diff dma-filelist-generation.py @ 0:55aa2dd24828 draft

planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dma-filelist-generation.py	Tue Mar 27 06:52:39 2018 -0400
@@ -0,0 +1,154 @@
+import argparse
+import textwrap
+import os
+import re
+import collections
+import csv
+from operator import itemgetter
+
+def check_folder(in_dir, reg_string):
+    filelist = []
+    for f in os.listdir(in_dir):
+
+        if re.match(reg_string, f, re.IGNORECASE):
+
+            fn, fe = os.path.splitext(f)
+            fnl = fn.split("_")
+            filename = fn
+            fullpth = os.path.join(in_dir, f)
+            wells = fnl[0]
+
+
+
+            if re.match("^.*pos.*", f, re.IGNORECASE):
+                polarity = "pos"
+            elif re.match("^.*neg.*", f, re.IGNORECASE):
+                polarity = "neg"
+            else:
+                error_message = "Files need to have either 'pos' or 'neg' in the file name"
+                print error_message
+                return 1, error_message, "", ""
+            if re.match("^.*blank.*", f, re.IGNORECASE):
+                sample_type = "blank"
+            else:
+                sample_type = "sample"
+
+
+            filelist.append([wells, sample_type, polarity, filename, fullpth])
+
+    return filelist
+
+def get_filelist(filesin, o, file_type='mzML', create_filelist=True):
+
+    filedict = collections.OrderedDict()
+
+
+    if file_type=="mzML":
+        reg_string = "^.*mzML$"
+    else:
+        reg_string = "^.*raw$"
+
+    if isinstance(filesin, list):
+        filelist = []
+        for f in filesin:
+            filelist.extend(check_folder(f, reg_string))
+    else:
+        filelist = check_folder(filesin, reg_string)
+
+    # Turn filelist into a dictionary
+    for f1 in filelist:
+        well = f1[0]
+        filedict[well] = []
+        for f2 in filelist:
+            if well == f2[0]:
+                filedict[well].append(f2[1:len(f2)+1])
+
+
+
+    filelist = sorted(filelist, key=itemgetter(0, 1))
+
+    for k, v in filedict.iteritems():
+        classes = [i[0] for i in v]
+        classes.sort()
+        if not classes == ['blank', 'sample']:
+            error_message = "!!!!ERROR!!!! Blank and sample required for each well, file type {}".format(file_type)
+            print error_message
+            return 1, error_message, "", ""
+
+    print 'files of type {} checked, files OK'.format(file_type)
+
+    if create_filelist:
+
+        outname = write_filedict(filedict, o, file_type)
+        print 'filelist created in folder {}, using file type {}, full path {}'.format(o, file_type, outname)
+
+    return 0, "files OK", filedict, filelist
+
+def write_filedict(filedict, out_dir, file_type, file_spacing='tsv'):
+
+    outname = os.path.join(out_dir,'filelist_{}.{}'.format(file_type, file_spacing))
+
+    if file_spacing=='tsv':
+        delim = '\t'
+    elif file_spacing=='csv':
+        delim = ','
+    else:
+        delim = ','
+
+
+    with open(outname, 'wb') as csvfile:
+        w = csv.writer(csvfile, delimiter=delim)
+
+        w.writerow(['filename','classLabel', 'multilist', 'multilistLabel'])
+        c = 1
+        for k, v in filedict.iteritems():
+            for i in v:
+                w.writerow([os.path.basename(i[3]), i[0], c, k])
+            c +=1
+
+    return outname
+
+
+def main():
+
+    p = argparse.ArgumentParser(prog='PROG',
+                                formatter_class=argparse.RawDescriptionHelpFormatter,
+                                description='''Create filelist for DMA DIMS nearline workflow''',
+                                epilog=textwrap.dedent('''
+                            -------------------------------------------------------------------------
+
+                            Example Usage
+
+                            python dma-filelist-generation.py -i [dir with sample files], [dir with blank files] -o .
+
+                            '''))
+
+    p.add_argument('-i', dest='i', help='dir with sample files',  nargs = '*', required=True)
+    p.add_argument('-o', dest='o', help='out dir', required=True)
+    p.add_argument('--check_mzml', dest='check_mzml', action='store_true')
+    p.add_argument('--check_raw', dest='check_raw', action='store_true')
+    p.add_argument('--create_filelist_mzml', dest='create_filelist_mzml', action='store_true')
+    p.add_argument('--create_filelist_raw', dest='create_filelist_raw', action='store_true')
+
+    args = p.parse_args()
+
+    if not os.path.exists(args.o):
+        os.makedirs(args.o)
+    print args.o
+
+    if not args.check_mzml and not args.check_raw:
+        print '--check_mzml or --check_raw (or both) are required as inputs'
+        exit()
+
+    if args.check_mzml:
+        get_filelist(args.i, args.o, file_type='mzML', create_filelist=args.create_filelist_mzml)
+
+    if args.check_raw:
+
+        get_filelist(args.i, args.o, file_type='raw',  create_filelist=args.create_filelist_raw)
+
+
+
+if __name__ == '__main__':
+    main()
+