Mercurial > repos > peterjc > mira4_assembler
changeset 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 | b506e3b779fa |
| children | 56b421d59805 |
| files | tools/mira4_0/mira4.py tools/mira4_0/mira4_bait.py tools/mira4_0/mira4_convert.py tools/mira4_0/mira4_make_bam.py |
| diffstat | 4 files changed, 40 insertions(+), 57 deletions(-) [+] |
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--- a/tools/mira4_0/mira4.py Wed Oct 07 09:08:29 2015 -0400 +++ b/tools/mira4_0/mira4.py Wed Feb 10 09:07:39 2016 -0500 @@ -14,10 +14,6 @@ WRAPPER_VER = "0.0.4" #Keep in sync with the XML file -def sys_exit(msg, err=1): - sys.stderr.write(msg+"\n") - sys.exit(err) - def get_version(mira_binary): """Run MIRA to find its version number""" @@ -71,22 +67,22 @@ try: mira_path = os.environ["MIRA4"] except KeyError: - sys_exit("Environment variable $MIRA4 not set") + sys.exit("Environment variable $MIRA4 not set") mira_binary = os.path.join(mira_path, "mira") if not os.path.isfile(mira_binary): - sys_exit("Missing mira under $MIRA4, %r\nFolder contained: %s" + sys.exit("Missing mira under $MIRA4, %r\nFolder contained: %s" % (mira_binary, ", ".join(os.listdir(mira_path)))) mira_convert = os.path.join(mira_path, "miraconvert") if not os.path.isfile(mira_convert): - sys_exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s" + sys.exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s" % (mira_convert, ", ".join(os.listdir(mira_path)))) mira_ver = get_version(mira_binary) if not mira_ver.strip().startswith("4.0"): - sys_exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_binary)) + sys.exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_binary)) mira_convert_ver = get_version(mira_convert) if not mira_convert_ver.strip().startswith("4.0"): - sys_exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_convert)) + sys.exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_convert)) if options.version: print "%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER) if mira_ver != mira_convert_ver: @@ -94,9 +90,9 @@ sys.exit(0) if not manifest: - sys_exit("Manifest is required") + sys.exit("Manifest is required") elif not os.path.isfile(manifest): - sys_exit("Missing input MIRA manifest file: %r" % manifest) + sys.exit("Missing input MIRA manifest file: %r" % manifest) try: @@ -149,14 +145,13 @@ def collect_output(temp, name, handle): """Moves files to the output filenames (global variables).""" - n3 = (temp, name, name, name) f = "%s/%s_assembly/%s_d_results" % (temp, name, name) if not os.path.isdir(f): log_manifest(manifest) - sys_exit("Missing output folder") + sys.exit("Missing output folder") if not os.listdir(f): log_manifest(manifest) - sys_exit("Empty output folder") + sys.exit("Empty output folder") missing = [] old_maf = "%s/%s_out.maf" % (f, name) @@ -201,7 +196,7 @@ #Not collecting the MAF file, use original location msg = make_bam(mira_convert, old_maf, ref_fasta, out_bam, handle) if msg: - sys_exit(msg) + sys.exit(msg) def clean_up(temp, name): folder = "%s/%s_assembly" % (temp, name) @@ -277,8 +272,9 @@ handle.close() clean_up(temp, name) log_manifest(manifest) - sys_exit("Return error code %i from command:\n%s" % (return_code, cmd), - return_code) + sys.stderr.write("Return error code %i from command:\n" % return_code) + sys.stderr.write(cmd + "\n") + sys.exit(eturn_code) handle.flush() if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"):
--- a/tools/mira4_0/mira4_bait.py Wed Oct 07 09:08:29 2015 -0400 +++ b/tools/mira4_0/mira4_bait.py Wed Feb 10 09:07:39 2016 -0500 @@ -9,10 +9,6 @@ WRAPPER_VER = "0.0.5" #Keep in sync with the XML file -def sys_exit(msg, err=1): - sys.stderr.write(msg+"\n") - sys.exit(err) - def get_version(mira_binary): """Run MIRA to find its version number""" @@ -34,20 +30,20 @@ if " version " in line: line = line.split() return line[line.index("version")+1].rstrip(")") - sys_exit("Could not determine MIRA version:\n%s" % ver) + sys.exit("Could not determine MIRA version:\n%s" % ver) return ver.split("\n", 1)[0] try: mira_path = os.environ["MIRA4"] except KeyError: - sys_exit("Environment variable $MIRA4 not set") + sys.exit("Environment variable $MIRA4 not set") mira_binary = os.path.join(mira_path, "mirabait") if not os.path.isfile(mira_binary): - sys_exit("Missing mirabait under $MIRA4, %r\nFolder contained: %s" + sys.exit("Missing mirabait under $MIRA4, %r\nFolder contained: %s" % (mira_binary, ", ".join(os.listdir(mira_path)))) mira_ver = get_version(mira_binary) if not mira_ver.strip().startswith("4.0"): - sys_exit("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver) + sys.exit("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver) if "-v" in sys.argv or "--version" in sys.argv: print "%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER) sys.exit(0) @@ -60,7 +56,7 @@ elif format == "mira": format = "maf" elif format != "fasta": - sys_exit("Was not expected format %r" % format) + sys.exit("Was not expected format %r" % format) assert out_file.endswith(".dat") out_file_stem = out_file[:-4] @@ -74,14 +70,14 @@ #Invert the selection... cmd_list.insert(1, "-i") else: - sys_exit("Output choice should be 'pos' or 'neg', not %r" % output_choice) + sys.exit("Output choice should be 'pos' or 'neg', not %r" % output_choice) if strand_choice == "both": pass elif strand_choice == "fwd": #Ingore reverse strand... cmd_list.insert(1, "-r") else: - sys_exit("Strand choice should be 'both' or 'fwd', not %r" % strand_choice) + sys.exit("Strand choice should be 'both' or 'fwd', not %r" % strand_choice) cmd = " ".join(cmd_list) #print cmd @@ -103,12 +99,12 @@ if return_code: sys.stderr.write(stdout) - sys_exit("Return error code %i from command:\n%s" % (return_code, cmd), + sys.exit("Return error code %i from command:\n%s" % (return_code, cmd), return_code) #Capture output out_tmp = out_file_stem + "." + format if not os.path.isfile(out_tmp): sys.stderr.write(stdout) - sys_exit("Missing output file from mirabait: %s" % out_tmp) + sys.exit("Missing output file from mirabait: %s" % out_tmp) shutil.move(out_tmp, out_file)
--- a/tools/mira4_0/mira4_convert.py Wed Oct 07 09:08:29 2015 -0400 +++ b/tools/mira4_0/mira4_convert.py Wed Feb 10 09:07:39 2016 -0500 @@ -7,8 +7,6 @@ import sys import subprocess import shutil -import time -import tempfile from optparse import OptionParser try: from io import BytesIO @@ -21,9 +19,6 @@ WRAPPER_VER = "0.0.7" # Keep in sync with the XML file -def sys_exit(msg, err=1): - sys.stderr.write(msg+"\n") - sys.exit(err) def run(cmd): #Avoid using shell=True when we call subprocess to ensure if the Python @@ -31,16 +26,16 @@ try: child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except Exception, err: - sys_exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) + sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) #Use .communicate as can get deadlocks with .wait(), stdout, stderr = child.communicate() return_code = child.returncode if return_code: cmd_str = " ".join(cmd) # doesn't quote spaces etc if stderr and stdout: - sys_exit("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr)) + sys.exit("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr)) else: - sys_exit("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr)) + sys.exit("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr)) def get_version(mira_binary): """Run MIRA to find its version number""" @@ -98,7 +93,7 @@ help="Show version and quit") options, args = parser.parse_args() if args: - sys_exit("Expected options (e.g. --input example.maf), not arguments") + sys.exit("Expected options (e.g. --input example.maf), not arguments") input_maf = options.input out_maf = options.maf @@ -110,35 +105,35 @@ try: mira_path = os.environ["MIRA4"] except KeyError: - sys_exit("Environment variable $MIRA4 not set") + sys.exit("Environment variable $MIRA4 not set") mira_convert = os.path.join(mira_path, "miraconvert") if not os.path.isfile(mira_convert): - sys_exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s" + sys.exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s" % (mira_convert, ", ".join(os.listdir(mira_path)))) mira_convert_ver = get_version(mira_convert) if not mira_convert_ver.strip().startswith("4.0"): - sys_exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_convert_ver, mira_convert)) + sys.exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_convert_ver, mira_convert)) if options.version: print("%s, MIRA wrapper version %s" % (mira_convert_ver, WRAPPER_VER)) sys.exit(0) if not input_maf: - sys_exit("Input MIRA file is required") + sys.exit("Input MIRA file is required") elif not os.path.isfile(input_maf): - sys_exit("Missing input MIRA file: %r" % input_maf) + sys.exit("Missing input MIRA file: %r" % input_maf) if not (out_maf or out_bam or out_fasta or out_ace or out_cstats): - sys_exit("No output requested") + sys.exit("No output requested") def check_min_int(value, name): try: i = int(value) - except: - sys_exit("Bad %s setting, %r" % (name, value)) + except ValueError: + sys.exit("Bad %s setting, %r" % (name, value)) if i < 0: - sys_exit("Negative %s setting, %r" % (name, value)) + sys.exit("Negative %s setting, %r" % (name, value)) return i min_length = check_min_int(options.min_length, "minimum length") @@ -176,7 +171,7 @@ def collect(old, new): if not os.path.isfile(old): - sys_exit("Missing expected output file %s" % old) + sys.exit("Missing expected output file %s" % old) shutil.move(old, new) if out_maf: @@ -190,12 +185,12 @@ #Might the output be filtered down to zero contigs? old = os.path.join(temp, "converted.fasta") if not os.path.isfile(old): - sys_exit("Missing expected output FASTA file") + sys.exit("Missing expected output FASTA file") elif os.path.getsize(old) == 0: print("Warning - no contigs (harsh filters?)") collect(old, out_fasta) else: - sys_exit("Missing expected output FASTA file (only generic file present)") + sys.exit("Missing expected output FASTA file (only generic file present)") if out_ace: collect(os.path.join(temp, "converted.maf"), out_ace) if out_cstats: @@ -207,7 +202,7 @@ if not os.path.isfile(old): old = os.path.join(temp, "converted.sam") if not os.path.isfile(old): - sys_exit("Missing expected intermediate file %s" % old) + sys.exit("Missing expected intermediate file %s" % old) h = BytesIO() msg = depad(out_fasta, old, out_bam, h) if msg:
--- a/tools/mira4_0/mira4_make_bam.py Wed Oct 07 09:08:29 2015 -0400 +++ b/tools/mira4_0/mira4_make_bam.py Wed Feb 10 09:07:39 2016 -0500 @@ -7,10 +7,6 @@ import subprocess import tempfile -def sys_exit(msg, err=1): - sys.stderr.write(msg+"\n") - sys.exit(err) - def run(cmd, log_handle): try: child = subprocess.Popen(cmd, shell=True, @@ -89,4 +85,4 @@ mira_convert, maf_file, fasta_file, bam_file = sys.argv[1:] msg = make_bam(mira_convert, maf_file, fasta_file, bam_file, sys.stdout) if msg: - sys_exit(msg) + sys.exit(msg)