diff metfrag.py @ 0:75c805123b45 draft

planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metfrag.py	Tue Jul 24 07:59:44 2018 -0400
@@ -0,0 +1,117 @@
+import argparse
+import csv
+import os
+import sys
+print(sys.version)
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--input')
+parser.add_argument('--db_local')
+parser.add_argument('--db_online')
+parser.add_argument('--ppm')
+parser.add_argument('--ppm_frag')
+parser.add_argument('--fragmasstol')
+parser.add_argument('--polarity')
+parser.add_argument('--results')
+parser.add_argument('--threads')
+
+args = parser.parse_args()
+print args
+
+os.makedirs("tmet")
+
+with open(args.input,"r") as infile:
+    numlines = 0
+    for line in infile:
+        line = line.strip()
+        if numlines == 0:
+            if "NAME" in line:
+                featid = line.split("NAME: ")[1]
+            if "PRECURSORMZ" in line:
+                mz = float(line.split("PRECURSORMZ: ")[1])
+                if args.polarity=="pos":
+                    mz2 = mz-1.007276
+                else:
+                    mz2 = mz+1.007276
+            if "Num Peaks" in line:
+                numlines = int(line.split("Num Peaks: ")[1])
+                linesread = 0
+                peaklist = []
+        else:
+            if linesread == numlines:
+                numlines = 0
+                #write spec file
+                with open('./tmpspec.txt', 'w') as outfile:
+                    for p in peaklist:
+                        outfile.write(p[0]+"\t"+p[1]+"\n")
+                #create commandline input
+                cmd_command = "PeakListPath=tmpspec.txt "
+                if args.db_local != "None":
+                    cmd_command += "MetFragDatabaseType=LocalCSV "
+                    cmd_command += "LocalDatabasePath={0} ".format(args.db_local)
+                else:
+                    cmd_command += "MetFragDatabaseType={0} ".format(args.db_online)
+                cmd_command += "FragmentPeakMatchAbsoluteMassDeviation={0} ".format(args.fragmasstol)
+                cmd_command += "FragmentPeakMatchRelativeMassDeviation={0} ".format(args.ppm_frag)
+                cmd_command += "DatabaseSearchRelativeMassDeviation={0} ".format(args.ppm)
+                cmd_command += "NeutralPrecursorMass={0} ".format(mz2)
+                cmd_command += "SampleName={0}_metfrag ".format(featid)
+                cmd_command += "ResultsPath=./tmet/ "
+                if args.polarity == "pos":
+                    cmd_command += "IsPositiveIonMode=True "
+                else:
+                    cmd_command += "IsPositiveIonMode=False "
+                if args.polarity == "pos": ### Annotation information. Create a dict for the PrecurorIonModes??
+                    cmd_command += "PrecursorIonMode=1 "
+                else:
+                    cmd_command += "PrecursorIonMode=-1 "
+                cmd_command += "MetFragCandidateWriter=CSV " ## TSV not available
+                cmd_command += "NumberThreads={} ".format(args.threads)
+                # run Metfrag
+                print "metfrag {0}".format(cmd_command)
+                os.system("metfrag {0}".format(cmd_command))
+            else:
+                line = tuple(line.split("\t"))
+                linesread += 1
+                peaklist.append(line)
+
+
+#outputs might have different headers. Need to get a list of all the headers before we start merging the files
+outfiles = sorted(os.listdir("./tmet"))
+
+headers = []
+c = 0
+for fname in outfiles:
+    with open("./tmet/"+fname) as infile:
+        reader = csv.reader(infile)
+        headers.extend(reader.next())
+        # check if file has any data rows 
+        for i, row in enumerate(reader):
+            c+=1
+            if i==1:
+                break
+            
+# if no data rows (e.g. matches) then do not save an output and leave the program        
+if c==0:
+    sys.exit()
+
+
+print headers
+headers = ['UID'] + sorted(list(set(headers)))
+print headers
+
+#merge outputs
+with open(args.results, 'a') as merged_outfile:
+
+    dwriter = csv.DictWriter(merged_outfile, fieldnames=headers, delimiter='\t')
+    dwriter.writeheader()
+
+    for fname in outfiles:
+        fileid = os.path.basename(fname).split("_")[0]
+        with open("./tmet/"+fname) as infile:
+            reader = csv.DictReader(infile, delimiter=',', quotechar='"')
+            for line in reader:
+                line['UID'] = fileid
+                dwriter.writerow(line)
+
+