Mercurial > repos > charles-bernard > alfa

comparison ALFA/ALFA_wrapper.py @ 31:7df7bee710ad draft

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Uploaded
author charles-bernard
date Sun, 18 Dec 2016 09:50:39 -0500
parents 1c9cea51dc24
children b26aec436ab5
comparison
equal deleted inserted replaced
30:1c9cea51dc24 31:7df7bee710ad
58 k = 0 58 k = 0
59 reads_filenames = [''] * (n/2) 59 reads_filenames = [''] * (n/2)
60 reads_labels = [''] * (n/2) 60 reads_labels = [''] * (n/2)
61 for i in range(0, n, 2): 61 for i in range(0, n, 2):
62 reads_filenames[k] = reads_list[i].split('__fname__')[1] 62 reads_filenames[k] = reads_list[i].split('__fname__')[1]
63 reads_labels[k] = reads_list[i+1].split('__label__')[1] 63 cur_label = reads_list[i+1].split('__label__')[1]
64 reads_labels[k] = re.sub(r' ', '_', cur_label)
64 if not reads_labels[k]: 65 if not reads_labels[k]:
65 reads_labels[k] = 'sample_%s' % str(k) 66 reads_labels[k] = 'sample_%s' % str(k)
66 input2_args='%s %s %s' % (input2_args, reads_filenames[k], reads_labels[k]) 67 input2_args='%s "%s" "%s"' % (input2_args, reads_filenames[k], reads_labels[k])
67 k += 1 68 k += 1
68 if format == 'bedgraph': 69 if format == 'bedgraph':
69 input2_args = input2_args + ' --bedgraph' 70 input2_args = input2_args + ' --bedgraph'
70 return input2_args, reads_filenames, reads_labels 71 return input2_args, reads_filenames, reads_labels
71 72
83 exit_and_explain("The script ALFA.py encountered the following error:\n\n%s" % alfa_err) 84 exit_and_explain("The script ALFA.py encountered the following error:\n\n%s" % alfa_err)
84 85
85 def merge_count_files(reads_labels): 86 def merge_count_files(reads_labels):
86 merged_count_file = open('count_file.txt', 'wb') 87 merged_count_file = open('count_file.txt', 'wb')
87 for i in range(0, len(reads_labels)): 88 for i in range(0, len(reads_labels)):
88 current_count_file = open(reads_labels[i] + '.categories_counts', 'r') 89 current_count_file = open('%s.categories_counts' % reads_labels[i], 'r')
89 merged_count_file.write('##LABEL: %s\n\n' % reads_labels[i]) 90 merged_count_file.write('##LABEL: %s\n\n' % reads_labels[i])
90 merged_count_file.write(current_count_file.read()) 91 merged_count_file.write(current_count_file.read())
91 merged_count_file.write('__________________________________________________________________\n') 92 merged_count_file.write('__________________________________________________________________\n')
92 current_count_file.close() 93 current_count_file.close()
93 merged_count_file.close() 94 merged_count_file.close()
104 105
105 #INPUT1: Annotation File 106 #INPUT1: Annotation File
106 if args.indexes: 107 if args.indexes:
107 # The indexes submitted by the user must exhibit the suffix '.(un)stranded.index' and will be called by alfa by their prefix 108 # The indexes submitted by the user must exhibit the suffix '.(un)stranded.index' and will be called by alfa by their prefix
108 index = symlink_user_indexes(args.indexes[0], args.indexes[1]) 109 index = symlink_user_indexes(args.indexes[0], args.indexes[1])
109 input1_args = '-g %s' % index 110 input1_args = '-g "%s"' % index
110 elif args.bi_indexes: 111 elif args.bi_indexes:
111 input1_args = '-g %s' % args.bi_indexes[0] 112 input1_args = '-g "%s"' % args.bi_indexes[0]
112 elif args.annotation_file: 113 elif args.annotation_file:
113 input1_args = '-a %s' % args.annotation_file[0] 114 input1_args = '-a "%s"' % args.annotation_file[0]
114 else: 115 else:
115 exit_and_explain('No annotation file submitted !') 116 exit_and_explain('No annotation file submitted !')
116 117
117 #INPUT 2: Mapped Reads 118 #INPUT 2: Mapped Reads
118 if args.reads: 119 if args.reads: