Mercurial > repos > peterjc > mira4_assembler
annotate tools/mira4_0/mira4_convert.py @ 38:cee8f9005e43 draft
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 206259620376b322fc8ed99a6efdd3712f38764b
| author | peterjc |
|---|---|
| date | Wed, 11 Jul 2018 12:35:35 -0400 |
| parents | 259891fce7fd |
| children | bbf14bb9607b |
| 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 """ | |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
6 |
|
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
7 from __future__ import print_function |
|
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
8 |
| 25 | 9 import os |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
10 import shutil |
| 25 | 11 import subprocess |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
12 import sys |
|
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
13 |
| 25 | 14 from optparse import OptionParser |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
15 |
| 25 | 16 try: |
| 17 from io import BytesIO | |
| 18 except ImportError: | |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
19 # Should we worry about Python 2.5 or older? |
| 25 | 20 from StringIO import StringIO as BytesIO |
| 21 | |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
22 # Do we need any PYTHONPATH magic? |
| 25 | 23 from mira4_make_bam import depad |
| 24 | |
|
35
259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
34
diff
changeset
|
25 WRAPPER_VER = "0.0.11" # Keep in sync with the XML file |
| 25 | 26 |
| 27 | |
| 28 def run(cmd): | |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
29 # Avoid using shell=True when we call subprocess to ensure if the Python |
|
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
30 # script is killed, so too is the child process. |
| 25 | 31 try: |
|
34
0785a6537f3e
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 6405ba93fcec7ea93452bf54d559c7507ee7a57c
peterjc
parents:
32
diff
changeset
|
32 child = subprocess.Popen(cmd, universal_newlines=True, |
|
0785a6537f3e
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 6405ba93fcec7ea93452bf54d559c7507ee7a57c
peterjc
parents:
32
diff
changeset
|
33 stdout=subprocess.PIPE, stderr=subprocess.PIPE) |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
34 except Exception as 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
|
35 sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
36 # Use .communicate as can get deadlocks with .wait(), |
| 25 | 37 stdout, stderr = child.communicate() |
| 38 return_code = child.returncode | |
| 39 if return_code: | |
| 40 cmd_str = " ".join(cmd) # doesn't quote spaces etc | |
| 41 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
|
42 sys.exit("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr)) |
| 25 | 43 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
|
44 sys.exit("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr)) |
| 25 | 45 |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
46 |
| 25 | 47 def get_version(mira_binary): |
|
38
cee8f9005e43
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 206259620376b322fc8ed99a6efdd3712f38764b
peterjc
parents:
35
diff
changeset
|
48 """Run MIRA to find its version number.""" |
| 25 | 49 # At the commend line I would use: mira -v | head -n 1 |
| 50 # however there is some pipe error when doing that here. | |
| 51 cmd = [mira_binary, "-v"] | |
| 52 try: | |
| 53 child = subprocess.Popen(cmd, | |
| 54 stdout=subprocess.PIPE, | |
| 55 stderr=subprocess.STDOUT) | |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
56 except Exception as err: |
| 25 | 57 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) |
| 58 sys.exit(1) | |
| 59 ver, tmp = child.communicate() | |
| 60 del child | |
| 61 return ver.split("\n", 1)[0].strip() | |
| 62 | |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
63 |
|
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
64 # Parse Command Line |
| 25 | 65 usage = """Galaxy MIRA4 wrapper script v%s - use as follows: |
| 66 | |
| 67 $ python mira4_convert.py ... | |
| 68 | |
| 69 This will run the MIRA miraconvert binary and collect its output files as directed. | |
| 70 """ % WRAPPER_VER | |
| 71 parser = OptionParser(usage=usage) | |
| 72 parser.add_option("--input", dest="input", | |
| 73 default=None, metavar="FILE", | |
| 74 help="MIRA input filename") | |
| 75 parser.add_option("-x", "--min_length", dest="min_length", | |
| 76 default="0", | |
| 77 help="Minimum contig length") | |
| 78 parser.add_option("-y", "--min_cover", dest="min_cover", | |
| 79 default="0", | |
| 80 help="Minimum average contig coverage") | |
| 81 parser.add_option("-z", "--min_reads", dest="min_reads", | |
| 82 default="0", | |
| 83 help="Minimum reads per contig") | |
| 84 parser.add_option("--maf", dest="maf", | |
| 85 default="", metavar="FILE", | |
| 86 help="MIRA MAF output filename") | |
| 87 parser.add_option("--ace", dest="ace", | |
| 88 default="", metavar="FILE", | |
| 89 help="ACE output filename") | |
| 90 parser.add_option("--bam", dest="bam", | |
| 91 default="", metavar="FILE", | |
| 92 help="Unpadded BAM output filename") | |
| 93 parser.add_option("--fasta", dest="fasta", | |
| 94 default="", metavar="FILE", | |
| 95 help="Unpadded FASTA output filename") | |
| 96 parser.add_option("--cstats", dest="cstats", | |
| 97 default="", metavar="FILE", | |
| 98 help="Contig statistics filename") | |
| 99 parser.add_option("-v", "--version", dest="version", | |
| 100 default=False, action="store_true", | |
| 101 help="Show version and quit") | |
| 102 options, args = parser.parse_args() | |
| 103 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
|
104 sys.exit("Expected options (e.g. --input example.maf), not arguments") |
| 25 | 105 |
| 106 input_maf = options.input | |
| 107 out_maf = options.maf | |
| 108 out_bam = options.bam | |
| 109 out_fasta = options.fasta | |
| 110 out_ace = options.ace | |
| 111 out_cstats = options.cstats | |
| 112 | |
|
35
259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
34
diff
changeset
|
113 if "MIRA4" in os.environ: |
| 25 | 114 mira_path = os.environ["MIRA4"] |
|
35
259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
34
diff
changeset
|
115 mira_convert = os.path.join(mira_path, "miraconvert") |
|
259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
34
diff
changeset
|
116 if not os.path.isfile(mira_convert): |
|
259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
34
diff
changeset
|
117 sys.exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s" |
|
259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
34
diff
changeset
|
118 % (mira_convert, ", ".join(os.listdir(mira_path)))) |
|
259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
34
diff
changeset
|
119 else: |
|
259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
34
diff
changeset
|
120 sys.stderr.write("DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n") |
|
259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
34
diff
changeset
|
121 mira_path = None |
|
259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
34
diff
changeset
|
122 mira_convert = "miraconvert" |
| 25 | 123 |
| 124 mira_convert_ver = get_version(mira_convert) | |
| 125 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
|
126 sys.exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_convert_ver, mira_convert)) |
| 25 | 127 if options.version: |
| 128 print("%s, MIRA wrapper version %s" % (mira_convert_ver, WRAPPER_VER)) | |
| 129 sys.exit(0) | |
| 130 | |
| 131 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
|
132 sys.exit("Input MIRA file is required") |
| 25 | 133 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
|
134 sys.exit("Missing input MIRA file: %r" % input_maf) |
| 25 | 135 |
| 136 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
|
137 sys.exit("No output requested") |
| 25 | 138 |
| 139 | |
| 140 def check_min_int(value, name): | |
| 141 try: | |
| 142 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
|
143 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
|
144 sys.exit("Bad %s setting, %r" % (name, value)) |
| 25 | 145 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
|
146 sys.exit("Negative %s setting, %r" % (name, value)) |
| 25 | 147 return i |
| 148 | |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
149 |
| 25 | 150 min_length = check_min_int(options.min_length, "minimum length") |
| 151 min_cover = check_min_int(options.min_cover, "minimum cover") | |
| 152 min_reads = check_min_int(options.min_reads, "minimum reads") | |
| 153 | |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
154 # TODO - Run MIRA in /tmp or a configurable directory? |
|
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
155 # Currently Galaxy puts us somewhere safe like: |
|
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
156 # /opt/galaxy-dist/database/job_working_directory/846/ |
| 25 | 157 temp = "." |
| 158 | |
| 159 | |
| 160 cmd_list = [mira_convert] | |
| 161 if min_length: | |
| 162 cmd_list.extend(["-x", str(min_length)]) | |
| 163 if min_cover: | |
| 164 cmd_list.extend(["-y", str(min_cover)]) | |
| 165 if min_reads: | |
| 166 cmd_list.extend(["-z", str(min_reads)]) | |
| 167 cmd_list.extend(["-f", "maf", input_maf, os.path.join(temp, "converted")]) | |
| 168 if out_maf: | |
| 169 cmd_list.append("maf") | |
| 170 if out_bam: | |
| 171 cmd_list.append("samnbb") | |
| 172 if not out_fasta: | |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
173 # Need this for samtools depad |
| 25 | 174 out_fasta = os.path.join(temp, "depadded.fasta") |
| 175 if out_fasta: | |
| 176 cmd_list.append("fasta") | |
| 177 if out_ace: | |
| 178 cmd_list.append("ace") | |
| 179 if out_cstats: | |
| 180 cmd_list.append("cstats") | |
| 181 run(cmd_list) | |
| 182 | |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
183 |
| 25 | 184 def collect(old, new): |
| 185 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
|
186 sys.exit("Missing expected output file %s" % old) |
| 25 | 187 shutil.move(old, new) |
| 188 | |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
189 |
| 25 | 190 if out_maf: |
| 191 collect(os.path.join(temp, "converted.maf"), out_maf) | |
| 192 if out_fasta: | |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
193 # Can we look at the MAF file to see if there are multiple strains? |
| 25 | 194 old = os.path.join(temp, "converted_AllStrains.unpadded.fasta") |
| 195 if os.path.isfile(old): | |
| 196 collect(old, out_fasta) | |
| 197 else: | |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
198 # Might the output be filtered down to zero contigs? |
| 25 | 199 old = os.path.join(temp, "converted.fasta") |
| 200 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
|
201 sys.exit("Missing expected output FASTA file") |
| 25 | 202 elif os.path.getsize(old) == 0: |
| 203 print("Warning - no contigs (harsh filters?)") | |
| 204 collect(old, out_fasta) | |
| 205 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
|
206 sys.exit("Missing expected output FASTA file (only generic file present)") |
| 25 | 207 if out_ace: |
| 208 collect(os.path.join(temp, "converted.maf"), out_ace) | |
| 209 if out_cstats: | |
| 210 collect(os.path.join(temp, "converted_info_contigstats.txt"), out_cstats) | |
| 211 | |
| 212 if out_bam: | |
| 213 assert os.path.isfile(out_fasta) | |
| 214 old = os.path.join(temp, "converted.samnbb") | |
| 215 if not os.path.isfile(old): | |
| 216 old = os.path.join(temp, "converted.sam") | |
| 217 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
|
218 sys.exit("Missing expected intermediate file %s" % old) |
| 25 | 219 h = BytesIO() |
| 220 msg = depad(out_fasta, old, out_bam, h) | |
| 221 if msg: | |
| 222 print(msg) | |
| 223 print(h.getvalue()) | |
| 224 h.close() | |
| 225 sys.exit(1) | |
| 226 h.close() | |
| 227 if out_fasta == os.path.join(temp, "depadded.fasta"): | |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
31
diff
changeset
|
228 # Not asked for by Galaxy, no longer needed |
| 25 | 229 os.remove(out_fasta) |
| 230 | |
| 231 if min_length or min_cover or min_reads: | |
| 232 print("Filtered.") | |
| 233 else: | |
| 234 print("Converted.") |