Mercurial > repos > peterjc > mira4_assembler
annotate tools/mira4_0/mira4_convert.py @ 31:fd95aaef8818 draft
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
| author | peterjc |
|---|---|
| date | Wed, 10 Feb 2016 09:07:39 -0500 |
| parents | 55ae131c5862 |
| children | 56b421d59805 |
| rev | line source |
|---|---|
| 25 | 1 #!/usr/bin/env python |
| 2 """A simple wrapper script to call MIRA and collect its output. | |
| 3 | |
| 4 This focuses on the miraconvert binary. | |
| 5 """ | |
| 6 import os | |
| 7 import sys | |
| 8 import subprocess | |
| 9 import shutil | |
| 10 from optparse import OptionParser | |
| 11 try: | |
| 12 from io import BytesIO | |
| 13 except ImportError: | |
| 14 #Should we worry about Python 2.5 or older? | |
| 15 from StringIO import StringIO as BytesIO | |
| 16 | |
| 17 #Do we need any PYTHONPATH magic? | |
| 18 from mira4_make_bam import depad | |
| 19 | |
| 20 WRAPPER_VER = "0.0.7" # Keep in sync with the XML file | |
| 21 | |
| 22 | |
| 23 def run(cmd): | |
| 24 #Avoid using shell=True when we call subprocess to ensure if the Python | |
| 25 #script is killed, so too is the child process. | |
| 26 try: | |
| 27 child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) | |
| 28 except Exception, err: | |
|
31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
25
diff
changeset
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29 sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) |
| 25 | 30 #Use .communicate as can get deadlocks with .wait(), |
| 31 stdout, stderr = child.communicate() | |
| 32 return_code = child.returncode | |
| 33 if return_code: | |
| 34 cmd_str = " ".join(cmd) # doesn't quote spaces etc | |
| 35 if stderr and stdout: | |
|
31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
25
diff
changeset
|
36 sys.exit("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr)) |
| 25 | 37 else: |
|
31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
25
diff
changeset
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38 sys.exit("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr)) |
| 25 | 39 |
| 40 def get_version(mira_binary): | |
| 41 """Run MIRA to find its version number""" | |
| 42 # At the commend line I would use: mira -v | head -n 1 | |
| 43 # however there is some pipe error when doing that here. | |
| 44 cmd = [mira_binary, "-v"] | |
| 45 try: | |
| 46 child = subprocess.Popen(cmd, | |
| 47 stdout=subprocess.PIPE, | |
| 48 stderr=subprocess.STDOUT) | |
| 49 except Exception, err: | |
| 50 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) | |
| 51 sys.exit(1) | |
| 52 ver, tmp = child.communicate() | |
| 53 del child | |
| 54 return ver.split("\n", 1)[0].strip() | |
| 55 | |
| 56 #Parse Command Line | |
| 57 usage = """Galaxy MIRA4 wrapper script v%s - use as follows: | |
| 58 | |
| 59 $ python mira4_convert.py ... | |
| 60 | |
| 61 This will run the MIRA miraconvert binary and collect its output files as directed. | |
| 62 """ % WRAPPER_VER | |
| 63 parser = OptionParser(usage=usage) | |
| 64 parser.add_option("--input", dest="input", | |
| 65 default=None, metavar="FILE", | |
| 66 help="MIRA input filename") | |
| 67 parser.add_option("-x", "--min_length", dest="min_length", | |
| 68 default="0", | |
| 69 help="Minimum contig length") | |
| 70 parser.add_option("-y", "--min_cover", dest="min_cover", | |
| 71 default="0", | |
| 72 help="Minimum average contig coverage") | |
| 73 parser.add_option("-z", "--min_reads", dest="min_reads", | |
| 74 default="0", | |
| 75 help="Minimum reads per contig") | |
| 76 parser.add_option("--maf", dest="maf", | |
| 77 default="", metavar="FILE", | |
| 78 help="MIRA MAF output filename") | |
| 79 parser.add_option("--ace", dest="ace", | |
| 80 default="", metavar="FILE", | |
| 81 help="ACE output filename") | |
| 82 parser.add_option("--bam", dest="bam", | |
| 83 default="", metavar="FILE", | |
| 84 help="Unpadded BAM output filename") | |
| 85 parser.add_option("--fasta", dest="fasta", | |
| 86 default="", metavar="FILE", | |
| 87 help="Unpadded FASTA output filename") | |
| 88 parser.add_option("--cstats", dest="cstats", | |
| 89 default="", metavar="FILE", | |
| 90 help="Contig statistics filename") | |
| 91 parser.add_option("-v", "--version", dest="version", | |
| 92 default=False, action="store_true", | |
| 93 help="Show version and quit") | |
| 94 options, args = parser.parse_args() | |
| 95 if args: | |
|
31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
25
diff
changeset
|
96 sys.exit("Expected options (e.g. --input example.maf), not arguments") |
| 25 | 97 |
| 98 input_maf = options.input | |
| 99 out_maf = options.maf | |
| 100 out_bam = options.bam | |
| 101 out_fasta = options.fasta | |
| 102 out_ace = options.ace | |
| 103 out_cstats = options.cstats | |
| 104 | |
| 105 try: | |
| 106 mira_path = os.environ["MIRA4"] | |
| 107 except KeyError: | |
|
31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
25
diff
changeset
|
108 sys.exit("Environment variable $MIRA4 not set") |
| 25 | 109 mira_convert = os.path.join(mira_path, "miraconvert") |
| 110 if not os.path.isfile(mira_convert): | |
|
31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
25
