Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/tmhmm2.py @ 18:eb6ac44d4b8e draft
Suite v0.2.8, record Promoter 2 verion + misc internal updates
| author | peterjc |
|---|---|
| date | Tue, 01 Sep 2015 09:56:36 -0400 |
| parents | 99b82a2b1272 |
| children | f3ecd80850e2 |
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| 17:e6cc27d182a8 | 18:eb6ac44d4b8e |
|---|---|
| 41 when there is no output from tmhmm2, and raise an error. | 41 when there is no output from tmhmm2, and raise an error. |
| 42 """ | 42 """ |
| 43 import sys | 43 import sys |
| 44 import os | 44 import os |
| 45 import tempfile | 45 import tempfile |
| 46 from seq_analysis_utils import stop_err, split_fasta, run_jobs, thread_count | 46 from seq_analysis_utils import sys_exit, split_fasta, run_jobs, thread_count |
| 47 | 47 |
| 48 FASTA_CHUNK = 500 | 48 FASTA_CHUNK = 500 |
| 49 | 49 |
| 50 if len(sys.argv) != 4: | 50 if len(sys.argv) != 4: |
| 51 stop_err("Require three arguments, number of threads (int), input protein FASTA file & output tabular file") | 51 sys_exit("Require three arguments, number of threads (int), input protein FASTA file & output tabular file") |
| 52 | 52 |
| 53 num_threads = thread_count(sys.argv[1], default=4) | 53 num_threads = thread_count(sys.argv[1], default=4) |
| 54 fasta_file = sys.argv[2] | 54 fasta_file = sys.argv[2] |
| 55 tabular_file = sys.argv[3] | 55 tabular_file = sys.argv[3] |
| 56 | 56 |
| 66 parts = line.rstrip("\r\n").split("\t") | 66 parts = line.rstrip("\r\n").split("\t") |
| 67 try: | 67 try: |
| 68 identifier, length, expAA, first60, predhel, topology = parts | 68 identifier, length, expAA, first60, predhel, topology = parts |
| 69 except: | 69 except: |
| 70 assert len(parts)!=6 | 70 assert len(parts)!=6 |
| 71 stop_err("Bad line: %r" % line) | 71 sys_exit("Bad line: %r" % line) |
| 72 assert length.startswith("len="), line | 72 assert length.startswith("len="), line |
| 73 length = length[4:] | 73 length = length[4:] |
| 74 assert expAA.startswith("ExpAA="), line | 74 assert expAA.startswith("ExpAA="), line |
| 75 expAA = expAA[6:] | 75 expAA = expAA[6:] |
| 76 assert first60.startswith("First60="), line | 76 assert first60.startswith("First60="), line |
| 110 try: | 110 try: |
| 111 output = open(temp).readline() | 111 output = open(temp).readline() |
| 112 except IOError: | 112 except IOError: |
| 113 output = "" | 113 output = "" |
| 114 clean_up(fasta_files + temp_files) | 114 clean_up(fasta_files + temp_files) |
| 115 stop_err("One or more tasks failed, e.g. %i from %r gave:\n%s" % (error_level, cmd, output), | 115 sys_exit("One or more tasks failed, e.g. %i from %r gave:\n%s" % (error_level, cmd, output), |
| 116 error_level) | 116 error_level) |
| 117 del results | 117 del results |
| 118 del jobs | 118 del jobs |
| 119 | 119 |
| 120 out_handle = open(tabular_file, "w") | 120 out_handle = open(tabular_file, "w") |
| 123 data_handle = open(temp) | 123 data_handle = open(temp) |
| 124 count = clean_tabular(data_handle, out_handle) | 124 count = clean_tabular(data_handle, out_handle) |
| 125 data_handle.close() | 125 data_handle.close() |
| 126 if not count: | 126 if not count: |
| 127 clean_up(fasta_files + temp_files) | 127 clean_up(fasta_files + temp_files) |
| 128 stop_err("No output from tmhmm2") | 128 sys_exit("No output from tmhmm2") |
| 129 out_handle.close() | 129 out_handle.close() |
| 130 | 130 |
| 131 clean_up(fasta_files + temp_files) | 131 clean_up(fasta_files + temp_files) |