|
0
|
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
|