diff
changeset
|
111 sys.exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s" |
| 25 | 112 % (mira_convert, ", ".join(os.listdir(mira_path)))) |
| 113 | |
| 114 mira_convert_ver = get_version(mira_convert) | |
| 115 if not mira_convert_ver.strip().startswith("4.0"): | |
|
31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
25
diff
changeset
|
116 sys.exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_convert_ver, mira_convert)) |
| 25 | 117 if options.version: |
| 118 print("%s, MIRA wrapper version %s" % (mira_convert_ver, WRAPPER_VER)) | |
| 119 sys.exit(0) | |
| 120 | |
| 121 if not input_maf: | |
|
31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
25
diff
changeset
|
122 sys.exit("Input MIRA file is required") |
| 25 | 123 elif not os.path.isfile(input_maf): |
|
31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
25
diff
changeset
|
124 sys.exit("Missing input MIRA file: %r" % input_maf) |
| 25 | 125 |
| 126 if not (out_maf or out_bam or out_fasta or out_ace or out_cstats): | |
|
31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
25
diff
changeset
|
127 sys.exit("No output requested") |
| 25 | 128 |
| 129 | |
| 130 def check_min_int(value, name): | |
| 131 try: | |
| 132 i = int(value) | |
|
31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
25
diff
changeset
|
133 except ValueError: |
|
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
25
diff
changeset
|
134 sys.exit("Bad %s setting, %r" % (name, value)) |
| 25 | 135 if i < 0: |
|
31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
25
diff
changeset
|
136 sys.exit("Negative %s setting, %r" % (name, value)) |
| 25 | 137 return i |
| 138 | |
| 139 min_length = check_min_int(options.min_length, "minimum length") | |
| 140 min_cover = check_min_int(options.min_cover, "minimum cover") | |
| 141 min_reads = check_min_int(options.min_reads, "minimum reads") | |
| 142 | |
| 143 #TODO - Run MIRA in /tmp or a configurable directory? | |
| 144 #Currently Galaxy puts us somewhere safe like: | |
| 145 #/opt/galaxy-dist/database/job_working_directory/846/ | |
| 146 temp = "." | |
| 147 | |
| 148 | |
| 149 cmd_list = [mira_convert] | |
| 150 if min_length: | |
| 151 cmd_list.extend(["-x", str(min_length)]) | |
| 152 if min_cover: | |
| 153 cmd_list.extend(["-y", str(min_cover)]) | |
| 154 if min_reads: | |
| 155 cmd_list.extend(["-z", str(min_reads)]) | |
| 156 cmd_list.extend(["-f", "maf", input_maf, os.path.join(temp, "converted")]) | |
| 157 if out_maf: | |
| 158 cmd_list.append("maf") | |
| 159 if out_bam: | |
| 160 cmd_list.append("samnbb") | |
| 161 if not out_fasta: | |
| 162 #Need this for samtools depad | |
| 163 out_fasta = os.path.join(temp, "depadded.fasta") | |
| 164 if out_fasta: | |
| 165 cmd_list.append("fasta") | |
| 166 if out_ace: | |
| 167 cmd_list.append("ace") | |
| 168 if out_cstats: | |
| 169 cmd_list.append("cstats") | |
| 170 run(cmd_list) | |
| 171 | |
| 172 def collect(old, new): | |
| 173 if not os.path.isfile(old): | |
|
31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
25
diff
changeset
|
174 sys.exit("Missing expected output file %s" % old) |
| 25 | 175 shutil.move(old, new) |
| 176 | |
| 177 if out_maf: | |
| 178 collect(os.path.join(temp, "converted.maf"), out_maf) | |
| 179 if out_fasta: | |
| 180 #Can we look at the MAF file to see if there are multiple strains? | |
| 181 old = os.path.join(temp, "converted_AllStrains.unpadded.fasta") | |
| 182 if os.path.isfile(old): | |
| 183 collect(old, out_fasta) | |
| 184 else: | |
| 185 #Might the output be filtered down to zero contigs? | |
| 186 old = os.path.join(temp, "converted.fasta") | |
| 187 if not os.path.isfile(old): | |
|
31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
25
diff
changeset
|
188 sys.exit("Missing expected output FASTA file") |
| 25 | 189 elif os.path.getsize(old) == 0: |
| 190 print("Warning - no contigs (harsh filters?)") | |
| 191 collect(old, out_fasta) | |
| 192 else: | |
|
31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
25
diff
changeset
|
193 sys.exit("Missing expected output FASTA file (only generic file present)") |
| 25 | 194 if out_ace: |
| 195 collect(os.path.join(temp, "converted.maf"), out_ace) | |
| 196 if out_cstats: | |
| 197 collect(os.path.join(temp, "converted_info_contigstats.txt"), out_cstats) | |
| 198 | |
| 199 if out_bam: | |
| 200 assert os.path.isfile(out_fasta) | |
| 201 old = os.path.join(temp, "converted.samnbb") | |
| 202 if not os.path.isfile(old): | |
| 203 old = os.path.join(temp, "converted.sam") | |
| 204 if not os.path.isfile(old): | |
|
31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
25
diff
changeset
|
205 sys.exit("Missing expected intermediate file %s" % old) |
| 25 | 206 h = BytesIO() |
| 207 msg = depad(out_fasta, old, out_bam, h) | |
| 208 if msg: | |
| 209 print(msg) | |
| 210 print(h.getvalue()) | |
| 211 h.close() | |
| 212 sys.exit(1) | |
| 213 h.close() | |
| 214 if out_fasta == os.path.join(temp, "depadded.fasta"): | |
| 215 #Not asked for by Galaxy, no longer needed | |
| 216 os.remove(out_fasta) | |
| 217 | |
| 218 if min_length or min_cover or min_reads: | |
| 219 print("Filtered.") | |
| 220 else: | |
| 221 print("Converted.") |