comparison list-chrom-cols.py @ 2:20d69a062da3 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8

1:253d531a0193

            cols.append( (coldesc['name'], colid, i == 0) )
            ++i
        
    elif dbtype == 'inhouse':
        # Get field for chromatographic column name
        col_field = 'col'
        if dbfields is not None:
            fields = dict(u.split("=") for u in dbfields.split(","))
            if 'col' in fields:
                col_field = fields['col']
                
        # Get all column names from file
        with open(dburl.get_file_name(), 'rb') as dbfile:
            reader = csv.reader(dbfile, delimiter = "\t", quotechar='"')
            header = reader.next()
            i = header.index(col_field)
            allcols = []
            for row in reader:
                col = row[i]
                if col not in allcols:
                    allcols.append(col)
            for i, c in enumerate(allcols):
                cols.append( (c, c, i == 0) )
    
    return cols

########
# MAIN #

2:20d69a062da3

            cols.append( (coldesc['name'], colid, i == 0) )
            ++i
        
    elif dbtype == 'inhouse':
        # Get field for chromatographic column name
        col_field = 'chromcol'
        if dbfields is not None:
            fields = dict(u.split("=") for u in dbfields.split(","))
            if 'chromcol' in fields:
                col_field = fields['chromcol']
                
        # Get all column names from file
        with open(dburl if isinstance(dburl, str) else dburl.get_file_name(), 'rb') as dbfile:
            reader = csv.reader(dbfile, delimiter = "\t", quotechar='"')
            header = reader.next()
            if col_field in header:
                i = header.index(col_field)
                allcols = []
                for row in reader:
                    col = row[i]
                    if col not in allcols:
                        allcols.append(col)
                for i, c in enumerate(allcols):
                    cols.append( (c, c, i == 0) )
    
    return cols

########
# MAIN #