW 95 95/240554 0.0395 +6 IGHJ6 CARGGGSYPYYYYGMDVW 93 93/240554 0.0387 +7 IGHJ4 CARDGGQLGIYFDYW 89 89/240554 0.037 +8 IGHJ4 CATDPARITDTDYW 88 88/240554 0.0366 +9 IGHJ4 CARGLPRPYSGSYSGFDYW 88 88/240554 0.0366 +10 IGHJ4 CARGEGYGDCW 86 86/240554 0.0358 +11 IGHJ4 CARGQGTVTTEIDYW 86 86/240554 0.0358 +12 IGHJ3 CARAGDYGSGTNAFDIW 85 85/240554 0.0353 +13 IGHJ4 CARYKRGGIAVAGTLSSSFDYW 84 84/240554 0.0349 +14 IGHJ4 CARDVEYYYDSSGQYFDYW 84 84/240554 0.0349 +15 IGHJ4 CARINYYDSSGYYHKGMYYFDYW 83 83/240554 0.0345 +16 IGHJ4 CARGPRHYDSSGYCVKLDYW 82 82/240554 0.0341 +17 IGHJ6 CARGVSGYYNFFYMDVW 81 81/240554 0.0337 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def3_BCR_parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def3_BCR_parameters.txt Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Remove Clonotypes With Reads Fewer Than Threshold?: Yes, +Keep Clonotypes with Number of Reads more than: 3 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def3_TCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def3_TCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + J-GENE AA JUNCTION Reads Reads/Total Frequency % +1 TRBJ2-3 CASSSTDTQYF 3569 3569/56731 6.2911 +2 TRBJ1-1 CASSLSGNTEAFF 673 673/56731 1.1863 +3 TRBJ2-1 CASSSFDEQFF 544 544/56731 0.9589 +4 TRBJ1-1 CASSEGGWTEAFF 399 399/56731 0.7033 +5 TRBJ2-1 CASSEIGQGANEQFF 203 203/56731 0.3578 +6 TRBJ2-7 CASSYMSSGSEQYF 105 105/56731 0.1851 +7 TRBJ2-3 CASSRTETQYF 95 95/56731 0.1675 +8 TRBJ1-1 CASSSRDPLNTEAFF 85 85/56731 0.1498 +9 TRBJ1-6 CASMGGLNIYNSPLHF 78 78/56731 0.1375 +10 TRBJ1-5 CASSVRRYSNQPQHF 69 69/56731 0.1216 +11 TRBJ2-1 CASSKSGGAFNEQFF 63 63/56731 0.1111 +12 TRBJ2-3 CASSLIPGQYQYF 59 59/56731 0.104 +13 TRBJ2-1 CASSEMGNEQFF 52 52/56731 0.0917 +14 TRBJ1-5 CASSPEVEGQPQHF 48 48/56731 0.0846 +15 TRBJ1-1 CAITGTAGNTEAFF 47 47/56731 0.0828 +16 TRBJ1-1 CSANRGEEAFF 45 45/56731 0.0793 +17 TRBJ1-1 CAWSVGAEAFF 44 44/56731 0.0776 +18 TRBJ1-1 CASSPGTAEAFF 42 42/56731 0.074 +19 TRBJ2-3 CASSRGLNGADTQYF 40 40/56731 0.0705 +20 TRBJ2-7 CASSASGYEQYF 40 40/56731 0.0705 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def3_TCR_input2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def3_TCR_input2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + J-GENE AA JUNCTION Reads Reads/Total Frequency % +1 TRBJ2-3 CASRLVPDTQYF 2898 2898/57339 5.0542 +2 TRBJ2-1 CASSSFDEQFF 618 618/57339 1.0778 +3 TRBJ2-3 CASSPGSTDTQYF 332 332/57339 0.579 +4 TRBJ1-1 CASSVLGVMNTEAFF 182 182/57339 0.3174 +5 TRBJ2-7 CASSYMSSGSEQYF 112 112/57339 0.1953 +6 TRBJ2-1 CSAFLGGTQFF 104 104/57339 0.1814 +7 TRBJ1-1 CASSSRDPLNTEAFF 86 86/57339 0.15 +8 TRBJ1-1 CASSEHGRAAEAFF 73 73/57339 0.1273 +9 TRBJ1-1 CSASRGEEAFF 69 69/57339 0.1203 +10 TRBJ2-1 CASSSPYANNEQFF 61 61/57339 0.1064 +11 TRBJ2-3 CASSFRTGFTDTQYF 55 55/57339 0.0959 +12 TRBJ2-1 CASSEMGNEQFF 50 50/57339 0.0872 +13 TRBJ2-1 CASSVTGYEQFF 49 49/57339 0.0855 +14 TRBJ2-3 CATATSGSTDTQYF 47 47/57339 0.082 +15 TRBJ2-3 CASSFRAPNTDTQYF 46 46/57339 0.0802 +16 TRBJ2-7 CSVGSGEGYEQYF 44 44/57339 0.0767 +17 TRBJ2-3 CSGIAGSTDTQYF 43 43/57339 0.075 +18 TRBJ1-3 CSARRLGTIYF 41 41/57339 0.0715 +19 TRBJ2-3 CASGGNTQYF 40 40/57339 0.0698 +20 TRBJ1-1 CASSRQIEAEAFF 39 39/57339 0.068 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def3_TCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def3_TCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,17 @@ + J-GENE AA JUNCTION Reads Reads/Total Frequency % +1 TRBJ2-3 CASSSTDTQYF 3569 3569/56731 6.2911 +2 TRBJ1-1 CASSLSGNTEAFF 673 673/56731 1.1863 +3 TRBJ1-1 CASSEGGWTEAFF 399 399/56731 0.7033 +4 TRBJ2-1 CASSEIGQGANEQFF 203 203/56731 0.3578 +5 TRBJ2-3 CASSRTETQYF 95 95/56731 0.1675 +6 TRBJ1-6 CASMGGLNIYNSPLHF 78 78/56731 0.1375 +7 TRBJ1-5 CASSVRRYSNQPQHF 69 69/56731 0.1216 +8 TRBJ2-1 CASSKSGGAFNEQFF 63 63/56731 0.1111 +9 TRBJ2-3 CASSLIPGQYQYF 59 59/56731 0.104 +10 TRBJ1-5 CASSPEVEGQPQHF 48 48/56731 0.0846 +11 TRBJ1-1 CAITGTAGNTEAFF 47 47/56731 0.0828 +12 TRBJ1-1 CSANRGEEAFF 45 45/56731 0.0793 +13 TRBJ1-1 CAWSVGAEAFF 44 44/56731 0.0776 +14 TRBJ1-1 CASSPGTAEAFF 42 42/56731 0.074 +15 TRBJ2-3 CASSRGLNGADTQYF 40 40/56731 0.0705 +16 TRBJ2-7 CASSASGYEQYF 40 40/56731 0.0705 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/exclusive_clonos_def3_TCR_parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclusive_clonos_def3_TCR_parameters.txt Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Remove Clonotypes With Reads Fewer Than Threshold?: Yes, +Keep Clonotypes with Number of Reads more than: 2 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_compare_geneJ_BCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_compare_geneJ_BCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,7 @@ + J-GENE Reads Reads/Total Frequency % +1 IGHJ4 3946 3946/8445 46.7259 +2 IGHJ3 1781 1781/8445 21.0894 +3 IGHJ6 1410 1410/8445 16.6963 +4 IGHJ5 798 798/8445 9.4494 +5 IGHJ2 292 292/8445 3.4577 +6 IGHJ1 218 218/8445 2.5814 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_compare_geneJ_BCR_input2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_compare_geneJ_BCR_input2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,7 @@ + J-GENE Reads Reads/Total Frequency % +1 IGHJ4 4114 4114/11970 34.3693 +2 IGHJ1 2276 2276/11970 19.0142 +3 IGHJ6 2008 2008/11970 16.7753 +4 IGHJ5 1743 1743/11970 14.5614 +5 IGHJ3 1691 1691/11970 14.127 +6 IGHJ2 138 138/11970 1.1529 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_compare_geneJ_BCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_compare_geneJ_BCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,7 @@ + J-GENE input1.csv input2.csv mean +1 IGHJ4 46.7259 34.3693 40.5476 +2 IGHJ3 21.0894 14.127 17.6082 +3 IGHJ6 16.6963 16.7753 16.7358 +4 IGHJ5 9.4494 14.5614 12.0054 +5 IGHJ1 2.5814 19.0142 10.7978 +6 IGHJ2 3.4577 1.1529 2.3053 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_compare_geneJ_TCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_compare_geneJ_TCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,8 @@ + J-GENE Reads Reads/Total Frequency % +1 TRBJ1-1 5562 5562/26646 20.8737 +2 TRBJ2-3 3665 3665/26646 13.7544 +3 TRBJ1-5 2692 2692/26646 10.1028 +4 TRBJ2-2 1575 1575/26646 5.9108 +5 TRBJ1-3 1009 1009/26646 3.7867 +6 TRBJ2-4 289 289/26646 1.0846 +7 TRBJ2-6 105 105/26646 0.3941 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_compare_geneJ_TCR_input2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_compare_geneJ_TCR_input2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,8 @@ + J-GENE Reads Reads/Total Frequency % +1 TRBJ2-1 4400 4400/25009 17.5937 +2 TRBJ2-7 3569 3569/25009 14.2709 +3 TRBJ2-5 1736 1736/25009 6.9415 +4 TRBJ1-6 1253 1253/25009 5.0102 +5 TRBJ1-4 650 650/25009 2.5991 +6 TRBJ1-2 140 140/25009 0.5598 +7 TRAJ27 1 1/25009 0.004 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_compare_geneJ_TCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_compare_geneJ_TCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,15 @@ + J-GENE input1.csv input2.csv mean +1 TRBJ1-1 20.8737 0.0 10.4368 +2 TRBJ2-1 0.0 17.5937 8.7968 +3 TRBJ2-7 0.0 14.2709 7.1354 +4 TRBJ2-3 13.7544 0.0 6.8772 +5 TRBJ1-5 10.1028 0.0 5.0514 +6 TRBJ2-5 0.0 6.9415 3.4707 +7 TRBJ2-2 5.9108 0.0 2.9554 +8 TRBJ1-6 0.0 5.0102 2.5051 +9 TRBJ1-3 3.7867 0.0 1.8934 +10 TRBJ1-4 0.0 2.5991 1.2995 +11 TRBJ2-4 1.0846 0.0 0.5423 +12 TRBJ1-2 0.0 0.5598 0.2799 +13 TRBJ2-6 0.3941 0.0 0.1971 +14 TRAJ27 0.0 0.004 0.0020 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_compare_geneV_BCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_compare_geneV_BCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ + V-GENE Reads Reads/Total Frequency % +1 IGHV4-39 859 859/10166 8.4497 +2 IGHV3-23 or IGHV3-23D 604 604/10166 5.9414 +3 IGHV3-33 582 582/10166 5.725 +4 IGHV4-34 444 444/10166 4.3675 +5 IGHV1-3 398 398/10166 3.915 +6 IGHV3-9 376 376/10166 3.6986 +7 IGHV1-8 342 342/10166 3.3642 +8 IGHV1-69 306 306/10166 3.01 +9 IGHV1-46 302 302/10166 2.9707 +10 IGHV3-11 272 272/10166 2.6756 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_compare_geneV_BCR_input2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_compare_geneV_BCR_input2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ + V-GENE Reads Reads/Total Frequency % +1 IGHV4-59 or IGHV4-61 726 726/12004 6.048 +2 IGHV3-21 582 582/12004 4.8484 +3 IGHV1-18 514 514/12004 4.2819 +4 IGHV1-69 or IGHV1-69D 415 415/12004 3.4572 +5 IGHV3-30 or IGHV3-30-3 398 398/12004 3.3156 +6 IGHV3-7 343 343/12004 2.8574 +7 IGHV7-4-1 308 308/12004 2.5658 +8 IGHV3-48 304 304/12004 2.5325 +9 IGHV2-5 291 291/12004 2.4242 +10 IGHV4-31 or IGHV4-59 212 212/12004 1.7661 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_compare_geneV_BCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_compare_geneV_BCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + V-GENE input1.csv input2.csv mean +1 IGHV4-39 8.4497 0.0 4.2248 +2 IGHV4-59 or IGHV4-61 0.0 6.048 3.0240 +3 IGHV3-23 or IGHV3-23D 5.9414 0.0 2.9707 +4 IGHV3-33 5.725 0.0 2.8625 +5 IGHV3-21 0.0 4.8484 2.4242 +6 IGHV4-34 4.3675 0.0 2.1837 +7 IGHV1-18 0.0 4.2819 2.1410 +8 IGHV1-3 3.915 0.0 1.9575 +9 IGHV3-9 3.6986 0.0 1.8493 +10 IGHV1-69 or IGHV1-69D 0.0 3.4572 1.7286 +11 IGHV1-8 3.3642 0.0 1.6821 +12 IGHV3-30 or IGHV3-30-3 0.0 3.3156 1.6578 +13 IGHV1-69 3.01 0.0 1.5050 +14 IGHV1-46 2.9707 0.0 1.4853 +15 IGHV3-7 0.0 2.8574 1.4287 +16 IGHV3-11 2.6756 0.0 1.3378 +17 IGHV7-4-1 0.0 2.5658 1.2829 +18 IGHV3-48 0.0 2.5325 1.2663 +19 IGHV2-5 0.0 2.4242 1.2121 +20 IGHV4-31 or IGHV4-59 0.0 1.7661 0.8831 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_compare_geneV_TCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_compare_geneV_TCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ + V-GENE Reads Reads/Total Frequency % +1 TRBV20-1 5516 5516/28836 19.1289 +2 TRBV29-1 2162 2162/28836 7.4976 +3 TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6 1679 1679/28836 5.8226 +4 TRBV2 1368 1368/28836 4.7441 +5 TRBV10-3 1011 1011/28836 3.506 +6 TRBV5-1 609 609/28836 2.1119 +7 TRBV9 575 575/28836 1.994 +8 TRBV28 568 568/28836 1.9698 +9 