# HG changeset patch # User damion # Date 1439150740 14400 # Node ID d31a1bd74e6349ad52de432e9a1708e2f34100c8 Uploaded first version diff -r 000000000000 -r d31a1bd74e63 LICENSE.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE.md Sun Aug 09 16:05:40 2015 -0400 @@ -0,0 +1,48 @@ +Source Code License + +An Open Source Initiative (OSI) approved license +ffp_phylogeny source code is licensed under the Academic Free License version 3.0. + +Licensed under the Academic Free License version 3.0 + +1) Grant of Copyright License. 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However, You may modify the text of this License and copy, distribute or communicate your modified version (the "Modified License") and apply it to other original works of authorship subject to the following conditions: (i) You may not indicate in any way that your Modified License is the "Academic Free License" or "AFL" and you may not use those names in the name of your Modified License; (ii) You must replace the notice specified in the first paragraph above with the notice "Licensed under " or with a notice of your own that is not confusingly similar to the notice in this License; and (iii) You may not claim that your original works are open source software unless your Modified License has been approved by Open Source Initiative (OSI) and You comply with its license review and certification process. diff -r 000000000000 -r d31a1bd74e63 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Sun Aug 09 16:05:40 2015 -0400 @@ -0,0 +1,47 @@ +Feature Frequency Profile Phylogenies +===================================== + + +Introduction +------------ + +FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison. This software is a Galaxy (http://galaxyproject.org) tool for calculating FFP on one or more fasta sequence or text datasets. + +The original command line ffp-phylogeny code is at http://ffp-phylogeny.sourceforge.net/ . This tool uses Aaron Petkau's modified version: https://github.com/apetkau/ffp-3.19-custom . Aaron has quite a good writeup of the technique as well at https://github.com/apetkau/microbial-informatics-2014/tree/master/labs/ffp-phylogeny . + +**Installation Note** : Your Galaxy server will need the groff package to be installed on it first (to generate ffp-phylogeny man pages). A cryptic error will occur if it isn't: "troff: fatal error: can't find macro file s". This is different from the "groff-base" package. + +This Galaxy tool prepares a mini-pipeline consisting of **[ffpry | ffpaa | ffptxt] > [ ffpfilt | ffpcol > ffprwn] > ffpjsd > ffptree** . The last step is optional - by deselecting the "Generate Tree Phylogeny" checkbox, the tool will output a distance matrix rather than a Newick (.nhx) formatted tree file. + +Each sequence or text file has a profile containing tallies of each feature found. A feature is a string of valid characters of given length. + +For nucleotide data, by default each character (ATGC) is grouped as either purine(R) or pyrmidine(Y) before being counted. + +For amino acid data, by default each character is grouped into one of the following: (ST),(DE),(KQR),(IVLM),(FWY),C,G,A,N,H,P. Each group is represented by the first character in its series. + +One other key concept is that a given feature, e.g. "TAA" is counted in forward AND reverse directions, mirroring the idea that a feature's orientation is not so important to distinguish when it comes to alignment-free comparison. The counts for "TAA" and "AAT" are merged. + +The labeling of the resulting counted feature items is perhaps the trickiest concept to master. Due to computational efficiency measures taken by the developers, a feature that we see on paper as "TAC" may be stored and labeled internally as "GTA", its reverse compliment. One must look for the alternative if one does not find the original. + +Also note that in amino acid sequences the stop codon "*" (or any other character that is not in the Amino acid alphabet) causes that character frame not to be counted. Also, character frames never span across fasta entries. + +A few tutorials: + * http://sourceforge.net/projects/ffp-phylogeny/files/Documentation/tutorial.pdf + * https://github.com/apetkau/microbial-informatics-2014/tree/master/labs/ffp-phylogeny + +------- +**Note** + +Taxonomy label details: If each file contains one profile, the file's name is used to label the profile. If each file contains fasta sequences to profile individually, their fasta identifiers will be used to label them. The "short labels" option will find the shortest label that uniquely identifies each profile. Either way, there are some quirks: ffpjsd clips labels to 10 characters if they are greater than 50 characters, so