| Previous changeset 5:26e35d5133a1 (2015-10-10) Next changeset 7:ba31415fedc5 (2017-02-02) |
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Commit message:
v0.0.10 explicit galaxy_sequence_utils dependency etc |
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modified:
tools/venn_list/README.rst tools/venn_list/tool_dependencies.xml tools/venn_list/venn_list.py tools/venn_list/venn_list.xml |
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| diff -r 26e35d5133a1 -r ea68a1a4c1d9 tools/venn_list/README.rst --- a/tools/venn_list/README.rst Sat Oct 10 08:52:01 2015 -0400 +++ b/tools/venn_list/README.rst Thu Feb 02 11:17:31 2017 -0500 |
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| @@ -1,7 +1,7 @@ Galaxy tool to draw a Venn Diagram with up to 3 sets ==================================================== -This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute +This tool is copyright 2011-2017 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. @@ -72,6 +72,9 @@ - Includes testing of failure mode. - Planemo for Tool Shed upload (``.shed.yml``, internal change only). - Tool Shed dependency for rpy and limma (thanks to Björn Grüning). +v0.0.10 - Updated to point at Biopython 1.67 (latest version in Tool Shed). + - Explicit dependency on ``galaxy_sequence_utils``. + - Python style updates (internal change only). ======= ====================================================================== |
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| diff -r 26e35d5133a1 -r ea68a1a4c1d9 tools/venn_list/tool_dependencies.xml --- a/tools/venn_list/tool_dependencies.xml Sat Oct 10 08:52:01 2015 -0400 +++ b/tools/venn_list/tool_dependencies.xml Thu Feb 02 11:17:31 2017 -0500 |
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| @@ -1,12 +1,15 @@ <?xml version="1.0"?> <tool_dependency> + <package name="galaxy_sequence_utils" version="1.0.1"> + <repository changeset_revision="c1ab450748ba" name="package_galaxy_sequence_utils_1_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> <package name="limma" version="3.25.3"> <repository changeset_revision="b19c06e97bce" name="package_r2_limma_3_25_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="rpy" version="1.0.3"> <repository changeset_revision="82170c94ca7c" name="package_rpy_1_0_3" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="biopython" version="1.65"> - <repository changeset_revision="dc595937617c" name="package_biopython_1_65" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="biopython" version="1.67"> + <repository changeset_revision="a42f244cce44" name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |
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| diff -r 26e35d5133a1 -r ea68a1a4c1d9 tools/venn_list/venn_list.py --- a/tools/venn_list/venn_list.py Sat Oct 10 08:52:01 2015 -0400 +++ b/tools/venn_list/venn_list.py Thu Feb 02 11:17:31 2017 -0500 |
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| @@ -11,127 +11,124 @@ import sys -def sys_exit(msg, error_level=1): - """Print error message to stdout and quit with given error level.""" - sys.stderr.write("%s\n" % msg) - sys.exit(error_level) - try: import rpy except ImportError: - sys_exit("Requires the Python library rpy (to call R)") + sys.exit("Requires the Python library rpy (to call R)") except RuntimeError, e: - sys_exit("The Python library rpy is not availble for the current R version\n\n%s" % e) + sys.exit("The Python library rpy is not availble for the current R version\n\n%s" % e) try: rpy.r.library("limma") -except: - sys_exit("Requires the R library limma (for vennDiagram function)") +except Exception: + sys.exit("Requires the R library limma (for vennDiagram function)") -if len(sys.argv)-1 not in [7, 10, 13]: - sys_exit("Expected 7, 10 or 13 arguments (for 1, 2 or 3 sets), not %i" % (len(sys.argv)-1)) +if len(sys.argv) - 1 not in [7, 10, 13]: + sys.exit("Expected 7, 10 or 13 arguments (for 1, 2 or 3 sets), not %i" % (len(sys.argv) - 1)) all_file, all_type, all_label = sys.argv[1:4] set_data = [] -if len(sys.argv)-1 >= 7: +if len(sys.argv) - 1 >= 7: set_data.append(tuple(sys.argv[4:7])) -if len(sys.argv)-1 >= 10: +if