TRBV3-1 467 467/28836 1.6195 +10 TRBV25-1 321 321/28836 1.1132 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_compare_geneV_TCR_input2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_compare_geneV_TCR_input2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ + V-GENE Reads Reads/Total Frequency % +1 TRBV12-3 or TRBV12-4 3388 3388/27418 12.3568 +2 TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6 2044 2044/27418 7.455 +3 TRBV6-1 or TRBV6-5 or TRBV6-6 1587 1587/27418 5.7882 +4 TRBV19 1331 1331/27418 4.8545 +5 TRBV27 787 787/27418 2.8704 +6 TRBV4-1 605 605/27418 2.2066 +7 TRBV7-9 572 572/27418 2.0862 +8 TRBV18 471 471/27418 1.7178 +9 TRBV11-1 or TRBV11-3 or TRBV7-9 411 411/27418 1.499 +10 TRBV6-2 or TRBV6-3 270 270/27418 0.9848 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_compare_geneV_TCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_compare_geneV_TCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + V-GENE input1.csv input2.csv mean +1 TRBV20-1 19.1289 0.0 9.5645 +2 TRBV12-3 or TRBV12-4 0.0 12.3568 6.1784 +3 TRBV29-1 7.4976 0.0 3.7488 +4 TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6 0.0 7.455 3.7275 +5 TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6 5.8226 0.0 2.9113 +6 TRBV6-1 or TRBV6-5 or TRBV6-6 0.0 5.7882 2.8941 +7 TRBV19 0.0 4.8545 2.4272 +8 TRBV2 4.7441 0.0 2.3721 +9 TRBV10-3 3.506 0.0 1.7530 +10 TRBV27 0.0 2.8704 1.4352 +11 TRBV4-1 0.0 2.2066 1.1033 +12 TRBV5-1 2.1119 0.0 1.0559 +13 TRBV7-9 0.0 2.0862 1.0431 +14 TRBV9 1.994 0.0 0.9970 +15 TRBV28 1.9698 0.0 0.9849 +16 TRBV18 0.0 1.7178 0.8589 +17 TRBV3-1 1.6195 0.0 0.8097 +18 TRBV11-1 or TRBV11-3 or TRBV7-9 0.0 1.499 0.7495 +19 TRBV25-1 1.1132 0.0 0.5566 +20 TRBV6-2 or TRBV6-3 0.0 0.9848 0.4924 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_usage_geneJ_BCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_usage_geneJ_BCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + J-GENE AA JUNCTION Reads Reads/Total Frequency % +1 IGHJ4 CTREEQYSSWYFDFW 191 191/240554 0.0794 +2 IGHJ6 CARGYYDSSGYYGVGQYYYYYMDVW 133 133/240554 0.0553 +3 IGHJ6 CARGMVRGVNYYYYYGMDVW 119 119/240554 0.0495 +4 IGHJ6 CARDRDLKDHHIAAAGSGYYYGMDVW 115 115/240554 0.0478 +5 IGHJ4 CARGTWYNDGWPHFDYW 107 107/240554 0.0445 +6 IGHJ3 CARSYYYGSGSYLAYAFDIW 104 104/240554 0.0432 +7 IGHJ4 CARDLGVLGYCSGGSCYSHVW 102 102/240554 0.0424 +8 IGHJ6 CASFPEQQLKWYGMDVW 101 101/240554 0.042 +9 IGHJ3 CASTESGGYYFDAFDIW 97 97/240554 0.0403 +10 IGHJ4 CARVLGDSFDYW 97 97/240554 0.0403 +11 IGHJ4 CATITMAYYFDYW 95 95/240554 0.0395 +12 IGHJ4 CARDPRSGYDFDYW 95 95/240554 0.0395 +13 IGHJ6 CARGGGSYPYYYYGMDVW 93 93/240554 0.0387 +14 IGHJ3 CARDHSTAEDAFDIW 92 92/240554 0.0382 +15 IGHJ4 CARDGGQLGIYFDYW 89 89/240554 0.037 +16 IGHJ6 CARDGYDSSGYYVGGALRLGVLQSYYGMDVW 88 88/240554 0.0366 +17 IGHJ4 CATDPARITDTDYW 88 88/240554 0.0366 +18 IGHJ3 CARVRELDAFDIW 88 88/240554 0.0366 +19 IGHJ4 CARGLPRPYSGSYSGFDYW 88 88/240554 0.0366 +20 IGHJ4 CARAGRVTMIVVVIKPLDYW 87 87/240554 0.0362 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_usage_geneJ_BCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_usage_geneJ_BCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,4 @@ + J-GENE Reads Reads/Total Frequency % +1 IGHJ4 10 10/20 50.0000 +2 IGHJ6 6 6/20 30.0000 +3 IGHJ3 4 4/20 20.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_usage_geneJ_BCR_output2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_usage_geneJ_BCR_output2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,4 @@ + J-GENE Frequency % +1 IGHJ4 50 +2 IGHJ6 30 +3 IGHJ3 20 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_usage_geneJ_BCR_output3.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_usage_geneJ_BCR_output3.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,3 @@ + input % +Dominant J-GENE IGHJ4 +Frequency 50.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_usage_geneJ_TCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_usage_geneJ_TCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + J-GENE AA JUNCTION Reads Reads/Total Frequency % +1 TRBJ2-3 CASSSTDTQYF 3569 3569/56731 6.2911 +2 TRBJ2-3 CASRLVPDTQYF 2898 2898/56731 5.1083 +3 TRBJ1-1 CASSLSGNTEAFF 673 673/56731 1.1863 +4 TRBJ2-1 CASSSFDEQFF 544 544/56731 0.9589 +5 TRBJ1-1 CASSEGGWTEAFF 399 399/56731 0.7033 +6 TRBJ2-3 CASSPGSTDTQYF 332 332/56731 0.5852 +7 TRBJ2-1 CASSEIGQGANEQFF 203 203/56731 0.3578 +8 TRBJ1-1 CASSVLGVMNTEAFF 182 182/56731 0.3208 +9 TRBJ2-7 CASSYMSSGSEQYF 105 105/56731 0.1851 +10 TRBJ2-1 CSAFLGGTQFF 104 104/56731 0.1833 +11 TRBJ2-3 CASSRTETQYF 95 95/56731 0.1675 +12 TRBJ1-1 CASSSRDPLNTEAFF 85 85/56731 0.1498 +13 TRBJ1-6 CASMGGLNIYNSPLHF 78 78/56731 0.1375 +14 TRBJ1-1 CASSEHGRAAEAFF 73 73/56731 0.1287 +15 TRBJ1-5 CASSVRRYSNQPQHF 69 69/56731 0.1216 +16 TRBJ1-1 CSASRGEEAFF 69 69/56731 0.1216 +17 TRBJ2-1 CASSKSGGAFNEQFF 63 63/56731 0.1111 +18 TRBJ2-1 CASSSPYANNEQFF 61 61/56731 0.1075 +19 TRBJ2-3 CASSLIPGQYQYF 59 59/56731 0.104 +20 TRBJ2-3 CASSFRTGFTDTQYF 55 55/56731 0.0969 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_usage_geneJ_TCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_usage_geneJ_TCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,7 @@ + J-GENE Reads Reads/Total Frequency % +1 TRBJ1-1 6 6/20 30.0000 +2 TRBJ2-3 6 6/20 30.0000 +3 TRBJ2-1 5 5/20 25.0000 +4 TRBJ1-5 1 1/20 5.0000 +5 TRBJ1-6 1 1/20 5.0000 +6 TRBJ2-7 1 1/20 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_usage_geneJ_TCR_output2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_usage_geneJ_TCR_output2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,7 @@ + J-GENE Frequency % +1 TRBJ1-1 30 +2 TRBJ2-3 30 +3 TRBJ2-1 25 +4 TRBJ1-5 5 +5 TRBJ1-6 5 +6 TRBJ2-7 5 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_usage_geneJ_TCR_output3.