--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filters.py	Tue Jul 18 09:06:47 2017 -0400
@@ -0,0 +1,156 @@
+#!/usr/binsenv python
+
+from __future__ import print_function
+
+import re
+import sys
+
+
+class LineFilter(object):
+    def __init__(self, source, filter_dict):
+        self.source = source
+        self.filter_dict = filter_dict
+        self.func = lambda i, l: l.rstrip('\r\n') if l else None
+        self.src_lines = []
+        self.src_line_cnt = 0
+        if not filter_dict:
+            return
+        if filter_dict['filter'] == 'regex':
+            rgx = re.compile(filter_dict['pattern'])
+            if filter_dict['action'] == 'exclude_match':
+                self.func = lambda i, l: l if not rgx.match(l) else None
+            elif filter_dict['action'] == 'include_match':
+                self.func = lambda i, l: l if rgx.match(l) else None
+            elif filter_dict['action'] == 'exclude_find':
+                self.func = lambda i, l: l if not rgx.search(l) else None
+            elif filter_dict['action'] == 'include_find':
+                self.func = lambda i, l: l if rgx.search(l) else None
+        elif filter_dict['filter'] == 'select_columns':
+            cols = [int(c) - 1 for c in filter_dict['columns']]
+            self.func = lambda i, l: self.select_columns(l, cols)
+        elif filter_dict['filter'] == 'replace':
+            p = filter_dict['pattern']
+            r = filter_dict['replace']
+            c = int(filter_dict['column']) - 1
+            self.func = lambda i, l: '\t'.join(
+                [x if j != c else re.sub(p, r, x) for j, x in enumerate(l.split('\t'))])
+        elif filter_dict['filter'] == 'prepend_line_num':
+            self.func = lambda i, l: '%d\t%s' % (i, l)
+        elif filter_dict['filter'] == 'append_line_num':
+            self.func = lambda i, l: '%s\t%d' % (l.rstrip('\r\n'), i)
+        elif filter_dict['filter'] == 'prepend_text':
+            s = filter_dict['column_text']
+            self.func = lambda i, l: '%s\t%s' % (s, l)
+        elif filter_dict['filter'] == 'append_text':
+            s = filter_dict['column_text']
+            self.func = lambda i, l: '%s\t%s' % (l.rstrip('\r\n'), s)
+        elif filter_dict['filter'] == 'skip':
+            cnt = filter_dict['count']
+            self.func = lambda i, l: l if i > cnt else None
+        elif filter_dict['filter'] == 'normalize':
+            cols = [int(c) - 1 for c in filter_dict['columns']]
+            sep = filter_dict['separator']
+            self.func = lambda i, l: self.normalize(l, cols, sep)
+
+    def __iter__(self):
+        return self
+
+    def __next__(self):
+        if not self.src_lines:
+            self.get_lines()
+        if self.src_lines:
+            return self.src_lines.pop(0)
+        raise StopIteration
+
+    next = __next__
+
+    def select_columns(self, line, cols):
+        fields = line.split('\t')
+        return '\t'.join([fields[x] for x in cols])
+
+    def normalize(self, line, split_cols, sep):
+        lines = []
+        fields = line.rstrip('\r\n').split('\t')
+        split_fields = dict()
+        cnt = 0
+        for c in split_cols:
+            if c < len(fields):
+                split_fields[c] = fields[c].split(sep)
+                cnt = max(cnt, len(split_fields[c]))
+        if cnt == 0:
+            lines.append('\t'.join(fields))
+        else:
+            for n in range(0, cnt):
+                flds = [x if c not in split_cols else split_fields[c][n]
+                        if n < len(split_fields[c])
+                        else '' for (c, x) in enumerate(fields)]
+                lines.append('\t'.join(flds))
+        return lines
+
+    def get_lines(self):
+        for i, next_line in enumerate(self.source):
+            self.src_line_cnt += 1
+            line = self.func(self.src_line_cnt, next_line)
+            if line:
+                if isinstance(line, list):
+                    self.src_lines.extend(line)
+                else:
+                    self.src_lines.append(line)
+                return
+
+
+class TabularReader:
+    """
+    Tabular file iterator. Returns a list
+    """
+    def __init__(self, input_file, skip=0, comment_char=None, col_idx=None,
+                 filters=None):
+        self.skip = skip
+        self.comment_char = comment_char
+        self.col_idx = col_idx
+        self.filters = filters
+        self.tsv_file = \
+            input_file if hasattr(input_file, 'readline') else open(input_file)
+        if skip and skip > 0:
+            for i in range(skip):
+                if not self.tsv_file.readline():
+                    break
+        source = LineFilter(self.tsv_file, None)
+        if comment_char:
+            source = LineFilter(source,
+                                {"filter": "regex", "pattern": comment_char,
+                                 "action": "exclude_match"})
+        if filters:
+            for f in filters:
+                source = LineFilter(source, f)
+        self.source = source
+
+    def __iter__(self):
+        return self
+
+    def __next__(self):
+        ''' Iteration '''
+        for i, line in enumerate(self.source):
+            fields = line.rstrip('\r\n').split('\t')
+            if self.col_idx:
+                fields = [fields[i] for i in self.col_idx]
+            return fields
+        raise StopIteration
+
+    next = __next__
+
+
+def filter_file(input_file, output, skip=0, comment_char='#', filters=None):
+    data_lines = 0
+    try:
+        tr = TabularReader(input_file, skip=skip, comment_char=comment_char,
+                           filters=filters)
+        for linenum, fields in enumerate(tr):
+            data_lines += 1
+            try:
+                output.write('%s\n' % '\t'.join(fields))
+            except Exception as e:
+                print('Failed at line: %d err: %s' % (linenum, e),
+                      file=sys.stderr)
+    except Exception as e:
+        exit('Error: %s' % (e))