all labels are trimmed to 50 characters first. Also "id" is prefixed to any numeric label since some tree visualizers won't show purely numeric labels. In the accidental case where a Fasta sequence label is a duplicate of a previous one it will be prefixed by "DupLabel-". + +The command line ffpjsd can hang if one provides an l-mer length greater than the length of file content. One must identify its process id ("ps aux | grep ffpjsd") and kill it ("kill [process id]"). + +Finally, it is possible for the ffptree program to generate a tree where some of the branch distances are negative. See https://www.biostars.org/p/45597/ + +------- +**References** + +The development of the ffp-phylogeny command line software should be attributed to: + +Sims GE, Jun S-R, Wu GA, Kim S-H. Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proceedings of the National Academy of Sciences of the United States of America 2009;106(8):2677-2682. doi:10.1073/pnas.0813249106. + diff -r 000000000000 -r d31a1bd74e63 ffp_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ffp_macros.xml Sun Aug 09 16:05:40 2015 -0400 @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + @BINARY@ + + @BINARY@ --version + + + \ No newline at end of file diff -r 000000000000 -r d31a1bd74e63 ffp_phylogeny.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ffp_phylogeny.py Sun Aug 09 16:05:40 2015 -0400 @@ -0,0 +1,364 @@ +#!/usr/bin/python +import optparse +import re +import time +import os +import tempfile +import sys +import shlex, subprocess +from string import maketrans + +VERSION_NUMBER = "0.1.03" + +class MyParser(optparse.OptionParser): + """ + From http://stackoverflow.com/questions/1857346/python-optparse-how-to-include-additional-info-in-usage-output + Provides a better class for displaying formatted help info in epilog() portion of optParse; allows for carriage returns. + """ + def format_epilog(self, formatter): + return self.epilog + + +def stop_err( msg ): + sys.stderr.write("%s\n" % msg) + sys.exit(1) + +def getTaxonomyNames(type, multiple, abbreviate, filepaths, filenames): + """ + Returns a taxonomic list of names corresponding to each file being analyzed by ffp. + This may also include names for each fasta sequence found within a file if the + "-m" multiple option is provided. Default is to use the file names rather than fasta id's inside the files. + NOTE: THIS DOES NOT (MUST NOT) REORDER NAMES IN NAME ARRAY. + EACH NAME ENTRY IS TRIMMED AND MADE UNIQUE + + @param type string ['text','amino','nucleotide'] + @param multiple boolean Flag indicates to look within files for labels + @param abbreviate boolean Flag indicates to shorten labels + @filenames array original input file names as user selected them + @filepaths array resulting galaxy dataset file .dat paths + + """ + # Take off prefix/suffix whitespace/comma : + taxonomy = filenames.strip().strip(',').split(',') + names=[] + ptr = 0 + + for file in filepaths: + # Trim labels to 50 characters max. ffpjsd kneecaps a taxonomy label to 10 characters if it is greater than 50 chars. + taxonomyitem = taxonomy[ptr].strip()[:50] #.translate(translations) + # Convert non-alphanumeric characters to underscore in taxonomy names. ffprwn IS VERY SENSITIVE ABOUT THIS. + taxonomyitem = re.sub('[^0-9a-zA-Z]+', '_', taxonomyitem) + + if (not type in 'text') and multiple: + #Must read each fasta file, looking for all lines beginning ">" + with open(file) as fastafile: + lineptr = 0 + for line in fastafile: + if line[0] == '>': + name = line[1:].split(None,1)[0].strip()[:50] + # Odd case where no fasta description found + if name == '': name = taxonomyitem + '.' + str(lineptr) + names.append(name) + lineptr += 1 + else: + + names.append(taxonomyitem) + + ptr += 1 + + if abbreviate: + names = trimCommonPrefixes(names) + names = trimCommonPrefixes(names, True) # reverse = Suffixes. + + return names + +def trimCommonPrefixes(names, reverse=False): + """ + Examines sorted array of names. Trims off prefix of each subsequent pair. + + @param names array of textual labels (file names or fasta taxonomy ids) + @param reverse boolean whether to reverse array strings before doing prefix trimming. + """ + wordybits = '|.0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + + if reverse: + names = map(lambda name: name[::-1], names) #reverses characters in names + + sortednames = sorted(names) + ptr = 0 + sortedlen = len(sortednames) + oldprefixlen=0 + prefixlen=0 + for name in sortednames: + ptr += 1 + + #If we're not at the very last item, reevaluate prefixlen + if ptr < sortedlen: + + # Skip first item in an any duplicate pair. Leave duplicate name in full. + if name == sortednames[ptr]: + if reverse: + continue + else: + names[names.index(name)] = 'DupLabel-' + name + continue + + # See http://stackoverflow.com/questions/9114402/regexp-finding-longest-common-prefix-of-two-strings + prefixlen = len( name[:([x[0]==x[1] for x in zip(name, sortednames[ptr])]+[0]).index(0)] ) + + if prefixlen <= oldprefixlen: + newprefix = name[:oldprefixlen] + else: + newprefix = name[:prefixlen] + # Expands label to include any preceeding characters that were probably part of it. + newprefix = newprefix.rstrip(wordybits) + newname = name[len(newprefix):] + # Some tree visualizers don't show numeric labels?!?! + if not reverse and newname.replace('.','',1).isdigit(): + newname = 'id_' + newname + names[names.index(name)] = newname #extract name after prefix part; has nl in it + oldprefixlen = prefixlen + + if reverse: + names = map(lambda name: name[::-1], names) #now back to original direction + + return names + +def getTaxonomyFile(names): + """ + FFP's ffpjsd -p [taxon file of labels] option creates a phylip tree with + given taxon labels + + @param names array of datafile names or fasta sequence ids + """ + + try: + temp = tempfile.NamedTemporaryFile(mode='w+t',delete=False) + taxonomyTempFile = temp.name + temp.writelines(name + '\n' for name in names) + + except: + stop_err("Galaxy configuration error for ffp_phylogeny tool. Unable to write taxonomy file " + taxonomyTempFile) + + finally: + temp.close() + + return taxonomyTempFile + + +def check_output(command): + """ + Execute a command line containing a series of pipes; and handle error cases by exiting at first error case. This is a substitute for Python 2.7 subprocess.check_output() - allowing piped commands without shell=True call . Based on Python subprocess docs 17.1.4.2 + + ISSUE: warnings on stderr are given with no exit code 0: + ffpry: Warning: No keys of length 6 found. + ffpcol: (null): Not a key valued FFP. + + Can't use communicate() because this closes processes' stdout + file handle even without errors because of read to end of stdout: + (stdoutdata, stderrdata) = processes[ptr-1].communicate() + + """ + commands = command.split("|") + processes = [] + ptr = 0 + substantive = re.compile('[a-zA-Z0-9]+') + + for command_line in commands: + print command_line.strip() + args = shlex.split(command_line.strip()) + if ptr == 0: + proc = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + processes.append(proc) + else: + + #this has to come before error processing? + newProcess = subprocess.Popen(args, stdin=processes[ptr-1].stdout, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + + # It seems the act of reading standard error output is enough to trigger + # error code signal for that process, i.e. so that retcode returns a code. + retcode = processes[ptr-1].poll() + stderrdata = processes[ptr-1].stderr.read() + #Issue with ffptree is it outputs ---- ... ---- on stderr even when ok. + if retcode or (len(stderrdata) > 0 and substantive.search(stderrdata)): + stop_err(stderrdata) + + processes.append(newProcess) + processes[ptr-1].stdout.close() # Allow prev. process to receive a SIGPIPE if current process exits. + + ptr += 1 + + retcode = processes[ptr-1].poll() + (stdoutdata, stderrdata) = processes[ptr-1].communicate() + if retcode or (len(stderrdata) > 0 and substantive.search(stderrdata)): + stop_err(stderrdata) + + return stdoutdata + + +class ReportEngine(object): + + def __init__(self): pass + + def __main__(self): + + + ## *************************** Parse Command Line ***************************** + parser = MyParser( + description = 'FFP (Feature frequency profile) is an alignment free comparison tool', + usage = 'python ffp_phylogeny.py [input_files] [output file] [options]', + epilog="""Details: + + FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison. + + """) + + parser.set_defaults(row_limit=0) + # Don't use "-h" , it is reserved for --help! + + parser.add_option('-t', '--type', type='choice', dest='type', default='text', + choices=['amino','nucleotide','text'], + help='Choice of Amino acid, nucleotide or plain text sequences to find features in') + + parser.add_option('-l', '--length', type='int', dest='length', default=6, + help='Features (any string of valid characters found in data) of this length will be counted. Synonyms: l-mer, k-mer, n-gram, k-tuple') + + #parser.add_option('-n', '--normalize', dest='normalize', default=True, action='store_true', + # help='Normalize counts into relative frequency') + + parser.add_option('-m', '--multiple', dest='multiple', default=False, action='store_true', + help='By default all sequences in a fasta file be treated as 1 sequence to profile. This option enables each sequence found in a fasta file to have its own