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_usage_geneJ_TCR_output3.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,3 @@ + input1.csv % +Dominant J-GENE TRBJ1-1 +Frequency 30.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_usage_geneV_BCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_usage_geneV_BCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + V-GENE AA JUNCTION Reads Reads/Total Frequency % +1 IGHV3-23 or IGHV3-23D CTREEQYSSWYFDFW 84 84/240554 0.0349 +2 IGHV3-11 CARGMVRGVNYYYYYGMDVW 78 78/240554 0.0324 +3 IGHV1-69 CASRMVRGVILPPYYYYYMDVW 74 74/240554 0.0308 +4 IGHV1-46 CARDRDLKDHHIAAAGSGYYYGMDVW 74 74/240554 0.0308 +5 IGHV7-4-1 CARASSHHYCSGGSCYSYYYYYYYMDVW 72 72/240554 0.0299 +6 IGHV4-59 or IGHV4-61 CARGTWYNDGWPHFDYW 71 71/240554 0.0295 +7 IGHV1-18 CARELYVWGSRHEVFDIW 71 71/240554 0.0295 +8 IGHV1-46 CASAGGVYTSGWHGTFYW 70 70/240554 0.0291 +9 IGHV3-33 CAKGGGSYYGVYYFDYW 69 69/240554 0.0287 +10 IGHV1-24 CATGDYDVLTGNYRAFW 67 67/240554 0.0279 +11 IGHV4-59 or IGHV4-61 CARDLGYSGSYLGRAFDIW 66 66/240554 0.0274 +12 IGHV3-33 CARDLHPRARGVIVIPGYW 65 65/240554 0.027 +13 IGHV1-69 CARLGRLERSPYYYMDVW 64 64/240554 0.0266 +14 IGHV4-34 CARVYPYDSSSWQAPYYYGMDVW 64 64/240554 0.0266 +15 IGHV1-69 CARDSSGGTDYYYYYMDVW 62 62/240554 0.0258 +16 IGHV3-49 CTRDRGERQYDAFDIW 61 61/240554 0.0254 +17 IGHV3-49 CTRPRGIVISAGIYFDYW 61 61/240554 0.0254 +18 IGHV1-69 CARDPVLYCGGDCSSSDAFDIW 60 60/240554 0.0249 +19 IGHV7-4-1 CARDTLYPPNYYGSGSYEGMDVW 60 60/240554 0.0249 +20 IGHV1-69 CARPRIAAAVYWYFDLW 60 60/240554 0.0249 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_usage_geneV_BCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_usage_geneV_BCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ + V-GENE Reads Reads/Total Frequency % +1 IGHV1-69 5 5/20 25.0000 +2 IGHV1-46 2 2/20 10.0000 +3 IGHV3-33 2 2/20 10.0000 +4 IGHV3-49 2 2/20 10.0000 +5 IGHV4-59 or IGHV4-61 2 2/20 10.0000 +6 IGHV7-4-1 2 2/20 10.0000 +7 IGHV1-18 1 1/20 5.0000 +8 IGHV1-24 1 1/20 5.0000 +9 IGHV3-11 1 1/20 5.0000 +10 IGHV3-23 or IGHV3-23D 1 1/20 5.0000 +11 IGHV4-34 1 1/20 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_usage_geneV_BCR_output2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_usage_geneV_BCR_output2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ + V-GENE Frequency % +1 IGHV1-69 25.0000 +2 IGHV1-46 10.0000 +3 IGHV3-33 10.0000 +4 IGHV3-49 10.0000 +5 IGHV4-59 or IGHV4-61 10.0000 +6 IGHV7-4-1 10.0000 +7 IGHV1-18 5.0000 +8 IGHV1-24 5.0000 +9 IGHV3-11 5.0000 +10 IGHV3-23 or IGHV3-23D 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_usage_geneV_BCR_output3.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_usage_geneV_BCR_output3.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,3 @@ + input % +Dominant V-GENE IGHV1-69 +Frequency 25.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_usage_geneV_TCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_usage_geneV_TCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + V-GENE AA JUNCTION Reads Reads/Total Frequency % +1 TRBV2 CASSSTDTQYF 3545 3545/56731 6.2488 +2 TRBV2 CASRLVPDTQYF 2893 2893/56731 5.0995 +3 TRBV13 CASSLSGNTEAFF 670 670/56731 1.181 +4 TRBV27 CASSSFDEQFF 544 544/56731 0.9589 +5 TRBV2 CASSEGGWTEAFF 398 398/56731 0.7016 +6 TRBV5-1 CASSPGSTDTQYF 329 329/56731 0.5799 +7 TRBV2 CASSEIGQGANEQFF 201 201/56731 0.3543 +8 TRBV10-2 CASSVLGVMNTEAFF 181 181/56731 0.319 +9 TRBV20-1 CSAFLGGTQFF 104 104/56731 0.1833 +10 TRBV12-3 or TRBV12-4 CASSRTETQYF 94 94/56731 0.1657 +11 TRBV12-3 or TRBV12-4 CASSSRDPLNTEAFF 84 84/56731 0.1481 +12 TRBV2 CASMGGLNIYNSPLHF 77 77/56731 0.1357 +13 TRBV25-1 CASSEHGRAAEAFF 72 72/56731 0.1269 +14 TRBV9 CASSVRRYSNQPQHF 69 69/56731 0.1216 +15 TRBV20-1 CSASRGEEAFF 69 69/56731 0.1216 +16 TRBV2 CASSKSGGAFNEQFF 62 62/56731 0.1093 +17 TRBV27 CASSLIPGQYQYF 59 59/56731 0.104 +18 TRBV7-8 CASSFRTGFTDTQYF 55 55/56731 0.0969 +19 TRBV10-2 CASSEMGNEQFF 52 52/56731 0.0917 +20 TRBV25-1 CASSVTGYEQFF 49 49/56731 0.0864 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_usage_geneV_TCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_usage_geneV_TCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ + V-GENE Reads Reads/Total Frequency % +1 TRBV2 6 6/20 30.0000 +2 TRBV10-2 2 2/20 10.0000 +3 TRBV12-3 or TRBV12-4 2 2/20 10.0000 +4 TRBV20-1 2 2/20 10.0000 +5 TRBV25-1 2 2/20 10.0000 +6 TRBV27 2 2/20 10.0000 +7 TRBV13 1 1/20 5.0000 +8 TRBV5-1 1 1/20 5.0000 +9 TRBV7-8 1 1/20 5.0000 +10 TRBV9 1 1/20 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_usage_geneV_TCR_output2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_usage_geneV_TCR_output2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ + V-GENE Frequency % +1 TRBV2 30.0000 +2 TRBV10-2 10.0000 +3 TRBV12-3 or TRBV12-4 10.0000 +4 TRBV20-1 10.0000 +5 TRBV25-1 10.0000 +6 TRBV27 10.0000 +7 TRBV13 5.0000 +8 TRBV5-1 5.0000 +9 TRBV7-8 5.0000 +10 TRBV9 5.