len(sys.argv) - 1 >= 10: set_data.append(tuple(sys.argv[7:10])) -if len(sys.argv)-1 >= 13: +if len(sys.argv) - 1 >= 13: set_data.append(tuple(sys.argv[10:13])) pdf_file = sys.argv[-1] n = len(set_data) print "Doing %i-way Venn Diagram" % n + def load_ids(filename, filetype): - if filetype=="tabular": + if filetype == "tabular": for line in open(filename): line = line.rstrip("\n") if line and not line.startswith("#"): - yield line.split("\t",1)[0] - elif filetype=="fasta": + yield line.split("\t", 1)[0] + elif filetype == "fasta": for line in open(filename): if line.startswith(">"): - yield line[1:].rstrip("\n").split(None,1)[0] + yield line[1:].rstrip("\n").split(None, 1)[0] elif filetype.startswith("fastq"): - #Use the Galaxy library not Biopython to cope with CS + # Use the Galaxy library not Biopython to cope with CS from galaxy_utils.sequence.fastq import fastqReader handle = open(filename, "rU") for record in fastqReader(handle): - #The [1:] is because the fastaReader leaves the @ on the identifer. + # The [1:] is because the fastaReader leaves the @ on the identifer. yield record.identifier.split()[0][1:] handle.close() - elif filetype=="sff": + elif filetype == "sff": try: from Bio.SeqIO import index except ImportError: - sys_exit("Require Biopython 1.54 or later (to read SFF files)") - #This will read the SFF index block if present (very fast) + sys.exit("Require Biopython 1.54 or later (to read SFF files)") + # This will read the SFF index block if present (very fast) for name in index(filename, "sff"): yield name else: - sys_exit("Unexpected file type %s" % filetype) + sys.exit("Unexpected file type %s" % filetype) + def load_ids_whitelist(filename, filetype, whitelist): for name in load_ids(filename, filetype): if name in whitelist: yield name else: - sys_exit("Unexpected ID %s in %s file %s" % (name, filetype, filename)) + sys.exit("Unexpected ID %s in %s file %s" % (name, filetype, filename)) if all_file in ["", "-", '""', '"-"']: - #Load without white list - sets = [set(load_ids(f,t)) for (f,t,c) in set_data] - #Take union - all = set() + # Load without white list + sets = [set(load_ids(f, t)) for (f, t, c) in set_data] + # Take union + all_ids = set() for s in sets: - all.update(s) - print "Inferred total of %i IDs" % len(all) + all_ids.update(s) + print "Inferred total of %i IDs" % len(all_ids) else: - all = set(load_ids(all_file, all_type)) - print "Total of %i IDs" % len(all) - sets = [set(load_ids_whitelist(f,t,all)) for (f,t,c) in set_data] + all_ids = set(load_ids(all_file, all_type)) + print "Total of %i IDs" % len(all_ids) + sets = [set(load_ids_whitelist(f, t, all_ids)) for (f, t, c) in set_data] -for s, (f,t,c) in zip(sets, set_data): +for s, (f, t, c) in zip(sets, set_data): print "%i in %s" % (len(s), c) -#Now call R library to draw simple Venn diagram +# Now call R library to draw simple Venn diagram try: - #Create dummy Venn diagram counts object for three groups - cols = 'c("%s")' % '","'.join("Set%i" % (i+1) for i in range(n)) - rpy.r('groups <- cbind(%s)' % ','.join(['1']*n)) + # Create dummy Venn diagram counts object for three groups + cols = 'c("%s")' % '","'.join("Set%i" % (i + 1) for i in range(n)) + rpy.r('groups <- cbind(%s)' % ','.join(['1'] * n)) rpy.r('colnames(groups) <- %s' % cols) rpy.r('vc <- vennCounts(groups)') - #Populate the 2^n classes with real counts - #Don't make any assumptions about the class order - #print rpy.r('vc') + # Populate the 2^n classes with real counts + # Don't make any assumptions about the class order + # print rpy.r('vc') for index, row in enumerate(rpy.r('vc[,%s]' % cols)): if isinstance(row, int) or isinstance(row, float): - #Hack for rpy being too clever for single element row + # Hack for rpy being too clever for single element row row = [row] - names = all + names = all_ids for wanted, s in zip(row, sets): if wanted: names = names.intersection(s) else: names = names.difference(s) - rpy.r('vc[%i,"Counts"] <- %i' % (index+1, len(names))) - #print rpy.r('vc') + rpy.r('vc[%i,"Counts"] <- %i' % (index + 1, len(names))) + # print rpy.r('vc') if n == 1: - #Single circle, don't need to add (Total XXX) line - names = [c