profile.') + + parser.add_option('-M', '--metric', type='string', dest='metric', + help='Various metrics to measure count distances by.') + + parser.add_option('-x', '--taxonomy', type='string', dest='taxonomy', + help='Taxanomic label for each profile/sequence.') + + parser.add_option('-d', '--disable', dest='disable', default=False, action='store_true', + help='By default amino acid and nucleotide characters are grouped by functional category (protein or purine/pyrimidine group) before being counted. Disable this to treat individual characters as distinct.') + + parser.add_option('-a', '--abbreviate', dest='abbreviate', default=False, action='store_true', + help='Shorten tree taxonomy labels as much as possible.') + + parser.add_option('-s', '--similarity', dest='similarity', default=False, action='store_true', + help='Enables pearson correlation coefficient matrix and any of the binary distance measures to be turned into similarity matrixes.') + + parser.add_option('-f', '--filter', type='choice', dest='filter', default='none', + choices=['none','count','f','n','e','freq','norm','evd'], + help='Choice of [f=raw frequency|n=normal|e=extreme value (Gumbel)] distribution: Features are trimmed from the data based on lower/upper cutoff points according to the given distribution.') + + parser.add_option('-L', '--lower', type='float', dest='lower', + help='Filter lower bound is a 0.00 percentages') + + parser.add_option('-U', '--upper', type='float', dest='upper', + help='Filter upper bound is a 0.00 percentages') + + parser.add_option('-o', '--output', type='string', dest='output', + help='Path of output file to create') + + parser.add_option('-T', '--tree', dest='tree', default=False, action='store_true', help='Generate Phylogenetic Tree output file') + + parser.add_option('-v', '--version', dest='version', default=False, action='store_true', help='Version number') + + # Could also have -D INT decimal precision included for ffprwn . + + options, args = parser.parse_args() + + if options.version: + print VERSION_NUMBER + return + + import time + time_start = time.time() + + try: + in_files = args[:] + + except: + stop_err("Expecting at least 1 input data file.") + + + #ffptxt / ffpaa / ffpry + if options.type in 'text': + command = 'ffptxt' + + else: + if options.type == 'amino': + command = 'ffpaa' + else: + command = 'ffpry' + + if options.disable: + command += ' -d' + + if options.multiple: + command += ' -m' + + command += ' -l ' + str(options.length) + + if len(in_files): #Note: app isn't really suited to stdio + command += ' "' + '" "'.join(in_files) + '"' + + #ffpcol / ffpfilt + if options.filter != 'none': + command += ' | ffpfilt' + if options.filter != 'count': + command += ' -' + options.filter + if options.lower > 0: + command += ' --lower ' + str(options.lower) + if options.upper > 0: + command += ' --upper ' + str(options.upper) + + else: + command += ' | ffpcol' + + if options.type in 'text': + command += ' -t' + + else: + + if options.type == 'amino': + command += ' -a' + + if options.disable: + command += ' -d' + + #if options.normalize: + command += ' | ffprwn' + + #Now create a taxonomy label file, ensuring a name exists for each profile. + taxonomyNames = getTaxonomyNames(options.type, options.multiple, options.abbreviate, in_files, options.taxonomy) + taxonomyTempFile = getTaxonomyFile(taxonomyNames) + + # -p = Include phylip format 'infile' of the taxon names to use. Very simple, just a list of fasta identifier names. + command += ' | ffpjsd -p ' + taxonomyTempFile + + if options.metric and len(options.metric) >0 : + command += ' --' + options.metric + if options.similarity: + command += ' -s' + + # Generate Newick (.nhx) formatted tree if we have at least 3 taxonomy items: + if options.tree: + if len(taxonomyNames) > 2: + command += ' | ffptree -q' + else: + stop_err("For a phylogenetic tree display, one must have at least 3 ffp profiles.") + + #print command + + result = check_output(command) + with open(options.output,'w') as fw: + fw.writelines(result) + os.remove(taxonomyTempFile) + +if __name__ == '__main__': + + time_start = time.time() + + reportEngine = ReportEngine() + reportEngine.__main__() + + print('Execution time (seconds): ' + str(int(time.time()-time_start))) + diff -r 000000000000 -r d31a1bd74e63 ffp_phylogeny.