Intermediate technical release (required for vidjil-server integration)

antevolo.py

@@ -78,7 +78,6 @@ def PrintParams(params, log):
     log.info("  Output directory:\t\t" + params.output_dir)
     log.info("  Number of threads:\t\t" + str(params.num_threads) + "\n")
     log.info("  Loci:\t\t\t\t" + params.loci)
-    log.info("  Max distance between CDR3:\t" + str(params.cdr3_tau))
     log.info("  Min number of shared SHMs:\t" + str(params.min_shared_shms))
     log.info("  Use SHM model:\t\t" + str(params.model))
 
@@ -167,7 +166,8 @@ def ModifyCDRLabelerConfigFile(params, log):
 def ModifyVjFinderConfigFile(params, log):
     vj_param_dict = dict()
     vj_param_dict['loci'] = params.loci
-    vj_param_dict['germline_dir'] = os.path.join(home_directory, "data/antevolo_germline")
+    # vj_param_dict['germline_dir'] = os.path.join(home_directory, "data/antevolo_germline")
+    vj_param_dict['germline_dir'] = os.path.join(home_directory, "data/antevolo_V_crop_allelic")
     params.germline_config_file = os.path.join(params.vj_finder_config_dir, "germline_files_config.txt")
     vj_param_dict['germline_filenames_config'] = params.germline_config_file
     process_cfg.substitute_params(params.vj_finder_config_file, vj_param_dict, log)
@@ -236,11 +236,6 @@ def main(argv):
     optional_args.set_defaults(compare=False)
 
     algorithm_args = parser.add_argument_group("Algorithm arguments")
-    algorithm_args.add_argument("--tau",
-                                type=int,
-                                default=3,
-                                dest="cdr3_tau",
-                                help="Threshold for construction Hamming graph on CDR3s [default: %(default)d]")
     algorithm_args.add_argument("-s", "--min-shared-shms",
                                 type=int,
                                 default=3,

configs/antevolo/config.info.template

@@ -32,7 +32,9 @@ algorithm_params {
     model 0
 
     similar_cdr3s_params {
-        num_mismatches   3
+        num_mismatches_igh   6
+        num_mismatches_igk   3
+        num_mismatches_igl   3
         num_indels       0
     }
 

configs/vj_finder/config.info.template

@@ -36,6 +36,7 @@ io_params {
 
 algorithm_params {
     aligner_params {
+        aligner_algorithm           quadratic_dag;   quadratic_dag, lis, quadratic_dp
         word_size_v                 7
         word_size_j                 5
         min_k_coverage_v            50
@@ -56,7 +57,7 @@ algorithm_params {
         enable_filtering            true
         left_uncovered_limit        16
         right_uncovered_limit       5
-        min_v_segment_length        250
+        min_v_segment_length        220
         min_j_segment_length        30
         min_aligned_length          300
     }

data/antevolo_V_crop_allelic/human/IG/IGHD.fa

@@ -0,0 +1,54 @@
+>IGHD1-1*01
+ggtacaactggaacgac
+>IGHD1-14*01
+ggtataaccggaaccac
+>IGHD1-20*01
+ggtataactggaacgac
+>IGHD1-26*01
+ggtatagtgggagctactac
+>IGHD1-7*01
+ggtataactggaactac
+>IGHD2-15*01
+aggatattgtagtggtggtagctgctactcc
+>IGHD2-2*01
+aggatattgtagtagtaccagctgctatgcc
+>IGHD2-21*01
+agcatattgtggtggtgattgctattcc
+>IGHD2-8*01
+aggatattgtactaatggtgtatgctatacc
+>IGHD3-10*01
+gtattactatggttcggggagttattataac
+>IGHD3-16*01
+gtattatgattacgtttgggggagttatgcttatacc
+>IGHD3-22*01
+gtattactatgatagtagtggttattactac
+>IGHD3-3*01
+gtattacgatttttggagtggttattatacc
+>IGHD3-9*01
+gtattacgatattttgactggttattataac
+>IGHD4-11*01
+tgactacagtaactac
+>IGHD4-17*01
+tgactacggtgactac
+>IGHD4-23*01
+tgactacggtggtaactcc
+>IGHD4-4*01
+tgactacagtaactac
+>IGHD5-12*01
+gtggatatagtggctacgattac
+>IGHD5-18*01
+gtggatacagctatggttac
+>IGHD5-24*01
+gtagagatggctacaattac
+>IGHD5-5*01
+gtggatacagctatggttac
+>IGHD6-13*01
+gggtatagcagcagctggtac
+>IGHD6-19*01
+gggtatagcagtggctggtac
+>IGHD6-25*01
+gggtatagcagcggctac
+>IGHD6-6*01
+gagtatagcagctcgtcc
+>IGHD7-27*01
+ctaactgggga

data/antevolo_V_crop_allelic/human/IG/IGHJ.fa

@@ -0,0 +1,13 @@
+>IGHJ1*01
+gctgaatacttccagcactggggccagggcaccctggtcaccgtctcctcag
+>IGHJ2*01
+ctactggtacttcgatctctggggccgtggcaccctggtcactgtctcctcag
+>IGHJ3*01
+tgatgcttttgatgtctggggccaagggacaatggtcaccgtctcttcag
+>IGHJ4*01
+actactttgactactggggccaaggaaccctggtcaccgtctcctcag
+>IGHJ5*01
+acaactggttcgactcctggggccaaggaaccctggtcaccgtctcctcag
+>IGHJ6*01
+attactactactactacggtatggacgtctggggcaaagggaccacggtcaccgtctcctcag
+