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/gene_usage_geneV_TCR_output3.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_usage_geneV_TCR_output3.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,3 @@ + input1.csv % +Dominant V-GENE TRBV2 +Frequency 30.0000 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def1_BCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def1_BCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + AA JUNCTION Reads Reads/Total Frequency % +1 CTREEQYSSWYFDFW 191 191/240554 0.0794 +2 CARGMVRGVNYYYYYGMDVW 119 119/240554 0.0495 +3 CARGTWYNDGWPHFDYW 107 107/240554 0.0445 +4 CARDLGVLGYCSGGSCYSHVW 102 102/240554 0.0424 +5 CARVLGDSFDYW 97 97/240554 0.0403 +6 CATITMAYYFDYW 95 95/240554 0.0395 +7 CARGGGSYPYYYYGMDVW 93 93/240554 0.0387 +8 CARDGGQLGIYFDYW 89 89/240554 0.037 +9 CARGLPRPYSGSYSGFDYW 88 88/240554 0.0366 +10 CARVRELDAFDIW 88 88/240554 0.0366 +11 CARVQYVWDSPGAFDIW 86 86/240554 0.0358 +12 CARGQGTVTTEIDYW 86 86/240554 0.0358 +13 CARDRANYGSGSPIDYW 85 85/240554 0.0353 +14 CARLGRLERSPYYYMDVW 85 85/240554 0.0353 +15 CARGPFYCSGGSCNLHYYYGMDVW 84 84/240554 0.0349 +16 CARDDSTGGNWDAFDIW 84 84/240554 0.0349 +17 CARYKRGGIAVAGTLSSSFDYW 84 84/240554 0.0349 +18 CARINYYDSSGYYHKGMYYFDYW 83 83/240554 0.0345 +19 CARVGSYSGIRAFDIW 83 83/240554 0.0345 +20 CARGPRHYDSSGYCVKLDYW 82 82/240554 0.0341 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def1_BCR_input2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def1_BCR_input2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + AA JUNCTION Reads Reads/Total Frequency % +1 CARGYYDSSGYYGVGQYYYYYMDVW 133 133/198331 0.0671 +2 CARGMVRGVNYYYYYGMDVW 122 122/198331 0.0615 +3 CARDRDLKDHHIAAAGSGYYYGMDVW 115 115/198331 0.058 +4 CARSYYYGSGSYLAYAFDIW 104 104/198331 0.0524 +5 CARDLGVLGYCSGGSCYSHVW 101 101/198331 0.0509 +6 CASFPEQQLKWYGMDVW 101 101/198331 0.0509 +7 CASTESGGYYFDAFDIW 97 97/198331 0.0489 +8 CARDPRSGYDFDYW 95 95/198331 0.0479 +9 CARDHSTAEDAFDIW 92 92/198331 0.0464 +10 CARDGYDSSGYYVGGALRLGVLQSYYGMDVW 88 88/198331 0.0444 +11 CATDPARITDTDYW 88 88/198331 0.0444 +12 CARAGRVTMIVVVIKPLDYW 87 87/198331 0.0439 +13 CARGEGYGDCW 86 86/198331 0.0434 +14 CARAGDYGSGTNAFDIW 85 85/198331 0.0429 +15 CARLGRLERSPYYYMDVW 84 84/198331 0.0424 +16 CARDGIAAATSGLDVW 84 84/198331 0.0424 +17 CARDVEYYYDSSGQYFDYW 84 84/198331 0.0424 +18 CARDRHCSGGSCRGLW 83 83/198331 0.0418 +19 CARVGSYSGIRAFDIW 82 82/198331 0.0413 +20 CARGDLVVVRGVINQGKLDYW 81 81/198331 0.0408 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def1_BCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def1_BCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ + AA JUNCTION input1.csv Reads/Total input1.csv Relative Frequency % input2.csv Reads/Total input2.csv Relative Frequency % Num of Patients +1 CARGMVRGVNYYYYYGMDVW 119/240554 0.0495 122/198331 0.0615 2 +3 CARDLGVLGYCSGGSCYSHVW 102/240554 0.0424 101/198331 0.0509 2 +13 CARLGRLERSPYYYMDVW 85/240554 0.0353 84/198331 0.0424 2 +18 CARVGSYSGIRAFDIW 83/240554 0.0345 82/198331 0.0413 2 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def1_BCR_parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def1_BCR_parameters.txt Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Remove Clonotypes With Reads Fewer Than Threshold?: Yes, +Keep Clonotypes with Number of Reads more than: 3 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def1_TCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def1_TCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + AA JUNCTION Reads Reads/Total Frequency % +1 CASSSTDTQYF 3569 3569/56731 6.2911 +2 CASSLSGNTEAFF 673 673/56731 1.1863 +3 CASSEGGWTEAFF 399 399/56731 0.7033 +4 CASSEIGQGANEQFF 203 203/56731 0.3578 +5 CASSYMSSGSEQYF 105 105/56731 0.1851 +6 CASSRTETQYF 95 95/56731 0.1675 +7 CASSSRDPLNTEAFF 85 85/56731 0.1498 +8 CASMGGLNIYNSPLHF 78 78/56731 0.1375 +9 CSASRGEEAFF 69 69/56731 0.1216 +10 CASSKSGGAFNEQFF 63 63/56731 0.1111 +11 CASSLIPGQYQYF 59 59/56731 0.104 +12 CASSEMGNEQFF 52 52/56731 0.0917 +13 CASSPEVEGQPQHF 48 48/56731 0.0846 +14 CAITGTAGNTEAFF 47 47/56731 0.0828 +15 CSANRGEEAFF 45 45/56731 0.0793 +16 CAWSVGAEAFF 44 44/56731 0.0776 +17 CASSPGTAEAFF 42 42/56731 0.074 +18 CASSASGYEQYF 40 40/56731 0.0705 +19 CASSRGLNGADTQYF 40 40/56731 0.0705 +20 CASSRQIEAEAFF 39 39/56731 0.0687 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def1_TCR_input2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def1_TCR_input2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + AA JUNCTION Reads Reads/Total Frequency % +1 CASRLVPDTQYF 2898 2898/54828 5.2856 +2 CASSSFDEQFF 544 544/54828 0.9922 +3 CASSPGSTDTQYF 332 332/54828 0.6055 +4 CASSVLGVMNTEAFF 182 182/54828 0.3319 +5 CSAFLGGTQFF 104 104/54828 0.1897 +6 CASSSRDPLNTEAFF 81 81/54828 0.1477 +7 CASSEHGRAAEAFF 73 73/54828 0.1331 +8 CASSVRRYSNQPQHF 69 69/54828 0.1258 +9 CASSKSGGAFNEQFF 62 62/54828 0.1131 +10 CASSSPYANNEQFF 61 61/54828 0.1113 +11 CASSFRTGFTDTQYF 55 55/54828 0.1003 +12 CASSVTGYEQFF 49 49/54828 0.0894 +13 CATATSGSTDTQYF 47 47/54828 0.0857 +14 CAITGTAGNTEAFF 47 47/54828 0.0857 +15 CASSFRAPNTDTQYF 46 46/54828 0.0839 +16 CSVGSGEGYEQYF 44 44/54828 0.0803 +17 CSGIAGSTDTQYF 43 43/54828 0.0784 +18 CSARRLGTIYF 41 41/54828 0.0748 +19 CASGGNTQYF 40 40/54828 0.073 +20 CASLSSNEQYF 39 39/54828 0.0711 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def1_TCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def1_TCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,4 @@ + AA JUNCTION input1.csv Reads/Total input1.csv Relative Frequency % input2.csv Reads/Total input2.csv Relative Frequency % Num of Patients +1 CASSSRDPLNTEAFF 85/56731 0.1498 81/54828 0.1477 2 +2 CASSKSGGAFNEQFF 63/56731 0.1111 62/54828 0.1131 2 +3 CAITGTAGNTEAFF 47/56731 0.0828 47/54828 0.0857 2 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def1_TCR_parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def1_TCR_parameters.txt Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Remove Clonotypes With Reads Fewer Than Threshold?: Yes, +Keep Clonotypes with Number of Reads more than: 2 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def2_BCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def2_BCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + V-GENE AA JUNCTION Reads Reads/Total Frequency % +1 IGHV3-23 or IGHV3-23D CTREEQYSSWYFDFW 84 84/240554 0.0349 +2 IGHV1-69 CASRMVRGVILPPYYYYYMDVW 74 74/240554 0.0308 +3 IGHV7-4-1 CARASSHHYCSGGSCYSYYYYYYYMDVW 72 72/240554 0.0299 +4 IGHV1-18 CARELYVWGSRHEVFDIW 71 71/240554 0.0295 +5 IGHV3-33 CAKGGGSYYGVYYFDYW 69 69/240554 0.0287 +6 IGHV4-59 or IGHV4-61 CARDLGYSGSYLGRAFDIW 66 66/240554 0.0274 +7 IGHV3-33 CARDLHPRARGVIVIPGYW 65 65/240554 0.027 +8 IGHV1-69 CARLGRLERSPYYYMDVW 64 64/240554 0.0266 +9 IGHV1-69 CARDSSGGTDYYYYYMDVW 62 62/240554 0.0258 +10 IGHV3-49 CTRPRGIVISAGIYFDYW 61 61/240554 0.0254 +11 IGHV1-69 CARDPVLYCGGDCSSSDAFDIW 60 60/240554 0.0249 +12 IGHV7-4-1 CARDTLYPPNYYGSGSYEGMDVW 60 60/240554 0.0249 +13 IGHV4-39 CAGRASPFGPSYYFNSW 60 60/240554 0.0249 +14 IGHV3-9 CAKDISLRDEGDSSVGYDYW 59 59/240554 0.0245 +15 IGHV4-39 CARLMLGTMVKTPDAFDIW 59 59/240554 0.0245 +16 IGHV1-3 CARALPPRYCSGGSCYYPSNWGQGTLVGYYPSNW 59 59/240554 0.0245 +17 IGHV3-30 or IGHV3-30-3 CARDQFGVVTVKGGYFQHW 58 58/240554 0.0241 +18 IGHV1-3 CARERYYNRGAFDIW 57 57/240554 0.0237 +19 IGHV3-9 CAIGRGVISTFFDYW 57 57/240554 0.0237 +20 IGHV3-23 or IGHV3-23D CAKERALGFGEPHYW 56 56/240554 0.0233 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def2_BCR_input2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def2_BCR_input2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + V-GENE AA JUNCTION Reads Reads/Total Frequency % +1 IGHV3-11 CARGMVRGVNYYYYYGMDVW 78 78/251182 0.0311 +2 IGHV1-46 CARDRDLKDHHIAAAGSGYYYGMDVW 74 74/251182 0.0295 +3 IGHV4-59 or IGHV4-61 CARGTWYNDGWPHFDYW 71 71/251182 0.0283 +4 IGHV1-46 CASAGGVYTSGWHGTFYW 70 70/251182 0.0279 +5 IGHV3-33 CAKGGGSYYGVYYFDYW 68 68/251182 0.0271 +6 IGHV1-24 CATGDYDVLTGNYRAFW 67 67/251182 0.0267 +7 IGHV3-33 CARDLHPRARGVIVIPGYW 65 65/251182 0.0259 +8 IGHV4-34 CARVYPYDSSSWQAPYYYGMDVW 64 64/251182 0.0255 +9 IGHV3-49 CTRDRGERQYDAFDIW 61 61/251182 0.0243 +10 IGHV1-69 CARDPVLYCGGDCSSSDAFDIW 60 60/251182 0.0239 +11 IGHV1-69 CARPRIAAAVYWYFDLW 60 60/251182 0.0239 +12 IGHV3-21 CARDHFVWGSPSPMDIW 60 60/251182 0.0239 +13 IGHV3-23 or IGHV3-23D CARVGSYSGIRAFDIW 59 59/251182 0.0235 +14 IGHV4-39 CARLMLGTMVKTPDAFDIW 59 59/251182 0.0235 +15 IGHV4-59 or IGHV4-61 CARHDGIAAAGHFDYW 59 59/251182 0.0235 +16 IGHV1-69 CAREEKFGELLERSYYYYYYMDVW 59 59/251182 0.0235 +17 IGHV1-69 CARGYYDSSGYYGVGQYYYYYMDVW 58 58/251182 0.0231 +18 IGHV3-33 CAKGPRMVRGVLDYW 57 57/251182 0.0227 +19 IGHV3-9 CAIGRGVISTFFDYW 57 57/251182 0.0227 +20 IGHV3-64 CATEHIAAAGEASAFDIW 57 57/251182 0.0227 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def2_BCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def2_BCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ + V-GENE AA JUNCTION input1.csv Reads/Total input1.csv Relative Frequency % input2.csv Reads/Total input2.csv Relative Frequency % Num of Patients +4 IGHV3-33 CAKGGGSYYGVYYFDYW 69/240554 0.0287 68/251182 0.0271 2 +6 IGHV3-33 CARDLHPRARGVIVIPGYW 65/240554 0.027 65/251182 0.0259 2 +10 IGHV1-69 CARDPVLYCGGDCSSSDAFDIW 60/240554 0.0249 60/251182 0.0239 2 +14 IGHV4-39 CARLMLGTMVKTPDAFDIW 59/240554 0.0245 59/251182 0.0235 2 +18 IGHV3-9 CAIGRGVISTFFDYW 57/240554 0.0237 57/251182 0.0227 2 