Mercurial > repos > damion > ffp_phylogeny
changeset 1:d1c88b118a3f draft
Uploaded
| author | damion |
|---|---|
| date | Fri, 13 Mar 2015 20:59:28 -0400 |
| parents | eb6e5e78a066 |
| children | 671667722d3d |
| files | LICENSE.md README.md ffp_phylogeny.py ffp_phylogeny.xml tarballit.sh test-data/test_length_2b_output.tabular test.txt |
| diffstat | 7 files changed, 146 insertions(+), 32 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Mar 13 20:59:28 2015 -0400 @@ -0,0 +1,44 @@ +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 . + +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. +
--- a/ffp_phylogeny.py Mon Feb 23 18:25:25 2015 -0500 +++ b/ffp_phylogeny.py Fri Mar 13 20:59:28 2015 -0400 @@ -1,5 +1,6 @@ #!/usr/bin/python import optparse +import re import time import os import tempfile @@ -160,6 +161,8 @@ 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()) @@ -167,22 +170,26 @@ 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() - retcode = processes[ptr-1].poll() - if retcode or len(stderrdata) > 0: - stop_err(stderrdata) + #Issue with ffptree is it outputs ----....---- on stderr + if retcode or (len(stderrdata) > 0 and substantive.search(stderrdata)): + stop_err(stderrdata) - newProcess = subprocess.Popen(args, stdin=processes[ptr-1].stdout, stdout=subprocess.PIPE, stderr=subprocess.PIPE) - processes.append(newProcess) + 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() - retcode = processes[ptr-1].poll() - if retcode or len(stderrdata) > 0: + if retcode or (len(stderrdata) > 0 and substantive.search(stderrdata)): stop_err(stderrdata) return stdoutdata @@ -322,6 +329,7 @@ #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 @@ -337,6 +345,8 @@ 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)
--- a/ffp_phylogeny.xml Mon Feb 23 18:25:25 2015 -0500 +++ b/ffp_phylogeny.xml Fri Mar 13 20:59:28 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="ffp_phylogeny" name="Feature Frequency Profile Phylogeny" version="0.1.00"> +<tool id="ffp_phylogeny" name="Feature Frequency Profile Phylogeny" version="0.1.02"> <description>An alignment free comparison tool for phylogenetic analysis and text comparison</description> <requirements> <requirement type="package" version="0.3.19_d4382db015acec0e5cc43d6c1ac80ae12cb7e6b3">ffp-phylogeny</requirement> @@ -22,35 +22,36 @@ -t "$(sequence.file_type.split('-')[0])" -l "$length" -o "$info" - ##if $normalize: + ##if $normalize ## -n ##end if - #if $sequence.file_type != 'text': - #if $sequence.file_type.find('multi') > 0: + #if $sequence.file_type != 'text' + #if $sequence.file_type == 'amino-multi' or $sequence.file_type == 'nucleotide-multi' -m #end if - #if $sequence.grouping: + #if $sequence.groupings + #pass + #else -d #end if - #if $metric: + #if $metric -M "$metric" #end if - #if $similarity: + #if $similarity -s #end if - #if $abbreviate: + #if $abbreviate -a #end if #end if - #if $phylogeny.phylo_type == 'filter': + #if $phylogeny.phylo_type == 'filter' -f "$phylogeny.filt.filter_type" -L "$phylogeny.filt.lower" -U "$phylogeny.filt.upper" #end if - #if $tree: + #if $tree -T #end if - ##ffpjsd -n FLOAT , --normval=FLOAT ## For option -e, --euclid, change the n-norm distance (Default is n=2) to any other value where n > 1 @@ -66,32 +67,32 @@ <param name="normalize" label="Normalize counts into relative frequency" type="boolean" checked="true" help="" /> --> <conditional name="sequence"> - <param type="select" name="file_type" label="File type" help="Note: For phylogeny display, at least three profiles are required, as files or fasta sequences within a file."> - <option value="amino">Amino Acids, one sequence per file</option> - <option value="amino-multi">Amino Acids, multiple fasta sequences per file</option> - <option value="nucleotide">Nucleic acids, one sequence per file</option> - <option value="nucleotide-multi">Nucleic acids, multiple fasta sequences per file</option> + <param type="select" name="file_type" label="File type" help="Note: For phylogeny display, at least three profiles are required."