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comparison ideas.xml @ 132:8ce93420010c draft

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Uploaded
author greg
date Tue, 12 Dec 2017 10:47:26 -0500
parents 5150fcdcd0fa
children 91db24a1384d
comparison
equal deleted inserted replaced
131:5150fcdcd0fa 132:8ce93420010c
16 #set prep_output_config = "prep_output_config.txt" 16 #set prep_output_config = "prep_output_config.txt"
17 ############################################## 17 ##############################################
18 ## Create the config file and prepare the data 18 ## Create the config file and prepare the data
19 ############################################## 19 ##############################################
20 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 20 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
21 mkdir '$output_pdf_dir' && 21 #if str($output_heatmaps) == "yes":
22 mkdir '$output_pdf_dir' &&
23 #end if
22 mkdir '$output_txt_dir' && 24 mkdir '$output_txt_dir' &&
23 cp '$gen_prep_input_config' $prep_input_config && 25 cp '$gen_prep_input_config' $prep_input_config &&
24 prepMat 26 prepMat
25 $prep_input_config 27 $prep_input_config
26 #if str($specify_genomic_window) == "yes": 28 #if str($specify_genomic_window) == "yes":
54 ## format expected by IDEAS. 56 ## format expected by IDEAS.
55 ############################################## 57 ##############################################
56 && cut -d' ' $prep_input_config -f1,2 > file1.txt 58 && cut -d' ' $prep_input_config -f1,2 > file1.txt
57 && ls tmp/*.bed.gz > file2.txt 59 && ls tmp/*.bed.gz > file2.txt
58 && paste <(cat file1.txt) <(cat file2.txt) -d' ' > $prep_output_config 60 && paste <(cat file1.txt) <(cat file2.txt) -d' ' > $prep_output_config
59 ##############################################
60 ## If using a genomic window bed file, categorize
61 ## the window positions by chromosome to enable
62 ## the IDEAS -inv option.
63 ##############################################
64 #if str($specify_genomic_window) == "yes": 61 #if str($specify_genomic_window) == "yes":
62 ##############################################
63 ## Using a genomic window bed file, so categorize
64 ## the window positions by chromosome to enable
65 ## the IDEAS -inv option.
66 ##############################################
65 #import collections 67 #import collections
66 #set window_positions_by_chroms = collections.OrderedDict() 68 #set window_positions_by_chroms = collections.OrderedDict()
67 #for count, line in enumerate(open($specify_genomic_window_cond.bed_input.file_name, 'r')): 69 #for count, line in enumerate(open($specify_genomic_window_cond.bed_input.file_name, 'r')):
68 #set $line = $line.strip() 70 #set $line = $line.strip()
69 #if not $line or $line.startswith('#'): 71 #if not $line or $line.startswith('#'):
125 fi 127 fi
126 #end if 128 #end if
127 129
128 #end for 130 #end for
129 #else: 131 #else:
132 ##############################################
133 ## Not using a genomic window bed file.
134 ##############################################
130 && ideas 135 && ideas
131 '$prep_output_config' 136 '$prep_output_config'
132 $tmp_dir/*.bed 137 $tmp_dir/*.bed
133 $hp 138 $hp
134 #if str($log2) != "0.0": 139 #if str($log2) != "0.0":