| Next changeset 1:ab12adaa5cc2 (2013-07-06) |
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glimmer2seq.py glimmer_build-icm.xml glimmer_w_icm.xml glimmer_wo_icm.py glimmer_wo_icm.xml readme.rst test-data/glimmer_w_icm_trans-table-11_genomic.fasta test-data/glimmer_wo_icm_trans-table-11_plasmid_genomic.fasta test-data/streptomyces_Tu6071_genomic.fasta test-data/streptomyces_Tu6071_plasmid_genes.fasta test-data/streptomyces_Tu6071_plasmid_genes.icm test-data/streptomyces_Tue6071_plasmid_genomic.fasta tool_dependencies.xml |
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| diff -r 000000000000 -r 841357e0acbf glimmer2seq.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/glimmer2seq.py Sat Jul 06 10:09:30 2013 -0400 |
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| @@ -0,0 +1,44 @@ +#!/usr/bin/env python +""" +Input: DNA FASTA file + Glimmer ORF file +Output: ORF sequences as FASTA file +Author: Bjoern Gruening +""" +import sys, os +from Bio import SeqIO +from Bio.SeqRecord import SeqRecord + +def glimmer2seq( glimmer_prediction = sys.argv [1], genome_sequence = sys.argv[2], outfile = sys.argv[3] ): + if len(sys.argv) >= 4: + glimmerfile = open( glimmer_prediction, "r") + sequence = open( genome_sequence ) + else: + print "Missing input values." + sys.exit() + + fastafile = SeqIO.parse(sequence, "fasta") + + sequences = dict() + seq_records = list() + for entry in fastafile: + sequences[entry.description] = entry + + for line in glimmerfile: + if line.startswith('>'): + entry = sequences[ line[1:].strip() ] + else: + orf_start = int(line[8:17]) + orf_end = int(line[18:26]) + + orf_name = line[0:8] + if orf_start <= orf_end: + seq_records.append( SeqRecord( entry.seq[ orf_start-1 : orf_end ], id = orf_name, description = entry.description ) ) + else: + seq_records.append( SeqRecord( entry.seq[ orf_end-1 : orf_start ].reverse_complement(), id = orf_name, description = entry.description ) ) + + SeqIO.write( seq_records, outfile, "fasta" ) + glimmerfile.close() + sequence.close() + +if __name__ == "__main__" : + glimmer2seq() |
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| diff -r 000000000000 -r 841357e0acbf glimmer_build-icm.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/glimmer_build-icm.xml Sat Jul 06 10:09:30 2013 -0400 |
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| @@ -0,0 +1,125 @@ +<tool id="glimmer_build-icm" name="Glimmer ICM builder" version="0.2"> + <description></description> + <requirements> + <requirement type="package" version="3.02b">glimmer</requirement> + </requirements> + <command> + build-icm + --depth $depth + #if $no_stops: + --no_stops + #end if + --period $period + --width $width + + #if $stop_codon_opts.stop_codon_opts_selector == "gb": + --trans_table "${stop_codon_opts.genbank_gencode}" + #else: + --stop_codons "${stop_codon_opts.stop_codons}" + #end if + + $outfile < $infile 2>&1; + </command> + <inputs> + <param name="infile" type="data" format="fasta" label="Trainings Dataset" help="A set of known genes in FASTA format." /> + <param name="depth" type="integer" value="7" label="Set the depth of the ICM" help="The depth is the maximum number of positions in the context window that will be used to determine the probability of the predicted position." /> + <param name="period" type="integer" value="3" label="Set the period of the ICM" help="The period is the number of different submodels for different positions in the text in a cyclic pattern. E.g., if the period is 3, the first submodel will determine positions 1, 4, 7, ..." /> + <param name="width" type="integer" value="12" label="Set the width of the ICM" help="The width includes the predicted position." /> + <param name="no_stops" type="boolean" truevalue="--no_stops" falsevalue="" checked="false" label="Do not use any input strings