Mercurial > repos > trinity_ctat > ctat_abundance_estimation_to_matrix
comparison ctat_abundance_estimation_to_matrix.py @ 0:5eca0c75b178 draft default tip
Upload ctat tools.
| author | trinity_ctat |
|---|---|
| date | Tue, 17 Jul 2018 11:47:32 -0400 |
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| children |
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| -1:000000000000 | 0:5eca0c75b178 |
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| 1 #!/usr/bin/env python | |
| 2 | |
| 3 import sys, os, string, subprocess | |
| 4 | |
| 5 #aliasing the filenames using the labels | |
| 6 | |
| 7 | |
| 8 def run_command(command): | |
| 9 print "Running command: " + command | |
| 10 | |
| 11 err_capture_file = open("my.stderr", 'w') # writing stderr to a file | |
| 12 cmd_run = subprocess.Popen(args=command, shell=True, stderr=err_capture_file, stdout=sys.stdout) | |
| 13 err = cmd_run.wait() # get exit code from command execution | |
| 14 err_capture_file.close() | |
| 15 | |
| 16 if err: | |
| 17 # report the error messages we captured, and exit non-zero | |
| 18 sys.stderr.write("Error, cmd: " + command + " died with ret: " + `err`) | |
| 19 for line in open(err_capture_file): | |
| 20 sys.stderr.write(line) | |
| 21 sys.exit(err) | |
| 22 return | |
| 23 | |
| 24 label_list = [] # symlink files to the labels | |
| 25 for i in range(1, len(sys.argv), 2): | |
| 26 filename=sys.argv[i] | |
| 27 label= sys.argv[i+1] | |
| 28 cmd= "ln -sf " + filename + " " + label | |
| 29 label_list.append(label) | |
| 30 run_command(cmd) | |
| 31 | |
| 32 | |
| 33 # run the abundance estimation script | |
| 34 | |
| 35 cmd = os.path.dirname(sys.argv[0]) + "/ctat_trinity_tool_wrapper.py " + " util/abundance_estimates_to_matrix.pl --gene_trans_map none --est_method RSEM --cross_sample_norm TMM " + " ".join(label_list) | |
| 36 | |
| 37 run_command(cmd) | |
| 38 | |
| 39 sys.exit(0) | |
| 40 |