Mercurial > repos > peterjc > mira_assembler
changeset 4:117cce3296af
Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
The Galaxy wrapper will no longer work with MIRA v3.2.x - if you are still using the old version of MIRA, please continue to use v0.0.2 of the wrapper.
| author | peterjc |
|---|---|
| date | Wed, 21 Dec 2011 11:33:19 -0500 |
| parents | 298f5c1d9521 |
| children | 216bf640baaf |
| files | tools/sr_assembly/mira.py tools/sr_assembly/mira.txt tools/sr_assembly/mira.xml |
| diffstat | 3 files changed, 60 insertions(+), 51 deletions(-) [+] |
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--- a/tools/sr_assembly/mira.py Tue Jun 21 09:50:32 2011 -0400 +++ b/tools/sr_assembly/mira.py Wed Dec 21 11:33:19 2011 -0500 @@ -11,24 +11,6 @@ sys.stderr.write(msg+"\n") sys.exit(err) -def tcs_to_tabular(old, new): - in_handle = open(old, "rU") - out_handle = open(new, "w") - assert in_handle.readline() == "#TCS V1.0\n" - assert in_handle.readline() == "#\n" - assert in_handle.readline() == "# contig name padPos upadPos | B Q | tcov covA covC covG covT cov* | qA qC qG qT q* | S | Tags\n" - assert in_handle.readline() == "#\n" - out_handle.write("#%s\n" % "\t".join(["contig", "pasPos", "upadPos", "B", "Q", - "tcov", "covA", "covC", "covG", "covT", "cov*", - "qA", "qC", "qG", "qT", "q*", "S", "Tags"])) - for line in in_handle: - parts = line.rstrip("\n").split(None,22) - assert parts[3] == parts[6] == parts[13] == parts[19] == parts[21] == "|" - wanted = parts[:3] + parts[4:6]+parts[7:13]+parts[14:19]+parts[20:21]+parts[22:] - out_handle.write("%s\n" % "\t".join(wanted)) - out_handle.close() - in_handle.close() - def collect_output(temp, name): n3 = (temp, name, name, name) f = "%s/%s_assembly/%s_d_results" % (temp, name, name) @@ -36,16 +18,18 @@ stop_err("Missing output folder") if not os.listdir(f): stop_err("Empty output folder") + missing = [] for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta), ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual), ("%s/%s_out.wig" % (f, name), out_wig), ("%s/%s_out.caf" % (f, name), out_caf), ("%s/%s_out.ace" % (f, name), out_ace)]: if not os.path.isfile(old): - stop_err("Missing %s output file" % os.path.splitext(old)[-1]) + missing.append(os.path.splitext(old)[-1]) else: shutil.move(old, new) - tcs_to_tabular("%s/%s_assembly/%s_d_results/%s_out.tcs" % n3, out_tcs) + if missing: + stop_err("Missing output files: %s" % ", ".join(missing)) def clean_up(temp, name): folder = "%s/%s_assembly" % (temp, name) @@ -56,14 +40,15 @@ #Currently Galaxy puts us somewhere safe like: #/opt/galaxy-dist/database/job_working_directory/846/ temp = "." -name, out_fasta, out_qual, out_tcs, out_ace, out_caf, out_wig, out_log = sys.argv[1:9] +name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8] start_time = time.time() -cmd = " ".join(sys.argv[9:]) +cmd_list =sys.argv[8:] +cmd = " ".join(cmd_list) assert os.path.isdir(temp) d = "%s_assembly" % name -assert not os.path.isdir(d) +assert not os.path.isdir(d), "Path %s already exists" % d try: #Check path access os.mkdir(d) @@ -77,7 +62,7 @@ handle = open(out_log, "w") try: #Run MIRA - child = subprocess.Popen(sys.argv[9:], + child = subprocess.Popen(cmd_list, stdout=handle, stderr=subprocess.STDOUT) except Exception, err: @@ -102,6 +87,10 @@ return_code) handle.close() +#print "Collecting output..." collect_output(temp, name) + +#print "Cleaning up..." clean_up(temp, name) + print "Done"
--- a/tools/sr_assembly/mira.txt Tue Jun 21 09:50:32 2011 -0400 +++ b/tools/sr_assembly/mira.txt Wed Dec 21 11:33:19 2011 -0500 @@ -7,7 +7,7 @@ This tool is a short Python script (to collect the MIRA output and move it to where Galaxy expects the files, and convert MIRA's TCS file into a tab -separate file for use in Galaxy). There are just two files to install: +separated file for use in Galaxy). There are just two files to install: * mira.py (the Python script) * mira.xml (the Galaxy tool definition) @@ -16,9 +16,9 @@ modify the tools_conf.xml file to tell Galaxy to offer the tool and also do this to tools_conf.xml.sample in order to run any tests: -<tool file="sr_assembly/seq_primer_clip.xml" /> +<tool file="sr_assembly/mira.xml" /> -You will also need to install MIRA, we used version 3.2.1. See: +You will also need to install MIRA, we used version 3.4.0. See: http://chevreux.org/projects_mira.html http://sourceforge.net/projects/mira-assembler/ @@ -33,8 +33,13 @@ History ======= -v0.0.1 - Initial version (working prototype) +v0.0.1 - Initial version (working prototype, using MIRA 3.2.1) v0.0.2 - Improve capture of stdout/stderr (should see it as it runs) +v0.0.3 - Support Ion Torrent reads, now requires MIRA 3.4.0 or later + (some other switched changed, e.g. -OUT rrol to rrot, which + means the wrapper no longer works with MIRA 3.2.x) + - The contig summary file (TCS file) was removed in MIRA 3.4 + - Report all missing output files (not just first missing one) Developers
--- a/tools/sr_assembly/mira.xml Tue Jun 21 09:50:32 2011 -0400 +++ b/tools/sr_assembly/mira.xml Wed Dec 21 11:33:19 2011 -0500 @@ -1,40 +1,46 @@ -<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.2"> - <description>Takes Sanger, Roche, and Illumina data</description> - <command interpreter="python">mira.py mira $out_fasta $out_qual $out_tcs $out_ace $out_caf $out_wig $out_log +<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.3"> + <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description> + <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log ##Give the wrapper script list of output filenames, then the mira command... mira --job=$job_method,$job_type,$job_quality ##Input files #if $condBackbone.use == "true": ## Can this be linked to job_method as well? If mapping we need the backbone... - -SB:lb=yes -SB:bft=fasta -FN:bbin=${condBackbone.filename} + -SB:lb=1:bft=1 -FN:bbin=${condBackbone.filename} #end if #if $condSanger.use == "true": - Sanger_SETTINGS - ## Not easy to add sanger to --job, so use load_sequence_data(lsd) instead - -LR:lsd=yes + SANGER_SETTINGS + ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file - -LR:mxti=no -LR:ft=fastq -FN:fqi=${condSanger.filename} + -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename} #end if #if $condRoche.use == "true": 454_SETTINGS - ## Not easy to add 454 to --job, so use load_sequence_data(lsd) instead - -LR:lsd=yes + ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file - -LR:mxti=no -LR:ft=fastq -FN:fqi=${condRoche.filename} + -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename} #end if #if $condIllumina.use == "true": SOLEXA_SETTINGS - ## Not easy to add solexa to --job, so use load_sequence_data(lsd) instead - -LR:lsd=yes -LR:ft=fastq -FN:fgi=${condIllumina.filename} + ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead + -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename} ##TODO - Look at -LR FASTQ qual offset (fqqo) #end if - +#if $condIonTorrent.use == "true": + IONTOR_SETTINGS + ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead + ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file + -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename} +#end if ##Output files COMMON_SETTINGS -##remove_rollover_logs, remove_log_directory --OUT:rrol=yes -OUT:rld=yes +##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output +##Explicitly disable formats we won't use like MAF (reduce IO) +-OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 +##remove_rollover_tmps, remove_tmp_directory +-OUT:rrot=1:rtd=1 </command> <inputs> @@ -47,9 +53,9 @@ <option value="est">EST (transcriptome)</option> </param> <param name="job_quality" type="select" label="Assembly quality grade"> - <option value="normal">Normal</option> + <option value="accurate">Accurate</option> + <option value="normal">Normal (deprecated)</option> <option value="draft">Draft</option> - <option value="accurate">Accurate</option> </param> <!-- Backbone --> <conditional name="condBackbone"> @@ -82,7 +88,8 @@ </param> <when value="false" /> <when value="true"> - <param name="filename" type="data" format="fastq,sff" label="Roche 454 reads file" help="FASTQ format" /> + <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences --> + <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" /> </when> </conditional> <!-- Illumina --> @@ -96,11 +103,22 @@ <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" /> </when> </conditional> + <!-- Ion Torrent --> + <conditional name="condIonTorrent"> + <param name="use" type="select" label="Ion Torrent reads?"> + <option value="false">No</option> + <option value="true">Yes</option> + </param> + <when value="false" /> + <when value="true"> + <!-- TODO? Support SFF files directly, e.g. with sff_extract --> + <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" /> + </when> + </conditional> </inputs> <outputs> <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" /> <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" /> - <data name="out_tcs" format="tabular" label="MIRA contigs summary" /> <data name="out_caf" format="txt" label="MIRA contigs (CAF)" /> <data name="out_ace" format="txt" label="MIRA contigs (ACE)" /> <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" /> @@ -117,9 +135,6 @@ Runs MIRA v3, collects the output, and throws away all the temporary files. -The MIRA transposed contig summary (TCS) file is converted into a tabular file for use within Galaxy. -This records one line per base per contig, and including things like the base, quality, coverage and any tags. - **Citation** This tool uses MIRA. If you use this tool in scientific work leading to a