with in-frame stop codons" /> + + <conditional name="stop_codon_opts"> + <param name="stop_codon_opts_selector" type="select" label="Specify start codons as"> + <option value="gb" selected="True">Genbank translation table entry</option> + <option value="free_form">Comma-separated list</option> + </param> + <when value="gb"> + <param name="genbank_gencode" type="select" label="Use Genbank translation table to specify stop codons"> + <option value="1" select="True">1. Standard</option> + <option value="2">2. Vertebrate Mitochondrial</option> + <option value="3">3. Yeast Mitochondrial</option> + <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> + <option value="5">5. Invertebrate Mitochondrial</option> + <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> + <option value="9">9. Echinoderm Mitochondrial</option> + <option value="10">10. Euplotid Nuclear</option> + <option value="11">11. Bacteria and Archaea</option> + <option value="12">12. Alternative Yeast Nuclear</option> + <option value="13">13. Ascidian Mitochondrial</option> + <option value="14">14. Flatworm Mitochondrial</option> + <option value="15">15. Blepharisma Macronuclear</option> + <option value="16">16. Chlorophycean Mitochondrial</option> + <option value="21">21. Trematode Mitochondrial</option> + <option value="22">22. Scenedesmus obliquus mitochondrial</option> + <option value="23">23. Thraustochytrium Mitochondrial</option> + <option value="24">24. Pterobranchia mitochondrial</option> + </param> + </when> + <when value="free_form"> + <param name="stop_codons" type="text" value="tag,tga,taa" label="Specify stop codons as a comma-separated list" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="data" name="outfile" /> + </outputs> + <tests> + <test> + <param name="infile" value='streptomyces_Tu6071_plasmid_genes.fasta' /> + <param name="depth" value="7" /> + <param name="period" value="3" /> + <param name="width" value="12" /> + <param name="no_stops" value="" /> + <param name="genbank_gencode" value="11" /> + <!-- compare files sizes, because the output is a binary --> + <output name="outfile" file='streptomyces_Tu6071_plasmid_genes.icm' compare="sim_size" delta="1000" ftype="data" /> + </test> + </tests> + + <help> + +**What it does** + +This program constructs an interpolated context model (ICM) from an input set of sequences. + +This model can be used by Glimmer3 to predict genes. + +**TIP** To extract CDS from a GenBank file use the tool *Extract ORF from a GenBank file*. + +----- + +**Example** + +*Input*:: + + - Genome Sequence + + >CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7 + GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT + GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT + TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT + TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC + GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA + ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG + AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA + CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA + TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC + AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA + GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC + AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC + CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA + AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC + GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT + ..... + +*Output*:: + interpolated context model (ICM) + +------- + +**References** + +A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007). + + + </help> +</tool> |
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| diff -r 000000000000 -r 841357e0acbf glimmer_w_icm.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/glimmer_w_icm.xml Sat Jul 06 10:09:30 2013 -0400 |