for (t,f,c) in set_data] + # Single circle, don't need to add (Total XXX) line + names = [c for (t, f, c) in set_data] else: - names = ["%s\n(Total %i)" % (c, len(s)) for s, (f,t,c) in zip(sets, set_data)] + names = ["%s\n(Total %i)" % (c, len(s)) for s, (f, t, c) in zip(sets, set_data)] rpy.r.assign("names", names) - rpy.r.assign("colors", ["red","green","blue"][:n]) + rpy.r.assign("colors", ["red", "green", "blue"][:n]) rpy.r.pdf(pdf_file, 8, 8) rpy.r("""vennDiagram(vc, include="both", names=names, main="%s", sub="(Total %i)", circle.col=colors) - """ % (all_label, len(all))) + """ % (all_label, len(all_ids))) rpy.r.dev_off() except Exception, exc: - sys_exit( "%s" %str( exc ) ) -rpy.r.quit( save="no" ) + sys.exit("%s" % str(exc)) +rpy.r.quit(save="no") print "Done" |
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| diff -r 26e35d5133a1 -r ea68a1a4c1d9 tools/venn_list/venn_list.xml --- a/tools/venn_list/venn_list.xml Sat Oct 10 08:52:01 2015 -0400 +++ b/tools/venn_list/venn_list.xml Thu Feb 02 11:17:31 2017 -0500 |
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| b'@@ -1,157 +1,158 @@\n-<tool id="venn_list" name="Venn Diagram" version="0.0.9">\r\n- <description>from lists</description>\r\n- <requirements>\r\n- <requirement type="python-module">rpy</requirement>\r\n- <requirement type="python-module">Bio</requirement>\r\n- <requirement type="package" version="1.0.3">rpy</requirement>\r\n- <requirement type="package" version="3.25.3">limma</requirement>\r\n- <requirement type="package" version="1.65">biopython</requirement>\r\n- </requirements>\r\n- <stdio>\r\n- <!-- Anything other than zero is an error -->\r\n- <exit_code range="1:" />\r\n- <exit_code range=":-1" />\r\n- </stdio>\r\n- <command interpreter="python">\r\n-venn_list.py\r\n-#if $universe.type_select=="implicit":\r\n- - -\r\n-#else:\r\n- "$main" $main.ext\r\n-#end if\r\n-"$main_lab"\r\n-#for $s in $sets:\r\n- "$s.set" $s.set.ext "$s.lab"\r\n-#end for\r\n-$PDF\r\n- </command>\r\n- <inputs>\r\n- <param name="main_lab" size="30" type="text" value="Venn Diagram" label="Plot title"/>\r\n- <conditional name="universe">\r\n- <param name="type_select" type="select" label="Implicit or explicit full ID list?">\r\n- <option value="explicit">Explicit</option>\r\n- <option value="implicit">Implicit (use union of sets below)</option>\r\n- </param>\r\n- <when value="explicit">\r\n- <param name="main" type="data" format="tabular,fasta,fastq,sff" label="Full dataset (with all identifiers)" help="Tabular file (uses column one), FASTA, FASTQ or SFF file."/>\r\n- </when>\r\n- <when value="implicit"/>\r\n- </conditional>\r\n- <repeat name="sets" min="1" max="3" title="Sets">\r\n- <param name="set" type="data" format="tabular,fasta,fastq,sff" label="Members of set" help="Tabular file (uses column one), FASTA, FASTQ or SFF file."/>\r\n- <param name="lab" size="30" type="text" value="Group" label="Caption for set"/>\r\n- </repeat>\r\n- </inputs>\r\n- <outputs>\r\n- <data format="pdf" name="PDF" />\r\n- </outputs>\r\n- <tests>\r\n- <!-- Doesn\'t seem to work properly, manages to get two sets, both\r\n- with same FASTA file, but second with default "Group" label. -->\r\n- <test>\r\n- <param name="type_select" value="explicit"/>\r\n- <param name="main" value="venn_list.tabular" ftype="tabular"/>\r\n- <param name="main_lab" value="Some Proteins"/>\r\n- <param name="set" value="rhodopsin_proteins.fasta"/>\r\n- <param name="lab" value="Rhodopsins"/>\r\n- <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" />\r\n- <assert_stdout>\r\n- <has_line line="Doing 1-way Venn Diagram" />\r\n- <has_line line="Total of 10 IDs" />\r\n- <has_line line="6 in Rhodopsins" />\r\n- </assert_stdout>\r\n- </test>\r\n- <test>\r\n- <param name="type_select" value="implicit"/>\r\n- <param name="sets_0|set" value="rhodopsin_proteins.fasta"/>\r\n- <param name="sets_0|lab" value="Rhodopsins"/>\r\n- <param name="sets_1|set" value="four_human_proteins.fasta"/>\r\n- <param name="sets_1|lab" value="Human"/>\r\n- <param name="sets_2|set" value="blastp_four_human_vs_rhodopsin.tabular"/>\r\n- <param name="sets_2|lab" value="Human vs Rhodopsin