diff --git a/tools/data_source/show_in_ucsc.py b/tools/data_source/show_in_ucsc.py deleted file mode 100755 index 93288a96827..00000000000 --- a/tools/data_source/show_in_ucsc.py +++ /dev/null @@ -1,65 +0,0 @@ -#!/usr/bin/env python2.4 -""" -Tool to display multiple datasets at the UCSC genome browser at a time, along with their custom track details. -Done by: Guru -""" - -import sys,os - -primary = sys.argv[2] -color_list = [sys.argv[3].replace('-',',')] -visib_list = [sys.argv[4]] - -if sys.argv[5]: - for color in sys.argv[5].split(','): - color_list.append(color.replace('-',',')) - -if sys.argv[6]: - visib_list.extend(sys.argv[6].split(",")) - -#visib_list = [sys.argv[4], sys.argv[6]] -input_list = [] -input_list.append(primary) - -name_list = [sys.argv[7].replace("_NAME_","").replace("_SPACE_"," ").replace("_OPEN_","(").replace("_CLOSE_",")")] -i=8 -for item in sys.argv[8:]: - if item.count("_NAME_") != 0 or item == "customTrack2.bed": - item=item.replace("_NAME_","").replace("_SPACE_"," ").replace("_OPEN_","(").replace("_CLOSE_",")") - for sym in ["(u__sq__","u__sq__","__sq__,","__sq__)","__sq__","__ob__", "__cb__"]: - item = item.replace(sym, "") - name_list.append(item) - i+=1 - else: - break - -for item in sys.argv[i:]: - if item.count("/") == 0: - item = item.replace(',','').replace("]",'').replace("[","") - try: - assert int(item) - item = "./database/files/dataset_" + item + ".dat" - except: - pass - input_list.append(item) - -out=[] -if color_list[1] == 'None': - color_list.pop() - visib_list.pop() - j=1 - while j < len(input_list): - color_list.append('0,0,0') - visib_list.append('1') - j+=1 - -fout = open(sys.argv[1],"w") -for k,inp in enumerate(input_list): - print >>fout, "track name='%s' visibility=%d color=%s" %(name_list[k],int(visib_list[k]),color_list[k]) - print >>fout, open(inp,"r").read() -fout.close() - -print "Display %d tracks in UCSC" %(len(input_list)) - - - diff --git a/tools/data_source/show_in_ucsc.xml b/tools/data_source/show_in_ucsc.xml deleted file mode 100644 index c53d871813f..00000000000 --- a/tools/data_source/show_in_ucsc.xml +++ /dev/null @@ -1,98 +0,0 @@ - - displays selected datasets in the UCSC genome browser - - show_in_ucsc.py $out_file1 $primary $primary_color $primary_visib $Color $Visibility $primary_name $other_names $newdata - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**Info** - -This tool displays the selected datasets with their custom track attributes (if any) in the UCSC genome browser. - -This tool allows you to set the **Color** and **Visibility** attributes and you can edit the **Name** attribute of the dataset by clicking on **"edit attributes"** button (pencil icon) next to the dataset name in the history panel. - -Please note that the primary dataset in step 1 of the tool sets the database build for the datasets in step 2. - - - - - \ No newline at end of file diff --git a/tools/data_source/show_in_ucsc_code.py b/tools/data_source/show_in_ucsc_code.py deleted file mode 100755 index 6c54f825634..00000000000 --- a/tools/data_source/show_in_ucsc_code.py +++ /dev/null @@ -1,17 +0,0 @@ -import os, sys - -def print_out(data): - build = str(data.dbkey) - id = data.id - extension = ["bed", "interval"] - return (build,id,extension) - -def print_name(data): - if isinstance(data, list): - name_list=[] - for item in data: - name_list.append("_NAME_" + item.name.replace("(","_OPEN_").replace(")","_CLOSE_").replace(" ","_SPACE_")) - return name_list - else: - return "_NAME_" + data.name.replace("(","_OPEN_").replace(")","_CLOSE_").replace(" ","_SPACE_") -