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| b'@@ -0,0 +1,224 @@\n+<tool id="glimmer_knowlegde-based" name="Glimmer3" version="0.2">\n+ <description>Predict ORFs in prokaryotic genomes (knowlegde-based)</description>\n+ <requirements>\n+ <requirement type="package" version="3.02b">glimmer</requirement>\n+ <requirement type="package" version="1.61">biopython</requirement>\n+ <requirement type="set_environment">GLIMMER_SCRIPT_PATH</requirement>\n+ </requirements>\n+ <command>\n+ #import tempfile, os\n+ #set $temp = tempfile.NamedTemporaryFile( delete=False )\n+ #silent $temp.close()\n+ #set $temp = $temp.name\n+\n+ glimmer3\n+ --max_olap $max_olap\n+ --gene_len $gene_len\n+ --threshold $threshold\n+ #if float( str($gc_percent) ) > 0.0:\n+ --gc_percent $gc_percent\n+ #end if\n+\n+ #if $stop_codon_opts.stop_codon_opts_selector == "gb":\n+ --trans_table "${stop_codon_opts.genbank_gencode}"\n+ #else:\n+ --stop_codons "${stop_codon_opts.stop_codons}"\n+ #end if\n+\n+ --start_codons $start_codons\n+\n+ $linear\n+ $no_indep\n+ $extend\n+ $seq_input\n+ $icm_input\n+ $temp 2>&1;\n+\n+ ## convert prediction to FASTA sequences\n+ \\$GLIMMER_SCRIPT_PATH/glimmer2seq.py $temp".predict" $seq_input $genes_output;\n+\n+ #if $report:\n+ mv $temp".predict" $report_output;\n+ #else:\n+ rm $temp".predict";\n+ #end if\n+\n+ #if $detailed_report:\n+ mv $temp".detail" $detailed_output;\n+ #else:\n+ rm $temp".detail";\n+ #end if\n+\n+ rm $temp\n+ </command>\n+ <inputs>\n+ <param name="seq_input" type="data" format="fasta" label="Genome Sequence" />\n+ <param name="icm_input" type="data" format="data" label="Interpolated context model (ICM)" />\n+\n+ <param name="max_olap" type="integer" value="50" label="Set maximum overlap length" help="Overlaps this short or shorter are ignored." />\n+ <param name="gene_len" type="integer" value="90" label="Set the minimum gene length to n nucleotides" hrlp="This does not include the bases in the stop codon."/>\n+ <param name="threshold" type="integer" value="30" label="Set threshold score for calling as gene" help="If the in-frame score >= N, then the region is given a number and considered a potential gene." />\n+ <param name="gc_percent" type="float" value="0.0" label="Set the GC percentage of the independent model, i.e., the model of intergenic sequence" help="If 0.0 specified, the GC percentage will be counted from the input file." />\n+\n+ <param name="linear" type="boolean" truevalue="--linear" falsevalue="" checked="true" label="Assume linear rather than circular genome, i.e., no wraparound" />\n+ <param name="no_indep" type="boolean" truevalue="--no_indep" falsevalue="" checked="false" label="Don\xe2\x80\x99t use the independent probability score column at all" help="Using this option will produce more short gene predictions." />\n+ <param name="extend" type="boolean" truevalue="--extend" falsevalue="" checked="false" label="Also score orfs that extend off the end of the sequence(s)" />\n+ <param name="start_codons" type="text" value="atg,gtg,ttg" label="Specify start codons as a comma-separated list" />\n+\n+ <conditional name="stop_codon_opts">\n+ <param name="stop_codon_opts_selector" type="select" label="Specify start codons as">\n+ <option value="gb" selected="True">Genbank translation table entry</option>\n+ <option value="free_form">Comma-separated list</option>\n+ </param>\n+ <when value="gb">\n+ <param name="genbank_gencode" type="select" label="Use Genbank translation table to specify stop codons">\n+ <option value="1" select="True">1. Standard</option>\n+ <option value="2">2. Vertebrate Mitochondrial</option>\n+ <option value="3">3. Yeast Mitochondrial</option>\n+ '..b"th extracted CDS from related organisms (ICM builder). If you can't generate an ICM model you can use the non knowlegde-based Glimmer with a de novo prediction.