> + <option value="amino">Amino Acids, one profile per file</option> + <option value="amino-multi">Amino Acids, one profile per fasta sequence in file</option> + <option value="nucleotide">Nucleic acids, one profile per file</option> + <option value="nucleotide-multi">Nucleic acids, one profile per fasta sequence in file</option> <option value="text">Text, single file</option> </param> <when value="amino"><!-- ffpaa --> <param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" /> - <param name="grouping" label="Enable amino acid grouping" type="boolean" checked="true" help="Counts amino acids in groups rather than individually (usually advantageous, see below)." /> + <param name="groupings" label="Enable amino acid grouping" type="boolean" checked="true" help="Counts amino acids in groups rather than individually (usually advantageous, see below)." /> </when> <when value="amino-multi"> <param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" /> - <param name="grouping" label="Enable amino acid grouping" type="boolean" checked="true" help="Counts amino acids in groups rather than individually (usually advantageous, see below)." /> + <param name="groupings" label="Enable amino acid grouping" type="boolean" checked="true" help="Counts amino acids in groups rather than individually (usually advantageous, see below)." /> </when> <when value="nucleotide"><!-- ffpry --> <param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" /> - <param name="grouping" label="Enable purine / pyrimidine grouping" type="boolean" checked="true" help="Counts each nucleotide as a purine(R) or pyrimidine(Y) rather than individually (usually advantageous)." /> + <param name="groupings" label="Enable purine / pyrimidine grouping" type="boolean" checked="true" help="Counts each nucleotide as a purine(R) or pyrimidine(Y) rather than individually (usually advantageous)." /> </when> <when value="nucleotide-multi"> <param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" /> - <param name="grouping" label="Enable purine / pyrimidine grouping" type="boolean" checked="true" help="Counts each nucleotide as a purine(R) or pyrimidine(Y) rather than individually (usually advantageous)." /> + <param name="groupings" label="Enable purine / pyrimidine grouping" type="boolean" checked="true" help="Counts each nucleotide as a purine(R) or pyrimidine(Y) rather than individually (usually advantageous)." /> </when> <when value="text"><!-- ffptxt --> @@ -200,7 +201,7 @@ <test> <param name="length" value="1"/> <param name="tree" value="0"/> - <param name="grouping" value="true"/> + <param name="groupings" value="false"/> <param name="file_type" value="nucleotide"/> <param name="filesin" value="genome1,genome2"/> <output name="info" file="test_length_1_output.tabular"/> @@ -208,11 +209,19 @@ <test> <param name="length" value="2"/> <param name="tree" value="0"/> - <param name="grouping" value="true"/> + <param name="groupings" value="false"/> <param name="file_type" value="nucleotide"/> <param name="filesin" value="genome1,genome2"/> <output name="info" file="test_length_2_output.tabular"/> </test> + <test> + <param name="length" value="2"/> + <param name="tree" value="0"/> + <param name="groupings" value="true"/> + <param name="file_type" value="nucleotide-multi"/> + <param name="filesin" value="genome1,genome2"/> + <output name="info" file="test_length_2b_output.tabular"/> + </test> </tests> <help><![CDATA[ @@ -224,7 +233,7 @@ 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 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. +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 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.
--- a/tarballit.sh Mon Feb 23 18:25:25 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -#!/bin/bash - tar -zcvf ffp_phylogeny.tar.gz * --exclude "*~" --exclude "tool_test_output*" --exclude "*gz"