Merge branch 'devel'

Genomon-Project · Jul 5, 2016 · 7d83d3b · 7d83d3b
2 parents f0ea90b + 3c73061
commit 7d83d3b
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Showing 18 changed files with 178 additions and 34 deletions.
diff --git a/config_template/genomon_v2_0_0.cfg b/config_template/genomon_v2_0_0.cfg
@@ -0,0 +1,125 @@
+# 
+# $Id: genomon_v2_0_0.cfg 117 2016-06-29 01:43:38Z aokada $
+# 
+
+###################### general
+[style]
+path = 
+remarks = 
+
+###################### mutation
+[mut]
+use_gene_rate = 0
+limited_genes = 
+#nouse_genes = NONE,-
+#limited_funcs = UTR3,UTR5,downstream,exonic,intergenic,intronic,ncRNA_exonic,ncRNA_intronic,ncRNA_splicing,splicing,upstream
+nouse_funcs = 
+#func_colors = UTR3:red:pink, UTR5:blue
+
+### special item
+# {#number_gene}
+# {#number_id}
+# {#number_mutaion_all}
+# {#number_mutaion_id}
+# {#number_mutaion_gene}
+# {#number_item}
+
+tooltip_format_checker_title1 = ID:{id}
+tooltip_format_checker_title2 = gene:{gene}
+tooltip_format_checker_partial = type[{func}], Chr:{chr}, Start:{start}, End:{end}, [{ref} -----> {alt}]
+tooltip_format_gene_title : gene:{gene}, {#number_mutaion_gene}
+tooltip_format_gene_partial : func:{func}, {#number_item}({#number_item/#number_id*100:.2}%)
+tooltip_format_id_title = ID:{id}, {#number_mutaion_id}
+tooltip_format_id_partial = func:{func}, {#number_item}
+
+### sample for subplot
+# [mut_subplot_type1_1]
+# title = bam's average depth
+# path = /path/to/file1
+# sept = ,
+# header = True
+# comment = #
+# col_value = average_depth
+# col_ID = id
+# mode = gradient
+# name_set = MIN:min, MAX:max
+# 
+# [mut_subplot_type2_1]
+# title = Clinical Gender
+# path = /path/to/file2
+# sept = ,
+# header = True
+# comment = 
+# col_value = gender
+# col_ID = barcode
+# mode = fix
+# name_set = 0:Male:blue, 1:Female:red, 2:Unknown:gray
+# 
+# [mut_subplot_type2_2]
+# title = Clinical Age
+# path = /path/to/file3
+# sept = ,
+# header = True
+# comment = 
+# col_value = age
+# col_ID = barcode
+# mode = range
+# name_set = 0:0-19, 20:20-39, 40:40-59, 60:60over
+
+[result_format_mutation]
+suffix = _genomon_mutations.result.txt
+
+sept = \t
+header = False
+comment = #
+sept_func = ";"
+sept_gene = ";"
+
+# column index (required)
+col_func = 5
+col_gene = 6
+
+# column index (option)
+col_opt_chr = 0
+col_opt_start = 1
+col_opt_end = 2
+col_opt_ref = 3
+col_opt_alt = 4
+
+[merge_format_mutation]
+lack_column_complement = NA
+sept = ,
+
+###################### sv
+[genome]
+path = 
+
+[sv]
+use_chrs = 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y
+snippet_threshold = 1000
+snippet_sv_type = inversion
+
+[result_format_sv]
+suffix = .genomonSV.result.txt
+
+sept = \t
+header = False
+comment = #
+
+# column index (required)
+col_chr1 = 0
+col_break1 = 1
+col_chr2 = 3
+col_break2 = 4
+
+# column index (option)
+col_opt_dir1 = 2
+col_opt_dir2 = 5
+col_opt_type = 7
+col_opt_gene_name1 = 8
+col_opt_gene_name2 = 9
+
+[merge_format_sv]
+lack_column_complement = NA
+sept = ,
+
diff --git a/config_template/genomon_v2_0_5_v2_0_4.cfg b/config_template/genomon_v2_0_5_v2_0_4.cfg
@@ -1,5 +1,5 @@
 # 
-# $Id: paplot.cfg 109 2016-06-02 06:59:42Z aokada $
+# $Id: genomon_v2_0_5_v2_0_4.cfg 119 2016-07-05 05:04:33Z aokada $
 # 
 
 ###################### general
@@ -14,7 +14,7 @@ limited_genes =
 #nouse_genes = -
 
 #limited_funcs = 
-nouse_funcs = (blank),unknown,synonymous_SNV
+nouse_funcs = _blank_,unknown,synonymous_SNV
 func_colors = stopgain:#E85299,frameshift_deletion:#F39600,frameshift_insertion:#E60011,nonframeshift_deletion:#9CAEB7,nonframeshift_insertion:#009943,nonsynonymous_SNV:#00ADA6,splicing:#D7C447,stoploss:#6BBB5A
 
 ### special item

diff --git a/config_template/genomon_v2_2_0_merge.cfg b/config_template/genomon_v2_2_0_merge.cfg
@@ -1,5 +1,5 @@
 # 
-# $Id: paplot.cfg 111 2016-06-08 02:04:29Z aokada $
+# $Id: genomon_v2_2_0_merge.cfg 119 2016-07-05 05:04:33Z aokada $
 # 
 
 ###################### general
@@ -14,7 +14,7 @@ limited_genes =
 #nouse_genes = -
 
 #limited_funcs = 
-nouse_funcs = (blank),unknown,synonymous_SNV
+nouse_funcs = _blank_,unknown,synonymous_SNV
 func_colors = stopgain:#E85299,frameshift_deletion:#F39600,frameshift_insertion:#E60011,nonframeshift_deletion:#9CAEB7,nonframeshift_insertion:#009943,nonsynonymous_SNV:#00ADA6,splicing:#D7C447,stoploss:#6BBB5A
 
 ### special item

diff --git a/config_template/genomon_v2_3_0_merge.cfg b/config_template/genomon_v2_3_0_merge.cfg
@@ -1,5 +1,5 @@
 # 
-# $Id: paplot.cfg 111 2016-06-08 02:04:29Z aokada $
+# $Id: genomon_v2_3_0_merge.cfg 119 2016-07-05 05:04:33Z aokada $
 # 
 
 ###################### general
@@ -14,7 +14,7 @@ limited_genes =
 #nouse_genes = -
 
 #limited_funcs = 
-nouse_funcs = (blank),unknown,synonymous_SNV
+nouse_funcs = _blank_,unknown,synonymous_SNV
 func_colors = stopgain:#E85299,frameshift_deletion:#F39600,frameshift_insertion:#E60011,nonframeshift_deletion:#9CAEB7,nonframeshift_insertion:#009943,nonsynonymous_SNV:#00ADA6,splicing:#D7C447,stoploss:#6BBB5A
 
 ### special item

diff --git a/example/example.cfg b/example/example.cfg
@@ -1,5 +1,5 @@
 # 
-# $Id: example.cfg 113 2016-06-10 08:41:34Z aokada $
+# $Id: example.cfg 117 2016-06-29 01:43:38Z aokada $
 # 
 
 ###################### general

diff --git a/pa_plot b/pa_plot
@@ -4,7 +4,7 @@ Created on Wed Dec 02 17:43:52 2015
 
 @author: okada
 
-$Id: pa_plot 111 2016-06-08 02:04:29Z aokada $
+$Id: pa_plot 117 2016-06-29 01:43:38Z aokada $
 """
 
 def main():

diff --git a/paplot.cfg b/paplot.cfg
@@ -1,5 +1,5 @@
 # 
-# $Id: paplot.cfg 111 2016-06-08 02:04:29Z aokada $
+# $Id: paplot.cfg 119 2016-07-05 05:04:33Z aokada $
 # 
 
 ###################### general
@@ -14,7 +14,7 @@ limited_genes =
 #nouse_genes = -
 
 #limited_funcs = 
-#nouse_funcs = (blank),unknown,synonymous_SNV
+#nouse_funcs = _blank_,unknown,synonymous_SNV
 #func_colors = stopgain:#E85299,frameshift_deletion:#F39600,frameshift_insertion:#E60011,nonframeshift_deletion:#9CAEB7,nonframeshift_insertion:#009943,nonsynonymous_SNV:#00ADA6,splicing:#D7C447,stoploss:#6BBB5A
 
 ### special item

diff --git a/paplot.egg-info/PKG-INFO b/paplot.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
 Metadata-Version: 1.0
 Name: paplot
-Version: 0.3.0release
+Version: 0.3.1release
 Summary: parser result files created by genomon
 Home-page: https://github.com/Genomon-Project/paplot.git
 Author: aokada

diff --git a/paplot/mut.py b/paplot/mut.py
@@ -4,7 +4,7 @@
 
 @author: okada
 
-$Id: mut.py 114 2016-06-14 02:08:37Z aokada $
+$Id: mut.py 119 2016-07-05 05:04:33Z aokada $
 """
 
 ########### js template
@@ -693,6 +693,7 @@ def genes_list(colmun, colmun_f, colmun_id, funcs, Ids, config):
 
         genes.append(key)
 
+    genes.sort()
     return genes
 
 def funcs_list(colmun, config):
@@ -851,21 +852,21 @@ def convert_tojs(input_file, output_file, positions, config):
         func = df.data[f][func_pos]
         df.data[f][func_pos] = func.replace(" ", "_")
         if func == "":
-            df.data[f][func_pos] = "(blank)"
+            df.data[f][func_pos] = "_blank_"
 
     [funcs, colors_n, colors_h] = funcs_list(df.column(cols_di["func"]), config)
 