\n+\n+-----\n+\n+**Example**\n+\n+*Input*::\n+\t\n+\t- interpolated context model (ICM): Use the 'Glimmer ICM builder' tool to create one\n+\t- Genome Sequence in FASTA format\n+\t\n+\t\t>CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7\n+\t\tGATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT\n+\t\tGATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT\n+\t\tTTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT\n+\t\tTTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC\n+\t\tGAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA\n+\t\tATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG\n+\t\tAACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA\n+\t\tCAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA\n+\t\tTGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC\n+\t\tAACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA\n+\t\tGTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC\n+\t\tAAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC\n+\t\tCATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA\n+\t\tAAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC\n+\t\tGAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT\n+\t\t.....\n+\n+*Output*:: \n+\n+\t- FASTA file with predicted proteins\n+\t- Glimmer prediction file (optional)\n+\n+\t\t>CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7.\n+\t\torf00001 40137 52 +2 8.68\n+\t\torf00004 603 34 -1 2.91\n+\t\torf00006 1289 1095 -3 3.16\n+\t\torf00007 1555 1391 -2 2.33\n+\t\torf00008 1809 1576 -1 1.02\n+\t\torf00010 1953 2066 +3 3.09\n+\t\torf00011 2182 2304 +1 0.89\n+\t\torf00013 2390 2521 +2 0.60\n+\t\torf00018 2570 3073 +2 2.54\n+\t\torf00020 3196 3747 +1 2.91\n+\t\torf00022 3758 4000 +2 0.83\n+\t\torf00023 4399 4157 -2 1.31\n+\t\torf00025 4463 4759 +2 2.92\n+\t\torf00026 4878 5111 +3 0.78\n+\t\torf00027 5468 5166 -3 1.64\n+\t\torf00029 5590 5832 +1 0.29\n+\t\torf00032 6023 6226 +2 6.02\n+\t\torf00033 6217 6336 +1 3.09\n+\t\t........\n+\n+\t- Glimmer detailed report (optional)\n+\n+\t\t>CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7.\n+\t\tSequence length = 40222\n+\t\t\t\n+\t\t\t ----- Start ----- --- Length ---- ------------- Scores -------------\n+\t\t ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 NC\n+\t\t0001 +2 40137 40137 52 135 135 9.26 96 - 96 - - 3 - 0\n+\t\t0002 +1 58 64 180 120 114 5.01 69 69 - - 30 - - 0\n+\t\t\t+3 300 309 422 120 111 -0.68 20 - - 20 38 - - 41\n+\t\t\t+3 423 432 545 120 111 1.29 21 - 51 21 13 - 8 5\n+\t\t0003 +2 401 416 595 192 177 2.51 93 - 93 - 5 - - 1\n+\t\t0004 -1 645 552 34 609 516 2.33 99 - - - 99 - - 0\n+\t\t\t+1 562 592 762 198 168 -2.54 1 1 - - - - - 98\n+\t\t\t+1 763 772 915 150 141 -1.34 1 1 - - - - 86 11\n+\t\t\t+3 837 846 1007 168 159 1.35 28 - 50 28 - - 17 3\n+\t\t0005 -3 1073 977 654 417 321 0.52 84 - - - - - 84 15\n+\t\t0006 -3 1373 1319 1095 276 222 3.80 99 - - - - - 99 0\n+\t\t0007 -2 1585 1555 1391 192 162 2.70 98 - - - - 98 - 1\n+\t\t0008 -1 1812 1809 1576 234 231 1.26 94 - - - 94 - - 5\n+\t\t0009 +2 1721 1730 1945 222 213 0.68 80 - 80 - - - - 19\n+\t\t.....\n+\n+-------\n+\n+**References**\n+\n+A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007).\n+\n+\n+ </help>\n+\n+</tool>\n" |
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| diff -r 000000000000 -r 841357e0acbf glimmer_wo_icm.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/glimmer_wo_icm.py Sat Jul 06 10:09:30 2013 -0400 |