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def2_BCR_parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def2_BCR_parameters.txt Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Remove Clonotypes With Reads Fewer Than Threshold?: Yes, +Keep Clonotypes with Number of Reads more than: 3 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def2_TCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def2_TCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + V-GENE AA JUNCTION Reads Reads/Total Frequency % +1 TRBV2 CASSSTDTQYF 3545 3545/56731 6.2488 +2 TRBV2 CASRLVPDTQYF 2893 2893/56731 5.0995 +3 TRBV13 CASSLSGNTEAFF 670 670/56731 1.181 +4 TRBV2 CASSEGGWTEAFF 398 398/56731 0.7016 +5 TRBV5-1 CASSPGSTDTQYF 329 329/56731 0.5799 +6 TRBV2 CASSEIGQGANEQFF 201 201/56731 0.3543 +7 TRBV20-1 CSAFLGGTQFF 104 104/56731 0.1833 +8 TRBV12-3 or TRBV12-4 CASSSRDPLNTEAFF 84 84/56731 0.1481 +9 TRBV25-1 CASSEHGRAAEAFF 72 72/56731 0.1269 +10 TRBV20-1 CSASRGEEAFF 69 69/56731 0.1216 +11 TRBV27 CASSLIPGQYQYF 59 59/56731 0.104 +12 TRBV10-2 CASSEMGNEQFF 52 52/56731 0.0917 +13 TRBV3-1 CASSPEVEGQPQHF 48 48/56731 0.0846 +14 TRBV7-8 CASSFRAPNTDTQYF 46 46/56731 0.0811 +15 TRBV30 CAWSVGAEAFF 44 44/56731 0.0776 +16 TRBV29-1 CSGIAGSTDTQYF 43 43/56731 0.0758 +17 TRBV20-1 CSARRLGTIYF 41 41/56731 0.0723 +18 TRBV2 CASGGNTQYF 40 40/56731 0.0705 +19 TRBV2 CASLSSNEQYF 39 39/56731 0.0687 +20 TRBV25-1 CASTSGTGSDTQYF 37 37/56731 0.0652 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def2_TCR_input2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def2_TCR_input2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + V-GENE AA JUNCTION Reads Reads/Total Frequency % +1 TRBV2 CASRLVPDTQYF 2931 2931/57218 5.1225 +2 TRBV13 CASSLSGNTEAFF 753 753/57218 1.316 +3 TRBV27 CASSSFDEQFF 544 544/57218 0.9507 +4 TRBV5-1 CASSPGSTDTQYF 322 322/57218 0.5628 +5 TRBV10-2 CASSVLGVMNTEAFF 181 181/57218 0.3163 +6 TRBV20-1 CSAFLGGTQFF 107 107/57218 0.187 +7 TRBV12-3 or TRBV12-4 CASSRTETQYF 94 94/57218 0.1643 +8 TRBV2 CASMGGLNIYNSPLHF 77 77/57218 0.1346 +9 TRBV25-1 CASSEHGRAAEAFF 74 74/57218 0.1293 +10 TRBV9 CASSVRRYSNQPQHF 69 69/57218 0.1206 +11 TRBV2 CASSKSGGAFNEQFF 62 62/57218 0.1084 +12 TRBV7-8 CASSFRTGFTDTQYF 55 55/57218 0.0961 +13 TRBV25-1 CASSVTGYEQFF 49 49/57218 0.0856 +14 TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6 CASSYMSSGSEQYF 47 47/57218 0.0821 +15 TRBV20-1 CSANRGEEAFF 45 45/57218 0.0786 +16 TRBV29-1 CSVGSGEGYEQYF 44 44/57218 0.0769 +17 TRBV12-3 or TRBV12-4 CASSPGTAEAFF 42 42/57218 0.0734 +18 TRBV7-9 CASSSPYANNEQFF 41 41/57218 0.0717 +19 TRBV25-1 CASSASGYEQYF 40 40/57218 0.0699 +20 TRBV12-3 or TRBV12-4 CASSRQIEAEAFF 38 38/57218 0.0664 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def2_TCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def2_TCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ + V-GENE AA JUNCTION input1.csv Reads/Total input1.csv Relative Frequency % input2.csv Reads/Total input2.csv Relative Frequency % Num of Patients +1 TRBV2 CASRLVPDTQYF 2893/56731 5.0995 2931/57218 5.1225 2 +2 TRBV13 CASSLSGNTEAFF 670/56731 1.181 753/57218 1.316 2 +3 TRBV5-1 CASSPGSTDTQYF 329/56731 0.5799 322/57218 0.5628 2 +4 TRBV20-1 CSAFLGGTQFF 104/56731 0.1833 107/57218 0.187 2 +5 TRBV25-1 CASSEHGRAAEAFF 72/56731 0.1269 74/57218 0.1293 2 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def2_TCR_parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def2_TCR_parameters.txt Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Remove Clonotypes With Reads Fewer Than Threshold?: Yes, +Keep Clonotypes with Number of Reads more than: 2 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def3_BCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def3_BCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + J-GENE AA JUNCTION Reads Reads/Total Frequency % +1 IGHJ4 CTREEQYSSWYFDFW 191 191/240554 0.0794 +2 IGHJ6 CARGMVRGVNYYYYYGMDVW 119 119/240554 0.0495 +3 IGHJ4 CARGTWYNDGWPHFDYW 107 107/240554 0.0445 +4 IGHJ4 CARDLGVLGYCSGGSCYSHVW 102 102/240554 0.0424 +5 IGHJ3 CASTESGGYYFDAFDIW 97 97/240554 0.0403 +6 IGHJ4 CATITMAYYFDYW 95 95/240554 0.0395 +7 IGHJ6 CARGGGSYPYYYYGMDVW 93 93/240554 0.0387 +8 IGHJ4 CARDGGQLGIYFDYW 89 89/240554 0.037 +9 IGHJ6 CARDGYDSSGYYVGGALRLGVLQSYYGMDVW 88 88/240554 0.0366 +10 IGHJ4 CATDPARITDTDYW 88 88/240554 0.0366 +11 IGHJ4 CARGLPRPYSGSYSGFDYW 88 88/240554 0.0366 +12 IGHJ4 CARGEGYGDCW 86 86/240554 0.0358 +13 IGHJ4 CARGQGTVTTEIDYW 86 86/240554 0.0358 +14 IGHJ3 CARAGDYGSGTNAFDIW 85 85/240554 0.0353 +15 IGHJ4 CARYKRGGIAVAGTLSSSFDYW 84 84/240554 0.0349 +16 IGHJ4 CARDVEYYYDSSGQYFDYW 84 84/240554 0.0349 +17 IGHJ6 CARDGIAAATSGLDVW 84 84/240554 0.0349 +18 IGHJ4 CARINYYDSSGYYHKGMYYFDYW 83 83/240554 0.0345 +19 IGHJ4 CARGPRHYDSSGYCVKLDYW 82 82/240554 0.0341 +20 IGHJ6 CARGVSGYYNFFYMDVW 81 81/240554 0.0337 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def3_BCR_input2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def3_BCR_input2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + J-GENE AA JUNCTION Reads Reads/Total Frequency % +1 IGHJ6 CARGYYDSSGYYGVGQYYYYYMDVW 133 133/229003 