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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,170 @@ | ||
| #!/usr/bin/env python | ||
|
|
||
| ############################################################################### | ||
| # # | ||
| # This program is free software: you can redistribute it and/or modify # | ||
| # it under the terms of the GNU General Public License as published by # | ||
| # the Free Software Foundation, either version 3 of the License, or # | ||
| # (at your option) any later version. # | ||
| # # | ||
| # This program is distributed in the hope that it will be useful, # | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of # | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # | ||
| # GNU General Public License for more details. # | ||
| # # | ||
| # You should have received a copy of the GNU General Public License # | ||
| # along with this program. If not, see <http://www.gnu.org/licenses/>. # | ||
| # # | ||
| ############################################################################### | ||
|
|
||
| __prog_name__ = 'checkHierarchy' | ||
| __prog_desc__ = '<program description>' | ||
|
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| __author__ = 'Donovan Parks' | ||
| __copyright__ = 'Copyright 2014' | ||
| __credits__ = ['Donovan Parks'] | ||
| __license__ = 'GPL3' | ||
| __version__ = '0.0.1' | ||
| __maintainer__ = 'Donovan Parks' | ||
| __email__ = '[email protected]' | ||
| __status__ = 'Development' | ||
|
|
||
| import os | ||
| import sys | ||
| import argparse | ||
| from collections import defaultdict | ||
|
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||
| def isNumber(s): | ||
| """Check is a string is a number.""" | ||
| try: | ||
| float(s) | ||
| return True | ||
| except ValueError: | ||
| return False | ||
|
|
||
| class CheckHierarchy(object): | ||
| def __init__(self): | ||
| pass | ||
|
|
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| def isUnclassified(self, value): | ||
| """Check if value (taxon, metabolic pathway) is unclassified.""" | ||
|
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| # currently unclassified sequences need to be explicitly stated as | ||
| # 'unclassified' (case insensitive) or '*__unclassified' which is | ||
| # the format used by GreenGenes | ||
| return value.lower() == 'unclassified' or value.lower()[1:] == '__unclassified' | ||
|
|
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| def determineHierarchicalColumns(self, headerValues, firstDataValues): | ||
| """Determine columns corresponding to user-defined hierarchy.""" | ||
|
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| # first column entry that is numeric is assumed to be from first sample | ||
| firstSampleIndex = 0 | ||
| for entry in firstDataValues: | ||
| if isNumber(entry): | ||
| break | ||
| firstSampleIndex += 1 | ||
|
|
||
| # sanity check profile | ||
| numSamples = len(headerValues) - firstSampleIndex | ||
| if numSamples < 2: | ||
| print '[Error] Profile must contain at least two samples. Identified %d samples' % numSamples | ||
| sys.exit() | ||
|
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| if firstSampleIndex == 0: | ||
| print '[Error] Profile file must contain at least one column indicating feature names.' | ||
| sys.exit() | ||
|
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| print 'Identified %d samples.' % numSamples | ||
| print 'Identified %d hierarchical columns.' % firstSampleIndex | ||
|
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| # get name of hierarchical columns | ||
| columnNames = headerValues[0:firstSampleIndex] | ||
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| return columnNames | ||
|
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| def run(self, stampProfile): | ||
| """Verify that data forms a strict hierarchy.""" | ||
| parent = defaultdict(dict) | ||
|
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| # identify entries breaking hierarchy | ||
| entriesWithUnclassifiedParents = [] | ||
| entriesBreakingHierarchy = [] | ||
| with open(stampProfile, 'U') as f: | ||
| header = f.readline() | ||
| headerValues = map(str.strip, header.split('\t')) | ||
|
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| columnNames = None | ||