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| @@ -0,0 +1,74 @@ +#!/usr/bin/env python +""" +Input: DNA Fasta File +Output: Tabular +Return Tabular File with predicted ORF's +Bjoern Gruening +""" +import sys, os +import tempfile +import subprocess +import shutil +from glimmer2seq import glimmer2seq + +def main(): + genome_seq_file = sys.argv[1] + outfile_classic_glimmer = sys.argv[2] + outfile_ext_path = sys.argv[3] + oufile_genes = sys.argv[8] + + tag = 'glimmer_non_knowlegde_based_prediction' + tempdir = tempfile.gettempdir() + + trainingset = os.path.join( tempdir, tag + ".train" ) + icm = os.path.join( tempdir, tag + ".icm" ) + + longorfs = tempfile.NamedTemporaryFile() + trainingset = tempfile.NamedTemporaryFile() + icm = tempfile.NamedTemporaryFile() + + #glimmeropts = "-o0 -g110 -t30 -l" + glimmeropts = "-o%s -g%s -t%s" % (sys.argv[4], sys.argv[5], sys.argv[6]) + if sys.argv[7] == "true": + glimmeropts += " -l" + + """ + 1. Find long, non-overlapping orfs to use as a training set + """ + subprocess.Popen(["long-orfs", "-n", "-t", "1.15", + genome_seq_file, "-"], stdout = longorfs, + stderr = subprocess.PIPE).communicate() + + """ + 2. Extract the training sequences from the genome file + """ + subprocess.Popen(["extract", "-t", + genome_seq_file, longorfs.name], stdout=trainingset, + stderr=subprocess.PIPE).communicate() + + """ + 3. Build the icm from the training sequences + """ + + # the "-" parameter is used to redirect the output to stdout + subprocess.Popen(["build-icm", "-r", "-"], + stdin=open(trainingset.name), stdout = icm, + stderr=subprocess.PIPE).communicate() + + """ + Run Glimmer3 + """ + b = subprocess.Popen(["glimmer3", glimmeropts, + genome_seq_file, icm.name, os.path.join(tempdir, tag)], + stdout = subprocess.PIPE, stderr=subprocess.PIPE).communicate() + + if outfile_classic_glimmer.strip() != 'None': + shutil.copyfile( os.path.join( tempdir, tag + ".predict" ), outfile_classic_glimmer ) + if outfile_ext_path.strip() != 'None': + shutil.copyfile( os.path.join( tempdir, tag + ".detail" ), outfile_ext_path ) + + glimmer2seq( os.path.join( tempdir, tag + ".predict" ), genome_seq_file, oufile_genes ) + + +if __name__ == "__main__" : + main() |
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| diff -r 000000000000 -r 841357e0acbf glimmer_wo_icm.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/glimmer_wo_icm.xml Sat Jul 06 10:09:30 2013 -0400 |
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| @@ -0,0 +1,119 @@ +<tool id="glimmer_not-knowlegde-based" name="Glimmer3" version="0.2"> + <description>Predict ORFs in prokaryotic genomes (not knowlegde-based)</description> + <requirements> + <requirement type="package" version="3.02b">glimmer</requirement> + <requirement type="package" version="1.61">biopython</requirement> + </requirements> + <command interpreter="python"> + glimmer_wo_icm.py + $input + #if $report: + $prediction + #else: + "None" + #end if + #if $detailed_report: + $detailed + #else: + "None" + #end if + $overlap + $gene_length + $threshold + $linear + $genes_output + </command> + <inputs> + <param name="input" type="data" format="fasta" label="Genome sequence" /> + <param name="overlap" type="integer" value="0" label="Set maximum overlap length. Overlaps this short or shorter are ignored." /> + <param name="gene_length" type="integer" value="110" label="Set minimum gene length." /> + <param name="threshold" type="integer" value="30" label="Set threshold score for calling as gene. If the in-frame score >= N, then the region is given a number and considered a potential gene." /> + <param name="linear" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Assume linear rather than circular genome, i.e., no wraparound" /> + + <param name="detailed_report" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a detailed gene prediction report as separate file" /> + <param name="report" type="boolean" truevalue="" falsevalue="" checked="false" label="Report the classic glimmer table output" /> + </inputs> + <outputs> + <data name="genes_output" format="fasta" label="Glimmer3 on ${on_string} (Gene Prediction FASTA)" /> + <data