Sasha works on revision

yana-safonova · Jul 5, 2017 · d4cf51b · d4cf51b
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commit d4cf51b
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Showing 7 changed files with 288 additions and 166 deletions.
diff --git a/py/dataset_stats.sh b/py/dataset_stats.sh
@@ -10,8 +10,12 @@ for file in "${ref_SIM_NEW}" "${ref_AGE3}" "${ref_AGE7}" "${ref_SIM}" "${ref_FLU
 do
     ./repertoire_stats.py $file
 done
-    
+
 
 ./repertoire_stats.py "/home/ashlemov/Git/ig_repertoire_constructor/src/extra/ig_quast_tool/FLU_FV_21_IGL/repertoire3.fa.gz"
 ./repertoire_stats.py "/home/ashlemov/Git/ig_repertoire_constructor/src/extra/ig_quast_tool/FLU_FV_21_IG/repertoire3.fa.gz"
 ./repertoire_stats.py "/home/ashlemov/Git/ig_repertoire_constructor/src/extra/ig_quast_tool/FLU_FV_21_IG/repertoire1.fa.gz"
+
+./repertoire_stats.py "/home/ashlemov/Git/ig_repertoire_constructor/test_dataset/igquast/SIMULATED_0.5/repertoire.fa.gz"
+./repertoire_stats.py "/home/ashlemov/Git/ig_repertoire_constructor/test_dataset/igquast/SYNTHETIC_0.5/repertoire.fa.gz"
+./repertoire_stats.py "/home/ashlemov/Git/ig_repertoire_constructor/test_dataset/igquast/SIMTCR_0.5/repertoire.fa.gz"
diff --git a/py/plot_sim.py b/py/plot_sim.py
@@ -3,17 +3,25 @@
 from plot_test import *
 
 if __name__ == "__main__":
-
-    # for i, toolname in enumerate(["igrec", "mixcr2", "presto"]):
-    #     plot_various_error_rate(igrec_dir + "/SIMULATED", what="sensitivity", out="sensitivity_%s" % toolname,
-    #                             which=[i],
-    #                             kinds=["igrec_tau3_f03", "mixcr2", "supernode"], labels=["IgReC", "MiXCR", "pRESTO"],
-    #                             legend=False)
-    #     plot_various_error_rate(igrec_dir + "/SIMULATED", what="precision", out="precision_%s" % toolname,
-    #                             which=[i],
-    #                             kinds=["igrec_tau3_f03", "mixcr2", "supernode"], labels=["IgReC", "MiXCR", "pRESTO"],
-    #                             legend=False)
-
+    plot_various_error_rate(igrec_dir + "/SIMULATED", what="sensitivity", out="TEST_Fig_9a",
+                            title="Sensitivity (SIMULATEDx10 SIMPLE)",
+                            kinds=["igrec", "mixcr2", "supernode"], labels=["IgReC", "MiXCR", "pRESTO"],
+                            multiple=True)
+    plot_various_error_rate(igrec_dir + "/SIMULATED", what="precision", out="TEST_Fig_9b",
+                            title="Precision (SIMULATEDx10 SIMPLE)",
+                            kinds=["igrec", "mixcr2", "supernode"], labels=["IgReC", "MiXCR", "pRESTO"],
+                            multiple=True)
+    plot_various_error_rate(igrec_dir + "/SIMULATED", what="sum", out="TEST_Fig_9c",
+                            title="Sensitivity + precision (SIMULATEDx10 SIMPLE)",
+                            kinds=["igrec", "mixcr2", "supernode"], labels=["IgReC", "MiXCR", "pRESTO"],
+                            multiple=True)
+    plot_various_error_rate(igrec_dir + "/SIMULATED", what="minsize", out="TEST_Fig_9d",
+                            title="Optimal minsize (SIMULATEDx10 SIMPLE)",
+                            kinds=["igrec", "mixcr2", "supernode"], labels=["IgReC", "MiXCR", "pRESTO"],
+                            which=[1, 2],  # remove IgReC's line
+                            multiple=True)
+
+    sys.exit()
     plot_various_error_rate(igrec_dir + "/SIMULATED", what="sensitivity", out="Fig_9a",
                             title="Sensitivity (SIMULATED SIMPLE)",
                             kinds=["igrec", "mixcr2", "supernode"], labels=["IgReC", "MiXCR", "pRESTO"])
@@ -81,78 +89,3 @@
                             prod_criterion=True,
                             title="Precision (SYNTHETIC)",
                             kinds=["igrec", "mixcr2", "supernode"], labels=["IgReC", "MiXCR", "pRESTO"])
-
-
-    sys.exit(0)
-    plot_various_error_rate(igrec_dir + "/SIMULATED", out="sensitivity_plus_precision", what="sum",
-                            title="SIMULATED, sensitivity + precision, simple",
-                            kinds=["igrec", "mixcr2", "supernode"], labels=["IgReC", "MiXCR", "pRESTO"])
-    plot_various_error_rate(igrec_dir + "/SIMULATED", out="optimal_minsize", what="minsize",
-                            title="SIMULATED, optimal min size, simple",
-                            kinds=["igrec", "mixcr2", "supernode"], labels=["IgReC", "MiXCR", "pRESTO"])
-
-
-    plot_various_error_rate(igrec_dir + "/SIMULATED", what="sensitivity", out="sensitivity_woans", woans=True,
-                            title="SIMULATED, sensitivity, complex",
-                            kinds=["igrec_tau3", "mixcr2", "supernode"], labels=["IgReC", "MiXCR", "pRESTO"])
-    plot_various_error_rate(igrec_dir + "/SIMULATED", what="precision", out="precision_woans", woans=True,
-                            title="SIMULATED, precision, complex",
-                            kinds=["igrec_tau3", "mixcr2", "supernode"], labels=["IgReC", "MiXCR", "pRESTO"])
-
-    plot_various_error_rate(igrec_dir + "/v_e_r_r", out="sensitivity_plus_precision_flu", what="sum",
-                            title="SYNTHETIC FLU, sensitivity + precision",
-                            kinds=["igrec", "mixcr2", "supernode"], labels=["IgReC", "MiXCR", "pRESTO"])
-
-    # plot_various_error_rate(igrec_dir + "/SIMULATED",
-    #                         kind1="igrec_tau3_f03", kind2="mixcr2",
-    #                         what="precision", out="precision_tau3")
-    # plot_various_error_rate(igrec_dir + "/SIMULATED",
-    #                         kind1="igrec_tau3_f03", kind2="mixcr2",
-    #                         what="sensitivity", out="sensitivity_tau3")
-    rocs(igrec_dir + "/SIMULATED/errate_2.0000",
-         tools=["igrec", "mixcr2", "supernode"],
-         labels=["IgReC", "MiXCR", "pRESTO"],
-         title="SIMULATED, error rate = 2, simple",
-         out="sensitivity_precision_plot_er2")
-    rocs(igrec_dir + "/SIMULATED/errate_1.0000",
-         tools=["igrec", "mixcr2", "supernode"],
-         labels=["IgReC", "MiXCR", "pRESTO"],
-         title="SIMULATED, error rate = 1, simple",
-         out="sensitivity_precision_plot_er1")
-    rocs(igrec_dir + "/SIMULATED/errate_0.5000",
-         tools=["igrec", "mixcr2", "supernode"],
-         labels=["IgReC", "MiXCR", "pRESTO"],
-         title="SIMULATED, error rate = 0.5, simple",
-         out="sensitivity_precision_plot_er05")
-
-    rocs(igrec_dir + "/SIMULATED/errate_2.0000_woans",
-         tools=["igrec"],
-         labels=["IgReC"],
-         title="SIMULATED, error rate = 2, complex",
-         out="sensitivity_precision_plot_er2_woanswer")
-    rocs(igrec_dir + "/SIMULATED/errate_1.0000_woans",
-         tools=["igrec"],
-         labels=["IgReC"],
-         title="SIMULATED, error rate = 1, complex",
-         out="sensitivity_precision_plot_er1_woanswer")
-    rocs(igrec_dir + "/SIMULATED/errate_0.5000_woans",
-         tools=["igrec"],
-         labels=["IgReC"],
-         title="SIMULATED, error rate = 0.5, complex",
-         out="sensitivity_precision_plot_er05_woanswer")
-
-    rocs(igrec_dir + "/v_e_r_r/errate_2.0000",
-         tools=["igrec", "mixcr2", "supernode"],
-         labels=["IgReC", "MiXCR", "pRESTO"],
-         title="SYNTHETIC, error rate = 2, simple",
-         out="sensitivity_precision_plot_er2_real")
-    rocs(igrec_dir + "/v_e_r_r/errate_1.0000",
-         tools=["igrec", "mixcr2", "supernode"],
-         labels=["IgReC", "MiXCR", "pRESTO"],
-         title="SYNTHETIC, error rate = 1, simple",
-         out="sensitivity_precision_plot_er1_real")
-    rocs(igrec_dir + "/v_e_r_r/errate_0.5000",
-         tools=["igrec", "mixcr2", "supernode"],
-         labels=["IgReC", "MiXCR", "pRESTO"],
-         title="SYNTHETIC, error rate = 0.5, simple",
-         out="sensitivity_precision_plot_er05_real")