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1 """
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2 bam_to_scidx.py
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3
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4 Input: BAM file
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5 Output: Converted scidx file
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6 """
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7 import optparse
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8 import os
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9 import shutil
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10 import subprocess
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11 import sys
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12 import tempfile
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13
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14 BUFF_SIZE = 1048576
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15
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16
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17 def get_stderr_exception(tmp_err, tmp_stderr):
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18 """
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19 Return a stderr string of reasonable size.
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20 """
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21 tmp_stderr.close()
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22 # Get stderr, allowing for case where it's very large.
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23 tmp_stderr = open(tmp_err, 'rb')
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24 stderr_str = ''
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25 buffsize = BUFF_SIZE
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26 try:
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27 while True:
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28 stderr_str += tmp_stderr.read(buffsize)
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29 if not stderr_str or len(stderr_str) % buffsize != 0:
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30 break
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31 except OverflowError:
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32 pass
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33 tmp_stderr.close()
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34 return stderr_str
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35
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36
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37 def stop_err(msg):
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38 sys.stderr.write(msg)
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39 sys.exit(1)
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40
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41
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42 parser = optparse.OptionParser()
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43 parser.add_option('-j', '--jar_file', dest='jar_file', type='string', help='BAMtoIDX.jar')
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44 parser.add_option('-b', '--input_bam', dest='input_bam', type='string', help='Input dataset in BAM format')
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45 parser.add_option('-i', '--input_bai', dest='input_bai', type='string', help='Input dataset index')
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46 parser.add_option('-r', '--read', dest='read', type='int', default=0, help='Reads.')
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47 parser.add_option('-o', '--output', dest='output', type='string', help='Output dataset in scidx format')
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48 options, args = parser.parse_args()
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49
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50 tmp_dir = tempfile.mkdtemp(prefix='tmp-scidx-')
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51 tmp_out = tempfile.NamedTemporaryFile().name
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52 tmp_stdout = open(tmp_out, 'wb')
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53 tmp_err = tempfile.NamedTemporaryFile().name
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54 tmp_stderr = open(tmp_err, 'wb')
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55
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56 # Link input BAM file and associated index file into the working directory.
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57 input_data_file_name = "input.bam"
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58 os.link(options.input_bam, os.path.join(tmp_dir, input_data_file_name))
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59 os.link(options.input_bai, os.path.join(tmp_dir, "%s.bai" % input_data_file_name))
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60
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61 cmd = "java -jar %s -b %s -s %d -o %s" % (options.jar_file, input_data_file_name, options.read, options.output)
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62 proc = subprocess.Popen(args=cmd, stdout=tmp_stdout, stderr=tmp_stderr, shell=True, cwd=tmp_dir)
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63 return_code = proc.wait()
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64 if return_code != 0:
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65 error_message = get_stderr_exception(tmp_err, tmp_stderr)
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66 stop_err(error_message)
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67
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68 if tmp_dir and os.path.exists(tmp_dir):
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69 shutil.rmtree(tmp_dir)
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