name="prediction" format="txt" label="Glimmer3 on ${on_string} (Gene Prediction table)"> + <filter>report == True</filter> + </data> + <data name="detailed" format="txt" label="Glimmer3 on ${on_string} (detailed report)"> + <filter>detailed_report == True</filter> + </data> + </outputs> + <tests> + <test> + <param name="input" value="streptomyces_Tue6071_plasmid_genomic.fasta" /> + <param name="overlap" value="0" /> + <param name="gene_length" value="110" /> + <param name="threshold" value="30" /> + <param name="linear" value="true" /> + <param name="detailed_report" value="" /> + <param name="report" value="" /> + <output name="genes_output" file="glimmer_wo_icm_trans-table-11_plasmid_genomic.fasta" ftype="fasta" /> + </test> + </tests> + <help> + +**What it does** + +This tool predicts open reading frames (orfs) from a given DNA Sequence. That tool is not knowlegde-based. + +The recommended way is to use a trained Glimmer3 with ICM model. Use the knowlegde-based version for that and insert/generate a training set. + +----- + +**Glimmer Overview** + +:: + +************** ************** ************** ************** +* * * * * * * * +* long-orfs * ===> * Extract * ===> * build-icm * ===> * glimmer3 * +* * * * * * * * +************** ************** ************** ************** + +----- + +**Example** + +Suppose you have the following DNA sequences:: + + >SQ Sequence 8667507 BP; 1203558 A; 3121252 C; 3129638 G; 1213059 T; 0 other; + cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg + ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag + cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc + cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc + ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg + ....... + +Running this tool will produce a FASTA file with predicted genes and glimmer output files like the following:: + + >SQ Sequence 8667507 BP; 1203558 A; 3121252 C; 3129638 G; 1213059 T; 0 other; + orf00001 577 699 +1 5.24 + orf00003 800 1123 +2 5.18 + orf00004 1144 3813 +1 10.62 + orf00006 3857 6220 +2 6.07 + orf00007 6226 7173 +1 1.69 + orf00008 7187 9307 +2 8.95 + orf00009 9424 10410 +1 8.29 + orf00010 10515 11363 +3 7.00 + orf00011 11812 11964 +1 2.80 + orf00012 12360 13457 +3 4.80 + orf00013 14379 14044 -1 7.41 + orf00015 15029 14739 -3 12.43 + orf00016 15066 15227 +3 1.91 + orf00020 16061 15351 -3 2.83 + orf00021 17513 17391 -3 2.20 + orf00023 17529 17675 +3 0.11 + + +------- + +**References** + +A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007). + + </help> +</tool> |
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| diff -r 000000000000 -r 841357e0acbf readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Sat Jul 06 10:09:30 2013 -0400 |
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| @@ -0,0 +1,73 @@ +======================================= +Galaxy wrapper for Glimmer gene calling +======================================= + +This wrapper is copyright 2012-2013 by Björn Grüning. + +This is a wrapper for the command line tool of Glimmer3_. + +.. _Glimmer: http://www.cbcb.umd.edu/software/glimmer/ + +Glimmer is a system for finding genes in microbial DNA, +especially the genomes of bacteria, archaea, and viruses. +Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated +Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. + +S. Salzberg, A. Delcher, S. Kasif, and O. White. Microbial gene identification using interpolated Markov models, Nucleic Acids Research 26:2 (1998), 544-548. + +A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg. Improved microbial gene identification with GLIMMER, Nucleic Acids Research 27:23 (1999), 4636-4641. + +A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007). + + +============ +Installation +============ + +Since version 0.2 the recommended installation procedure is via