0.0581 +2 IGHJ6 CARGMVRGVNYYYYYGMDVW 124 124/229003 0.0541 +3 IGHJ6 CARDRDLKDHHIAAAGSGYYYGMDVW 115 115/229003 0.0502 +4 IGHJ3 CARSYYYGSGSYLAYAFDIW 104 104/229003 0.0454 +5 IGHJ6 CASFPEQQLKWYGMDVW 101 101/229003 0.0441 +6 IGHJ4 CARVLGDSFDYW 97 97/229003 0.0424 +7 IGHJ4 CARDPRSGYDFDYW 95 95/229003 0.0415 +8 IGHJ3 CARDHSTAEDAFDIW 92 92/229003 0.0402 +9 IGHJ6 CARDGYDSSGYYVGGALRLGVLQSYYGMDVW 88 88/229003 0.0384 +10 IGHJ3 CARVRELDAFDIW 88 88/229003 0.0384 +11 IGHJ4 CARAGRVTMIVVVIKPLDYW 87 87/229003 0.038 +12 IGHJ3 CARVQYVWDSPGAFDIW 86 86/229003 0.0376 +13 IGHJ6 CARLGRLERSPYYYMDVW 85 85/229003 0.0371 +14 IGHJ4 CARDRANYGSGSPIDYW 85 85/229003 0.0371 +15 IGHJ6 CARGPFYCSGGSCNLHYYYGMDVW 84 84/229003 0.0367 +16 IGHJ3 CARDDSTGGNWDAFDIW 84 84/229003 0.0367 +17 IGHJ6 CARDGIAAATSGLDVW 83 83/229003 0.0362 +18 IGHJ5 CARDRHCSGGSCRGLW 83 83/229003 0.0362 +19 IGHJ3 CARVGSYSGIRAFDIW 83 83/229003 0.0362 +20 IGHJ4 CARGDLVVVRGVINQGKLDYW 81 81/229003 0.0354 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def3_BCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def3_BCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,4 @@ + J-GENE AA JUNCTION input1.csv Reads/Total input1.csv Relative Frequency % input2.csv Reads/Total input2.csv Relative Frequency % Num of Patients +1 IGHJ6 CARGMVRGVNYYYYYGMDVW 119/240554 0.0495 124/229003 0.0541 2 +8 IGHJ6 CARDGYDSSGYYVGGALRLGVLQSYYGMDVW 88/240554 0.0366 88/229003 0.0384 2 +16 IGHJ6 CARDGIAAATSGLDVW 84/240554 0.0349 83/229003 0.0362 2 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def3_BCR_parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def3_BCR_parameters.txt Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Remove Clonotypes With Reads Fewer Than Threshold?: Yes, +Keep Clonotypes with Number of Reads more than: 3 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def3_TCR_input1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def3_TCR_input1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + J-GENE AA JUNCTION Reads Reads/Total Frequency % +1 TRBJ2-3 CASSSTDTQYF 3569 3569/56731 6.2911 +2 TRBJ1-1 CASSLSGNTEAFF 673 673/56731 1.1863 +3 TRBJ2-1 CASSSFDEQFF 544 544/56731 0.9589 +4 TRBJ1-1 CASSEGGWTEAFF 399 399/56731 0.7033 +5 TRBJ2-1 CASSEIGQGANEQFF 203 203/56731 0.3578 +6 TRBJ2-7 CASSYMSSGSEQYF 105 105/56731 0.1851 +7 TRBJ2-3 CASSRTETQYF 95 95/56731 0.1675 +8 TRBJ1-1 CASSSRDPLNTEAFF 85 85/56731 0.1498 +9 TRBJ1-6 CASMGGLNIYNSPLHF 78 78/56731 0.1375 +10 TRBJ1-5 CASSVRRYSNQPQHF 69 69/56731 0.1216 +11 TRBJ2-1 CASSKSGGAFNEQFF 63 63/56731 0.1111 +12 TRBJ2-3 CASSLIPGQYQYF 59 59/56731 0.104 +13 TRBJ2-1 CASSEMGNEQFF 52 52/56731 0.0917 +14 TRBJ1-5 CASSPEVEGQPQHF 48 48/56731 0.0846 +15 TRBJ1-1 CAITGTAGNTEAFF 47 47/56731 0.0828 +16 TRBJ1-1 CSANRGEEAFF 45 45/56731 0.0793 +17 TRBJ1-1 CAWSVGAEAFF 44 44/56731 0.0776 +18 TRBJ1-1 CASSPGTAEAFF 42 42/56731 0.074 +19 TRBJ2-3 CASSRGLNGADTQYF 40 40/56731 0.0705 +20 TRBJ2-7 CASSASGYEQYF 40 40/56731 0.0705 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def3_TCR_input2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def3_TCR_input2.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ + J-GENE AA JUNCTION Reads Reads/Total Frequency % +1 TRBJ2-3 CASRLVPDTQYF 2898 2898/57339 5.0542 +2 TRBJ2-1 CASSSFDEQFF 618 618/57339 1.0778 +3 TRBJ2-3 CASSPGSTDTQYF 332 332/57339 0.579 +4 TRBJ1-1 CASSVLGVMNTEAFF 182 182/57339 0.3174 +5 TRBJ2-7 CASSYMSSGSEQYF 112 112/57339 0.1953 +6 TRBJ2-1 CSAFLGGTQFF 104 104/57339 0.1814 +7 TRBJ1-1 CASSSRDPLNTEAFF 86 86/57339 0.15 +8 TRBJ1-1 CASSEHGRAAEAFF 73 73/57339 0.1273 +9 TRBJ1-1 CSASRGEEAFF 69 69/57339 0.1203 +10 TRBJ2-1 CASSSPYANNEQFF 61 61/57339 0.1064 +11 TRBJ2-3 CASSFRTGFTDTQYF 55 55/57339 0.0959 +12 TRBJ2-1 CASSEMGNEQFF 50 50/57339 0.0872 +13 TRBJ2-1 CASSVTGYEQFF 49 49/57339 0.0855 +14 TRBJ2-3 CATATSGSTDTQYF 47 47/57339 0.082 +15 TRBJ2-3 CASSFRAPNTDTQYF 46 46/57339 0.0802 +16 TRBJ2-7 CSVGSGEGYEQYF 44 44/57339 0.0767 +17 TRBJ2-3 CSGIAGSTDTQYF 43 43/57339 0.075 +18 TRBJ1-3 CSARRLGTIYF 41 41/57339 0.0715 +19 TRBJ2-3 CASGGNTQYF 40 40/57339 0.0698 +20 TRBJ1-1 CASSRQIEAEAFF 39 39/57339 0.068 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def3_TCR_output1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def3_TCR_output1.csv Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ + J-GENE AA JUNCTION input1.csv Reads/Total input1.csv Relative Frequency % input2.csv Reads/Total input2.csv Relative Frequency % Num of Patients +1 TRBJ2-1 CASSSFDEQFF 544/56731 0.9589 618/57339 1.0778 2 +2 TRBJ2-7 CASSYMSSGSEQYF 105/56731 0.1851 112/57339 0.1953 2 +3 TRBJ1-1 CASSSRDPLNTEAFF 85/56731 0.1498 86/57339 0.15 2 +4 TRBJ2-1 CASSEMGNEQFF 52/56731 0.0917 50/57339 0.0872 2 |
| b |
| diff -r 0e37e5b73273 -r acaa8e8a0b88 test-data/public_clonos_def3_TCR_parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/public_clonos_def3_TCR_parameters.txt Mon Apr 30 04:47:52 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Remove Clonotypes With Reads Fewer Than Threshold?: Yes, +Keep Clonotypes with Number of Reads more than: 2 |