| for i, line in enumerate(f): | ||
| rowNumber = i+2 # +1 for header row, +1 for zero indexing | ||
| lineSplit = line.split('\t') | ||
| dataValues = map(str.strip, lineSplit) | ||
|
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| if len(headerValues) != len(dataValues): | ||
| print '[Error] Line %d does not contain as many entries as the header line.' % rowNumber | ||
| sys.exit() | ||
|
|
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| if not columnNames: | ||
| columnNames = self.determineHierarchicalColumns(headerValues, dataValues) | ||
|
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| categories = dataValues[0:len(columnNames)] | ||
| for r, value in enumerate(categories): | ||
| # top of hierarchy has no parent | ||
| if r == 0: | ||
| continue | ||
|
|
||
| # ignore unclassified sequences | ||
| if self.isUnclassified(value): | ||
| continue | ||
|
|
||
| # make sure parent is not unclassified | ||
| parentValue = categories[r-1] | ||
| if self.isUnclassified(parentValue): | ||
| entriesWithUnclassifiedParents.append([rowNumber, r, value]) | ||
| continue | ||
|
|
||
| if r not in parent: | ||
| parent[r] = {} | ||
|
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| if value not in parent[r]: | ||
| parent[r][value] = parentValue | ||
| else: | ||
| if parent[r][value] != parentValue: | ||
| entriesBreakingHierarchy.append([rowNumber, r, value, parent[r][value], parentValue]) | ||
|
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| # report entries breaking hierarchy | ||
| if len(entriesWithUnclassifiedParents) > 0: | ||
| print '' | ||
| print 'The following entries have an unclassified parent:' | ||
| for entry in entriesWithUnclassifiedParents: | ||
| rowNumber, r, value = entry | ||
| print '%s\t%s\t%s' % (rowNumber, columnNames[r], value) | ||
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| if len(entriesBreakingHierarchy) > 0: | ||
| print '' | ||
| print 'The following entries have two (and potentially more) parents:' | ||
| for entry in entriesBreakingHierarchy: | ||
| rowNumber, r, value, parent1, parent2 = entry | ||
| print '%s\t%s\t%s\t%s' % (rowNumber, columnNames[r], value, ','.join([parent1, parent2])) | ||
|
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| if len(entriesWithUnclassifiedParents) == 0 and len(entriesBreakingHierarchy) == 0: | ||
| print '' | ||
| print 'Profile forms a strict hierarchy. You are good to go!' | ||
|
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| if __name__ == '__main__': | ||
| print __prog_name__ + ' v' + __version__ + ': ' + __prog_desc__ | ||
| print ' by ' + __author__ + ' (' + __email__ + ')' + '\n' | ||
|
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| parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) | ||
| parser.add_argument('stamp_profile', help='STAMP profile to evaluate') | ||
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| args = parser.parse_args() | ||
|
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| try: | ||
| checkHierarchy = CheckHierarchy() | ||
| checkHierarchy.run(args.stamp_profile) | ||
| except SystemExit: | ||
| print "\nControlled exit resulting from an unrecoverable error or warning." | ||
| except: | ||
| print "\nUnexpected error:", sys.exc_info()[0] | ||
| raise |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -37,7 +37,7 @@ | |
| ('.', ['README.md'])] | ||
| setup( | ||
| name='STAMP', | ||
| version='2.0.7', | ||
| version='2.0.8', | ||
| author='Donovan Parks, Rob Beiko', | ||
| author_email='[email protected]', | ||
| packages=['stamp', 'stamp.GUI'] + pluginPkgs + metagenomicPkgs, | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -23,8 +23,8 @@ | |
| __copyright__ = 'Copyright 2013' | ||
| __credits__ = ['Donovan Parks'] | ||
| __license__ = 'GPL3' | ||
| __version__ = '2.0.7' | ||
| __date__ = 'July 26, 2014' | ||
| __version__ = '2.0.8' | ||
| __date__ = 'August 4, 2014' | ||
| __maintainer__ = 'Donovan Parks' | ||
| __email__ = '[email protected]' | ||
| __status__ = 'Development' | ||
|
|
||
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This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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