Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.py @ 109:06f121a1974e draft

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Uploaded
author greg
date Mon, 27 Feb 2017 14:34:41 -0500
parents 82144bc3626a
children 6cb3520313b9
comparison
equal deleted inserted replaced
108:82144bc3626a 109:06f121a1974e
83 sys.exit(1) 83 sys.exit(1)
84 84
85 85
86 def write_html_output(output, title, dir): 86 def write_html_output(output, title, dir):
87 with open(output, 'w') as fh: 87 with open(output, 'w') as fh:
88 fh.write('<html><head><title>%s</title></head><body><p/><ul>\n' % title) 88 fh.write('<html><head><title>%s</title></head>\n' % title)
89 fh.write('<body><p/><table>\n')
90 fh.write('<tr><th>Size</th><th>Name</th></tr>\n')
89 for fname in os.listdir(dir): 91 for fname in os.listdir(dir):
90 fh.write('<li><a type="text/plain" href="%s">%s</a></li>\n' % (fname, fname)) 92 size = str(os.path.getsixe(fname))
91 fh.write('</ul></body></html>\n') 93 link = '<a href="%s" type="text/plain">%s</a>\n' % (fname, fname)
94 fh.write('<tr><td>%s</td><td>%s</td></tr>\n' % (size, link))
95 fh.write('</table></body></html>\n')
92 96
93 97
94 # Define command response buffers. 98 # Define command response buffers.
95 tmp_out = tempfile.NamedTemporaryFile().name 99 tmp_out = tempfile.NamedTemporaryFile().name
96 tmp_stdout = open(tmp_out, 'wb') 100 tmp_stdout = open(tmp_out, 'wb')
140 # Handle orthogroups outputs. 144 # Handle orthogroups outputs.
141 if create_ortho_sequences: 145 if create_ortho_sequences:
142 if create_corresponding_coding_sequences: 146 if create_corresponding_coding_sequences:
143 out_file = args.output_ptorthocs 147 out_file = args.output_ptorthocs
144 orthogroups_fasta_dest_dir = args.output_ptorthocs_dir 148 orthogroups_fasta_dest_dir = args.output_ptorthocs_dir
145 title = 'Orthogroups with corresponding coding sequences' 149 title = 'Orthogroups and corresponding coding sequences files'
146 else: 150 else:
147 out_file = args.output_ptortho 151 out_file = args.output_ptortho
148 orthogroups_fasta_dest_dir = args.output_ptortho_dir 152 orthogroups_fasta_dest_dir = args.output_ptortho_dir
149 title = 'Orthogroups' 153 title = 'Orthogroups files'
150 orthogroups_fasta_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_fasta') 154 orthogroups_fasta_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_fasta')
151 move_directory_files(orthogroups_fasta_src_dir, orthogroups_fasta_dest_dir) 155 move_directory_files(orthogroups_fasta_src_dir, orthogroups_fasta_dest_dir)
152 write_html_output(out_file, title, orthogroups_fasta_dest_dir) 156 write_html_output(out_file, title, orthogroups_fasta_dest_dir)
153 # Handle single copy orthogroup outputs. 157 # Handle single copy orthogroup outputs.
154 if args.output_ptsco is not None: 158 if args.output_ptsco is not None:
155 single_copy_fasta_src_dir = os.path.join(OUTPUT_DIR, 'single_copy_fasta') 159 single_copy_fasta_src_dir = os.path.join(OUTPUT_DIR, 'single_copy_fasta')
156 single_copy_fasta_dest_dir = args.output_ptsco_dir 160 single_copy_fasta_dest_dir = args.output_ptsco_dir
157 title = 'Single copy orthogroups' 161 title = 'Single copy orthogroups files'
158 move_directory_files(single_copy_fasta_src_dir, single_copy_fasta_dest_dir) 162 move_directory_files(single_copy_fasta_src_dir, single_copy_fasta_dest_dir)
159 write_html_output(args.output_ptsco, title, single_copy_fasta_dest_dir) 163 write_html_output(args.output_ptsco, title, single_copy_fasta_dest_dir)