     # ID list
     Ids = []
     for row in df.data:
-        iid = row[df.name_to_index("id")]
+        iid = row[df.name_to_index(cols_di["id"])]
         if iid != "": Ids.append(iid)
     Ids = list(set(Ids))
     Ids.sort()
 
     genes = genes_list(df.column(cols_di["gene"]), \
                         df.column(cols_di["func"]), \
-                        df.column(df.name_to_index("id")), \
+                        df.column(cols_di["id"]), \
                         funcs, Ids, config)    
 
     option_keys = cols_di.keys()
@@ -895,7 +896,7 @@ def convert_tojs(input_file, output_file, positions, config):
     mutations = {}
     tooltips = {}
     for row in df.data:
-        iid = row[df.name_to_index("id")]
+        iid = row[df.name_to_index(cols_di["id"])]
         if iid == "": continue
 
         if (iid in mutations) == False:

diff --git a/paplot/qc.py b/paplot/qc.py
@@ -4,7 +4,7 @@
 
 @author: okada
 
-$Id: qc.py 114 2016-06-14 02:08:37Z aokada $
+$Id: qc.py 118 2016-07-05 02:05:54Z aokada $
 """
 
 def convert_tojs(input_file, output_file, positions, config):
@@ -42,13 +42,23 @@ def convert_tojs(input_file, output_file, positions, config):
             continue
 
         data = line.split(sept)
-
-        item_text = "{"
+
+        items = {}
+        str_list = []
         for i in range(len(data)):
             if names[header[i]] == "id":
-                item_text += names[header[i]] + ':"' + data[i] + '",'
+                str_list.append(names[header[i]])
+
+            items[names[header[i]]] = data[i]
+
+        keys = items.keys()
+        keys.sort()
+        item_text = "{"
+        for key in keys:
+            if key in str_list:
+                item_text += key + ':"' + items[key] + '",'
             else:
-                item_text += names[header[i]] + ':' + data[i] + ','
+                item_text += key + ':' + items[key] + ','
 
         data_text += item_text + "},\n"
 

diff --git a/paplot/run_conf.py b/paplot/run_conf.py
@@ -4,7 +4,7 @@
 
 @author: okada
 
-$Id: run_conf.py 81 2016-04-07 08:31:10Z aokada $
+$Id: run_conf.py 117 2016-06-29 01:43:38Z aokada $
 """
 prog = "pa_plot conf"
 

diff --git a/paplot/run_mut.py b/paplot/run_mut.py
@@ -4,7 +4,7 @@
 
 @author: okada
 
-$Id: run_mut.py 106 2016-05-25 08:54:02Z aokada $
+$Id: run_mut.py 116 2016-06-29 01:34:43Z aokada $
 """
 prog = "pa_plot mutation"
 
@@ -14,7 +14,7 @@ def main(argv):
     import paplot.mut as mut
     import paplot.prep as prep
     import argparse
-    
+
     parser = argparse.ArgumentParser(prog = prog)
 
     parser.add_argument("--version", action = "version", version = tools.version_text())

diff --git a/paplot/run_qc.py b/paplot/run_qc.py
@@ -4,7 +4,7 @@
 
 @author: okada
 
-$Id: run_qc.py 84 2016-04-22 00:43:25Z aokada $
+$Id: run_qc.py 117 2016-06-29 01:43:38Z aokada $
 """
 prog = "pa_plot qc"
 

diff --git a/paplot/run_sv.py b/paplot/run_sv.py
@@ -4,7 +4,7 @@
 
 @author: okada
 
-$Id: run_sv.py 84 2016-04-22 00:43:25Z aokada $
+$Id: run_sv.py 117 2016-06-29 01:43:38Z aokada $
 """
 prog = "pa_plot sv"
 

diff --git a/paplot/subcode/tools.py b/paplot/subcode/tools.py
@@ -4,7 +4,7 @@
 
 @author: okada
 
-$Id: tools.py 109 2016-06-02 06:59:42Z aokada $
+$Id: tools.py 118 2016-07-05 02:05:54Z aokada $
 """
 
 def config_getboolean(config, section, item):
@@ -77,12 +77,15 @@ def get_inputlist(pattern):
     import glob
 
     inputs = pattern.lstrip("'").lstrip('"').rstrip("'").rstrip('"').split(",")
-
+    
     all_list = []
     for item in inputs:
         all_list.extend(glob.glob(win_to_unix(item).lstrip(" ").rstrip(" ")))
+
+    input_list = list(set(all_list))
+    input_list.sort()
 
-    return list(set(all_list))
+    return input_list
 
 def get_section(mode):
     section_in = ""

diff --git a/paplot/sv.py b/paplot/sv.py
@@ -4,7 +4,7 @@
 
 @author: okada
 
-$Id: sv.py 114 2016-06-14 02:08:37Z aokada $
+$Id: sv.py 117 2016-06-29 01:43:38Z aokada $
 """
 
 ########### js template

diff --git a/setup.cfg b/setup.cfg
@@ -1,5 +1,5 @@
 # 
-# $Id: setup.cfg 37 2016-02-16 05:19:48Z aokada $
+# $Id: setup.cfg 118 2016-07-05 02:05:54Z aokada $
 # 
 
 [egg_info]