Mercurial > repos > trinity_ctat > ctat_abundance_estimation_to_matrix
diff ctat_abundance_estimation_to_matrix.py @ 0:5eca0c75b178 draft default tip
Upload ctat tools.
author | trinity_ctat |
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date | Tue, 17 Jul 2018 11:47:32 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_abundance_estimation_to_matrix.py Tue Jul 17 11:47:32 2018 -0400 @@ -0,0 +1,40 @@ +#!/usr/bin/env python + +import sys, os, string, subprocess + +#aliasing the filenames using the labels + + +def run_command(command): + print "Running command: " + command + + err_capture_file = open("my.stderr", 'w') # writing stderr to a file + cmd_run = subprocess.Popen(args=command, shell=True, stderr=err_capture_file, stdout=sys.stdout) + err = cmd_run.wait() # get exit code from command execution + err_capture_file.close() + + if err: + # report the error messages we captured, and exit non-zero + sys.stderr.write("Error, cmd: " + command + " died with ret: " + `err`) + for line in open(err_capture_file): + sys.stderr.write(line) + sys.exit(err) + return + +label_list = [] # symlink files to the labels +for i in range(1, len(sys.argv), 2): + filename=sys.argv[i] + label= sys.argv[i+1] + cmd= "ln -sf " + filename + " " + label + label_list.append(label) + run_command(cmd) + + +# run the abundance estimation script + +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) + +run_command(cmd) + +sys.exit(0) +