Mercurial > repos > iuc > filter_tabular
changeset 15:90f657745fea draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit dd35055c76d86fe98985b5825c1751efb8208242
| author | iuc |
|---|---|
| date | Thu, 27 Jun 2024 17:23:47 +0000 |
| parents | 557ec8d7087d |
| children | |
| files | filter_tabular.xml filters.py load_db.py macros.xml |
| diffstat | 4 files changed, 33 insertions(+), 23 deletions(-) [+] |
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--- a/filter_tabular.xml Wed Sep 13 12:15:22 2023 +0000 +++ b/filter_tabular.xml Thu Jun 27 17:23:47 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="filter_tabular" name="Filter Tabular" version="3.3.0"> +<tool id="filter_tabular" name="Filter Tabular" version="3.3.1"> <description></description> <macros> @@ -16,10 +16,9 @@ <configfile name="filter_json"> #import json #set $dataset_name = $input.element_identifier +#set $table=$input @LINEFILTERS@ -#if $input_filters: #echo $json.dumps($input_filters) -#end if </configfile> </configfiles> <inputs> @@ -166,6 +165,17 @@ </repeat> <output name="output" file="filtered_IEDB.tsv"/> </test> + <test> + <param name="input" ftype="tabular" value="math_input.tsv"/> + <param name="comment_char" value="False"/> + <repeat name="linefilters"> + <conditional name="filter"> + <param name="filter_type" value="skip"/> + <param name="skiplines" value=""/> + </conditional> + </repeat> + <output name="output" file="math_input.tsv"/> + </test> </tests> <help><![CDATA[ ==============
--- a/filters.py Wed Sep 13 12:15:22 2023 +0000 +++ b/filters.py Thu Jun 27 17:23:47 2024 +0000 @@ -11,7 +11,7 @@ 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.func = lambda i, line: line.rstrip('\r\n') if line else None self.src_lines = [] self.src_line_cnt = 0 @@ -28,23 +28,23 @@ 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 + self.func = lambda i, line: line if not rgx.match(line) else None elif filter_dict['action'] == 'include_match': - self.func = lambda i, l: l if rgx.match(l) else None + self.func = lambda i, line: line if rgx.match(line) else None elif filter_dict['action'] == 'exclude_find': - self.func = lambda i, l: l if not rgx.search(l) else None + self.func = lambda i, line: line if not rgx.search(line) else None elif filter_dict['action'] == 'include_find': - self.func = lambda i, l: l if rgx.search(l) else None + self.func = lambda i, line: line if rgx.search(line) 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) + self.func = lambda i, line: self.select_columns(line, cols) elif filter_dict['filter'] == 'select_column_slices': cols = [x if isinstance(x, int) else [y if y is not None else None for y in [xint(k) for k in x.split(':')]] for x in [xint(c) for c in filter_dict['columns']]] if all([isinstance(x, int) for x in cols]): - self.func = lambda i, l: self.select_columns(l, cols) + self.func = lambda i, line: self.select_columns(line, cols) else: cols = [slice(x[0], x[1], x[2] if len(x) > 2 else None) if isinstance(x, list) else x for x in cols] - self.func = lambda i, l: self.select_slices(l, cols) + self.func = lambda i, line: self.select_slices(line, cols) elif filter_dict['filter'] == 'replace': p = filter_dict['pattern'] r = filter_dict['replace'] @@ -54,32 +54,32 @@ 'append', 'before', 'after']: - self.func = lambda i, l: '\t'.join( + self.func = lambda i, line: '\t'.join( [x if j != c else re.sub(p, r, x) - for j, x in enumerate(l.split('\t'))]) + for j, x in enumerate(line.split('\t'))]) else: a = 0 if filter_dict['add'] == 'prepend'\ else min(0, c - 1) if filter_dict['add'] == 'before'\ else c + 1 if filter_dict['add'] == 'after'\ else None - self.func = lambda i, l: self.replace_add(l, p, r, c, a) + self.func = lambda i, line: self.replace_add(line, p, r, c, a) elif filter_dict['filter'] == 'prepend_line_num': - self.func = lambda i, l: '%d\t%s' % (i, l) + self.func = lambda i, line: '%d\t%s' % (i, line) elif filter_dict['filter'] == 'append_line_num': - self.func = lambda i, l: '%s\t%d' % (l.rstrip('\r\n'), i) + self.func = lambda i, line: '%s\t%d' % (line.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) + self.func = lambda i, line: '%s\t%s' % (s, line) elif filter_dict['filter'] == 'append_text': s = filter_dict['column_text'] - self.func = lambda i, l: '%s\t%s' % (l.rstrip('\r\n'), s) + self.func = lambda i, line: '%s\t%s' % (line.rstrip('\r\n'), s) elif filter_dict['filter'] == 'skip': cnt = filter_dict['count'] - self.func = lambda i, l: l if i > cnt else None + self.func = lambda i, line: line 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) + self.func = lambda i, line: self.normalize(line, cols, sep) def __iter__(self): return self
--- a/load_db.py Wed Sep 13 12:15:22 2023 +0000 +++ b/load_db.py Thu Jun 27 17:23:47 2024 +0000 @@ -328,4 +328,4 @@ c.close() except Exception as e: print('Failed: %s err: %s' % (index_def, e), file=sys.stderr) - raise(e) + raise e
--- a/macros.xml Wed Sep 13 12:15:22 2023 +0000 +++ b/macros.xml Thu Jun 27 17:23:47 2024 +0000 @@ -8,8 +8,8 @@ #set $skip_lines = None #if str($fi.filter.skip_lines) != '': #set $skip_lines = int($fi.filter.skip_lines) - #elif $tbl.table.metadata.comment_lines and $tbl.table.metadata.comment_lines > 0: - #set $skip_lines = int($tbl.table.metadata.comment_lines) + #elif $table.metadata.comment_lines and int($table.metadata.comment_lines) > 0: + #set $skip_lines = int($table.metadata.comment_lines) #end if #if $skip_lines is not None: #set $filter_dict = dict()