BLAST"/>\r\n- <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" />\r\n- <assert_stdout>\r\n- <has_line line="Doing 3-way Venn Diagram" />\r\n- <has_line line="Inferred total of 10 IDs" />\r\n- <has_line line="6 in Rhodopsins" />\r\n- <has_line line="4 in Human" />\r\n- <has_line line="1 in Human vs Rhodopsin BLAST" />\r\n- </assert_stdout>\r\n- </test>\r\n- <test expect_failure="true" expect_exit_code="1">\r\n- <param name="type_select" value="expl'..b'2|set" value="blastp_four_human_vs_rhodopsin.tabular"/>\n+ <param name="sets_2|lab" value="Human vs Rhodopsin BLAST"/>\n+ <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" />\n+ <assert_stdout>\n+ <has_line line="Doing 3-way Venn Diagram" />\n+ <has_line line="Inferred total of 10 IDs" />\n+ <has_line line="6 in Rhodopsins" />\n+ <has_line line="4 in Human" />\n+ <has_line line="1 in Human vs Rhodopsin BLAST" />\n+ </assert_stdout>\n+ </test>\n+ <test expect_failure="true" expect_exit_code="1">\n+ <param name="type_select" value="explicit"/>\n+ <param name="main" value="venn_list.tabular" ftype="tabular"/>\n+ <param name="main_lab" value="Some Proteins"/>\n+ <param name="sets_0|set" value="rhodopsin_proteins.fasta"/>\n+ <param name="sets_0|lab" value="Rhodopsins"/>\n+ <param name="sets_1|set" value="four_human_proteins.fasta"/>\n+ <param name="sets_1|lab" value="Human"/>\n+ <param name="sets_2|set" value="blastp_four_human_vs_rhodopsin.tabular"/>\n+ <param name="sets_2|lab" value="Human vs Rhodopsin BLAST"/>\n+ <assert_stdout>\n+ <has_line line="Doing 3-way Venn Diagram" />\n+ <has_line line="Total of 10 IDs" />\n+ </assert_stdout>\n+ <assert_stderr>\n+ <has_text_matching expression="Unexpected ID sp|Q9BS26|ERP44_HUMAN in fasta file *" />\n+ </assert_stderr>\n+ </test>\n+ </tests>\n+ <help>\n+\n+.. class:: infomark\n+\n+**TIP:** If your data is in tabular files, the identifier is assumed to be in column one.\n+\n+**What it does**\n+\n+Draws Venn Diagram for one, two or three sets (as a PDF file).\n+\n+You must supply one, two or three sets of identifiers -- corresponding\n+to one, two or three circles on the Venn Diagram.\n+\n+In general you should also give the full list of all the identifiers\n+explicitly. This is used to calculate the number of identifers outside\n+the circles (and check the identifiers in the other files match up).\n+The full list can be omitted by implicitly taking the union of the\n+category sets. In this case, the count outside the categories (circles)\n+will always be zero.\n+\n+The identifiers can be taken from the first column of a tabular file\n+(e.g. query names in BLAST tabular output, or signal peptide predictions\n+after filtering, etc), or from a sequence file (FASTA, FASTQ, SFF).\n+\n+For example, you may have a set of NGS reads (as a FASTA, FASTQ or SFF\n+file), and the results of several different read mappings (e.g. to\n+different references) as tabular files (filtered to have just the mapped\n+reads). You could then show the different mappings (and their overlaps)\n+as a Venn Diagram, and the outside count would be the unmapped reads.\n+\n+**Citations**\n+\n+The Venn Diagrams are drawn using Gordon Smyth\'s limma package from\n+R/Bioconductor, http://www.bioconductor.org/\n+\n+The R library is called from Python via rpy, http://rpy.sourceforge.net/\n+\n+If you use this Galaxy tool in work leading to a scientific publication please\n+cite:\n+\n+Peter J.A. Cock, Bj\xc3\xb6rn A. Gr\xc3\xbcning, Konrad Paszkiewicz and Leighton Pritchard (2013).\n+Galaxy tools and workflows for sequence analysis with applications\n+in molecular plant pathology. PeerJ 1:e167\n+http://dx.doi.org/10.7717/peerj.167\n+\n+This tool uses Biopython to read and write SFF files, so you may also wish to\n+cite the Biopython application note (and Galaxy too of course):\n+\n+Cock et al 2009. Biopython: freely available Python tools for computational\n+molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.\n+http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.\n+\n+ </help>\n+ <citations>\n+ <citation type="doi">10.7717/peerj.167</citation>\n+ <citation type="doi">10.1093/bioinformatics/15.5.356</citation>\n+ </citations>\n+</tool>\n' |