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ffp_phylogeny.xml Sun Aug 09 16:05:40 2015 -0400 @@ -0,0 +1,293 @@ + + An alignment free comparison tool for phylogenetic analysis and text comparison + + ffp-phylogeny + + + + ./ffp_phylogeny.py + ffp_macros.xml + + + 1 + + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + [ ffpfilt | ffpcol > ffprwn] > ffpjsd > ffptree** . The last step is optional - by deselecting the "Generate Tree Phylogeny" checkbox, the tool will output only the precursor distance matrix file rather than a Newick (.nhx) formatted tree file. + +Each sequence or text file has a profile containing tallies of each feature found. A feature is a string of valid characters of given length. + +For nucleotide data, by default each character (ATGC) is grouped as either purine(R) or pyrmidine(Y) before being counted. + +For amino acid data, by default each character is grouped into one of the following: +(ST),(DE),(KQR),(IVLM),(FWY),C,G,A,N,H,P. Each group is represented by the first character in its series. + +One other key concept is that a given feature, e.g. "TAA" is counted in forward +AND reverse directions, mirroring the idea that a feature's orientation is not +so important to distinguish when it comes to alignment-free comparison. +The counts for "TAA" and "AAT" are merged. + +The labeling of the resulting counted feature items is perhaps the trickiest +concept to master. Due to computational efficiency measures taken by the +developers, a feature that we see on paper as "TAC" may be stored and labeled +internally as "GTA", its reverse compliment. One must look for the alternative +if one does not find the original. + +Also note that in amino acid sequences the stop codon "*" (or any other character +that is not in the Amino acid alphabet) causes that character frame not to be +counted. Also, character frames never span across fasta entries. + +A few tutorials: + * http://sourceforge.net/projects/ffp-phylogeny/files/Documentation/tutorial.pdf + * https://github.com/apetkau/microbial-informatics-2014/tree/master/labs/ffp-phylogeny + +------- + +.. class:: warningmark + +**Note** + +Taxonomy label details: If each file contains one profile, the file's name is used to label the profile. +If each file contains fasta sequences to profile individually, their fasta identifiers will be used to label them. +The "short labels" option will find the shortest label that uniquely identifies each profile. +Either way, there are some quirks: ffpjsd clips labels to 10 characters if they are greater than 50 characters, so all labels are trimmed to 50 characters first. +Also "id" is prefixed to any numeric label since some tree visualizers won't show purely numeric labels. +In the accidental case where a Fasta sequence label is a duplicate of a previous one it will be prefixed by "DupLabel-". + +The command line ffpjsd can hang if one provides an l-mer length greater than the length of file content. +One must identify its process id (">ps aux | grep ffpjsd") and kill it (">kill [process id]"). +------- + +**References** + +The original ffp-phylogeny code is at http://ffp-phylogeny.sourceforge.net/ . +This tool uses Aaron Petkau's modified version: https://github.com/apetkau/ffp-3.19-custom . + +The development of the ff-phylogeny should be attributed to: + +Sims GE, Jun S-R, Wu GA, Kim S-H. Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proceedings of the National Academy of Sciences of the United States of America 2009;106(8):2677-2682. doi:10.1073/pnas.0813249106. + + ]]> + + + diff -r 000000000000 -r d31a1bd74e63 test-data/genome1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome1 Sun Aug 09 16:05:40 2015 -0400 @@ -0,0 +1,2 @@ +>genome1 +AATT diff -r 000000000000 -r d31a1bd74e63 test-data/genome2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome2 Sun Aug 09 16:05:40 2015 -0400 @@ -0,0 +1,2 @@ +>genome2 +AAGG diff -r 000000000000 -r d31a1bd74e63 test-data/test_length_1_output.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_length_1_output.tabular Sun Aug 09 16:05:40 2015 -0400 @@ -0,0 +1,3 @@ +2 +genome1 0.00e+00 1.89e-01 +genome2 1.89e-01 0.00e+00 diff -r 000000000000 -r d31a1bd74e63 test-data/test_length_2_output.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_length_2_output.tabular Sun Aug 09 16:05:40 2015 -0400 @@ -0,0 +1,3 @@ +2 +genome1 0.00e+00 4.58e-01 +genome2 4.58e-01 0.00e+00 diff -r 000000000000 -r d31a1bd74e63 test-data/test_length_2b_output.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_length_2b_output.tabular Sun Aug 09 16:05:40 2015 -0400 @@ -0,0 +1,3 @@ +2 +genome1 0.00e+00 1.42e-01 +genome2 1.42e-01 0.00e+00 diff -r 000000000000 -r d31a1bd74e63 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun Aug 09 16:05:40 2015 -0400 @@ -0,0 +1,24 @@ + + + + + + git clone https://github.com/apetkau/ffp-3.19-custom.git ffp-phylogeny + git reset --hard d4382db015acec0e5cc43d6c1ac80ae12cb7e6b3 + ./configure --disable-gui --prefix=$INSTALL_DIR + + + + $INSTALL_DIR/bin + + + + + apetkau/ffp-3.19-custom is a customized version of http://sourceforge.net/projects/ffp-phylogeny/ + + + +