the `Galaxy Tool Shed`. + +.. _`Galaxy Tool Shed`: http://toolshed.g2.bx.psu.edu/view/bjoern-gruening/glimmer3 + +To install Glimmer3 manually, please download Glimmer3 from:: + + http://www.cbcb.umd.edu/software/glimmer/glimmer302.tar.gz + +and follow the installation instructions. You can also use packages from your distribution like http://packages.debian.org/stable/science/tigr-glimmer + +To install the wrapper copy the glimmer3 folder in the galaxy tools +folder and modify the tools_conf.xml file to make the tool available to Galaxy. +For example:: + + <tool file="gene_prediction/tools/glimmer3/glimmer_w_icm.xml" /> + <tool file="gene_prediction/tools/glimmer3/glimmer_wo_icm.xml" /> + <tool file="gene_prediction/tools/glimmer3/glimmer_build-icm.xml" /> + +======= +History +======= + +- v0.1: Initial public release +- v0.2: Add tool shed integration + +=============================== +Wrapper Licence (MIT/BSD style) +=============================== + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the +names of the contributors or copyright holders not be used in +advertising or publicity pertaining to distribution of the software +without specific prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +OR PERFORMANCE OF THIS SOFTWARE. + |
| b |
| diff -r 000000000000 -r 841357e0acbf test-data/glimmer_w_icm_trans-table-11_genomic.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/glimmer_w_icm_trans-table-11_genomic.fasta Sat Jul 06 10:09:30 2013 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>orf00001 gi|333022496:2500-3701 Streptomyces sp. Tu6071 chromosome, whole genome shotgun sequence +GTGCTCGGTGGCGGCCCAGGTGGCGAGAAGCCGCAGGGTGTCGTGGTCGGGGGTGCCGGG +GGCGGCGCTGTAGGCGGTCAGGGTCAGTCCCGGCTGAGCCGGTAG |
| b |
| diff -r 000000000000 -r 841357e0acbf test-data/glimmer_wo_icm_trans-table-11_plasmid_genomic.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/glimmer_wo_icm_trans-table-11_plasmid_genomic.fasta Sat Jul 06 10:09:30 2013 -0400 |
| b |
| b'@@ -0,0 +1,2213 @@\n+>orf00001 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+TTGGCTCGTCTGCCTCGTGAGGAGATTCAAATGTCTGTTTCCCGGGTTCCGCTGCGGAAA\n+CATCAGGTAGAGCTTATGTCGGACCTCAGGAAATGGGTCCGGGTAGCCGCCCGGGAAAGC\n+GCCCGCACGGAGCGTGGGGCGCGGGCCACGGTGGTGTCCGCTACGGGTACGGGAAAGACG\n+ATCAGCGCGGCTGCTGCGGCGTTGGAGTTGTTCCCTTCGGGGCGGGTTCTCGTGATGGTG\n+CCGACGCTGGATCTGCTGGTGCAGACGGCGCAGTCGTGGCGGGCGGTGGGGCACACGGCG\n+CCGATGGTCGGGGTGTGCTCGCTGCCCAGGGATCTGCTCCTGGAGGAGCTGCGGGTGCGG\n+ACGACGACCCACCCGATCCGGCTCGCGCTTTGGGCCGGATCGGGGCCGGTGGTCGTGCTG\n+GCGACGTACTCCTCGCTCGTGGGCGAGGACGGGCAGGGCGGACCCTTGGAGGCCGCTCTC\n+GCCGGGGCTGGCTTGTACGGGCAGCGGATGGATGGCTTCGACCTTGCGGTCGTGGACGAG\n+GCGCACCGCACGGCGGGCAGCGCGGAGAAGGCGTGGGCGGCGATCCACGACAACGCCCGT\n+TTTCCGGCGGCGCACCGGCTGTACCTCACCGCGACCCCGCGCGTCCTGGCCCCGGCCCGT\n+CCCGCCAGGCACGAGGGCGAGGAGGGACGCGGGGAGGCGCCGGCACTCGTGACGATGGCG\n+AATGATCCGGCGGGCGAGTACGGGGCGTGGATTCACGAACTCGGTTTGTCCGAGGCAATC\n+GCGCGAAAAATCGTCGCGCCTTTTGAGATTGACGTTTTGGAGATTACTGATCCTGAGCCG\n+GAATTGATGGAGGGATTGGATCGGGAGGCGCGGCGTGGGCGGCGGCTTGCGTTGCTTCAG\n+ACCGGGCTTTTGGAGCACGCGGCCGAGCATAATATTTGCACCATGATGACGCTTCATCAG\n+CAGGTTGAGGAGGCGGCGGCTTTCGCGGAGAAAATGCCGGAGACGGCGGCGGAGCTTTAC\n+CGGAATGAGGTGTCGGCGGAGGATTTTGCCCTGGCCGAGGAGCTCCCGGCCTCCGAGGTG\n+GGTGGGGGGTTCTACGAGCTGGAGCCGGGGCGTCATGTGCCGCCGTCGCGGGTGTGGTCG\n+CGGTGGCTGTATGGGGAGCATCCTGTGGCCGAACGGCGTTCTGTGCTGCGGGAGTTCGCG\n+AACGGGATGGACGCGGAGGGGCGGCGGGTGCACCGGGCGTTCCTCGCTTCCGTACGGGTC\n+CTGGGTGAGGGCGTCGACATCGTCGGGGAGCGCGGGGTCGAGGCGATCTGCTTTGCCGAC\n+GCACGCGGGTCTCAGGTGGAGATCGTGCAGAACATCGGGCGCGCGTTGCGCCAGAACCCG\n+GATGGGCGGGCGAAGACGGCGCGGATCATCGTGCCGGTCTTCCTGCGGCCGGACGAGGAC\n+GGGGAGGGCATGGTGGCGTCGGAGGCGTACCGGCCGCTCGTCGCCGTACTCCAGGGCCTG\n+CGCTCGCACGACGAGCACCTGGTCGAGAAACTCATGCTGCGGGCGCGCGTACGGGCCGAG\n+AGCGCGAGCGCGCGCAGCGCGGAGGAGGGCGGTGCGGGGCCCTCGCGGCTCCTGTCGGAC\n+TCCGGGACGGCGGCTGCGGCCTCCGAGGGCGTCGAGGGCCAGGAGCAGGGCGAGGACGGC\n+GCCGAGGCGGAGTCGGTGCTGCTGCGGTTCTCCTCGCCGCGCGCGGCGTCGACGGTCGCG\n+GCGTTCCTGCGGACGCGGGTGTACCAGCCCGAGTCGCTGGTGTGGCTGGAGGGGTACGAG\n+GCCCTGCGCGCCTGGCGGGCCGAGCAAGGGGTGAGCGGGGTGTGCGCGGTCCCGTACGAC\n+GCCGAGGTCGCCGCGGGGGCCTCGCGGCGGTACCCGGTCGGGCGGTGGACCGCCGCGCAA\n+CGCCGCGCCCGCCGCGAGGGCACCCTCAGCGCACACCGCGTCGAGCTCCTCGACGCGGAG\n+GGCATGGTGTGGGAGCCGCGCGAGGAGGAATGGGAGCGCACGCTCGCGGGGCTTCGCTCC\n+TACCGGACGGCGTACGGGCACCTCGCCCCCCACAGGCGCGAAACCTGGGGCGAAGACGAG\n+GGTGAGGACGTCGTACGCGTCGGGGACCTGATGGCGAACCTCCGCCGCAAGGACGGACTC\n+GGGAAGGACGCGAAGCGGGCCGCCGCGCGCGCCGCGCAGCTGAGGGCCGTCGATGCGGAC\n+TGGGACTGCCCGTGGCCGCTGGACTGGCAGCGCTGCTGCCGGAAACTCGTGCTCCTGGCC\n+GCGGACGAGCCCGGCGGGCGCCTGCCGGAGATCGCGCCCGGGGTCTGCCTGGACGGGGAT\n+GACCTCGGGGTGTGGGTCGCGCGGCAGCAGGAGCCGCGGGTGTGGGCGCGGCTCAGCACC\n+GAGCAGCGGGCGCGGCTCGAAGCGCTCGGGCTGCGGCCCACCGAAGCGGCCCCGGGGCGG\n+GGTGTGGAGGGCACGGGGGCGGCGGGGAGCATGAAGCGGACGGCGACGGCGCGAACGGCT\n+TTTCAGCGGGGTGTGGCGGCGCTCGCGCAGTGGGTCGAGCGGGAAGGCGCGGGGAAACCC\n+GTACCCCGCAAACACGTCGAGACCGTCAGCGTCGACGGCGAGGACGTCGACGTACGCCTC\n+GGCGTATGGATCTCGAACACCAAGAGCCGGTACGACGGGCTGAGCGAGGACGAACGCGCG\n+CAGCTCACCGCACTCGGAATGCCCTGGGCAGGATGA\n+>orf00005 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+GTGCTCGCCGCCGTACGGGACACGATCGCCGAGACCGGCCAGGGACCGTCCGTACGGCAG\n+ATCCAGCGCGTCACCGGGCTCGCGCTCGGCACCATCGCCCACCACCTGAAGGCGCTGGAG\n+GAGAGCGGCCCCCTCGTCCGTACGGGCCTGCACTGGCGCACCTGCCGCCTGGGCTGA\n+>orf00006 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+GTGACCGATGAACTGCTCCGCCTCGCCCAGGAGAGGCGTGCGACCTACCGCGACCTCACC\n+CTCGGCGGCCCCGCCCGCCCCCCGACACCTCTGCGCCGGGCACTGATCCGGCAGTCCGCC\n+CGCCTGCTCGACGGCCCGCCCACCACGGCCCGCCGGGCTCTGCTGTGCCGCCCGCCCACG\n+CCCGCGTCCCCGCCCTCGCGGGGGACCAGGTGA\n+>orf00007 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+GTGACCGATTTCCCCGACGATCTCCTCGCGGCTCAGCGCGACCTCACCGCCGTACGCGCC\n+ACCCTTTCCGCCCGCCTCGCGGCGCTGCCGCCCTCGGCCGAGCCGATGCCCGCGTGGGAG\n+CGGCCCGACGGCTACTGGGCGGGCGCCCGTACGCACCCGGCCTCCCCGGGGTGGAGCGAG\n+GAGGAGCGCGAGGAGGTCGCCGCGCTCCGCGAGCGGGAGCGGGATCTGGCCGGGGTGATC\n+GTGACGCACGAGCTGTGGGCGAGCGTGCCGGCCGGGGAGCGGA'..b'CCTGGCAGGCAGAGGAGGGCGCCTACATG\n+CACCAGCAGAACACCCGTCCCCTCACCCTCGCGCCCGCACTGAACGACTCGCCCGCCGGA\n+CTGCTCTCCTGGATCCTCGAGAAGTACCGCGCGTGGACCGACTGCGGCGGCGACCTGTCC\n+ACCCGCTTCGGCGACGACTTCCTCCTCACCCAGGCATCGCTCTACTGGTTCACCGGCACG\n+ATCTCCACGTCCTTCCGCCCGTACTACGAGTACGCGCACCAGCTCACCCGGCGCGTGCGG\n+CGGGTCGACGTCCCCACCGCCCTCGCCCTGTTCCCCGCAGACCTCGCCCAACCGCCCCGG\n+AGCTGGGCCGAGCGCACCTACCACCTCACGCGTTACACCCGTATGCCTCGCGGCGGCCAC\n+TTCGCCGCGCACGAGGAACCGGCCTTGCTTGCCGACGACATCACCGCGTTCTTCGGCGAC\n+CTCCGTTAG\n+>orf00336 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+GTGGATGGACTGCATGGGAGCCCACTTCATAAGAGGCTCGACGAACACTGCGCTGGCCGA\n+TTCGGGATCGCACCACCGCTAACCGGGGAAATCACCACGAAGATCAACCACTGA\n+>orf00337 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+ATGCCCACCGAGACCCTGCCGCCCGAGGTGCGGAATTTCATCGACGATGCGCGGCGTCAC\n+CTGGCTTTCTGCGCCGGGCTGCGCGCGGGCGAGGACCCGGCGTACGCGACCGTGCTCCTG\n+GCCGCCGCCGAGCAGGGAGAAGAAGTCCTCGCCCGGTACGAAGGCCGCGTAGCTTAG\n+>orf00339 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+TTGGCTTGTCTGCCTCGTGAGGAGTTTCAAATTTCTGTTTCTCGGGTTCCGTTGCGGAAA\n+CATCAGGTGGAGCTTATGTCGGACCTCAGGAAATGGGTTCGGGTGGCTGCCCGGGAAAGC\n+GCCCGTTCGGGGCGGGGGGCGCGGGCGACGGTGGTGTCCGCTACGGGTACGGGGAAGACG\n+ATCAGCGCGGCTGTTGCGGCGTTGGAGTTGTTCCCTTCGGGGCGGGTTCTCGTGATGGTG\n+CCGACGCTGGATCTGCTGGTGCAGACGGCGCAGTCGTGGCGGGCGGTGGGGCACACGGCG\n+CCGATGGTCGGGGTGTGCTCGCTGCCCGGGGATCTGCTCCTGGAGGAGTTGCGGGTGCGG\n+ACGACGACGCACCCGATCCGGCTCGCGCTGTGGGCCGGGCAGGGGCCTGTGGTCGTGCTG\n+GCGACGTACTCCTCGCTCGTGGGCGGGGACGGGCAGGGCGGGCCCCTGGAGGCCGCCCTG\n+GCGGGCTCGGGGTTGTACGGGCAGCGGATGGACGGCTTCGACCTCGCGGTCGTGGACGAG\n+GCGCACCGTACGGCGGGCAGCGCGGCGAAGCCCTGGGCCGCGATCCACGACAACGCCCGT\n+ATCCCGGCGGCGCACCGGCTCTACCTCACCGCCACCCCGCGCGTCCTCGCGCCCGCCCGC\n+CCCGACAGGGACGAGGACCAGGAGGAGGGCGGCGGGGAGGCGCCGGCACTCGTGACGATG\n+GCGAACGACCCGGAAGGCGAGTACGGGGCGTGGATTCACGAACTCGGGTTGTCCGAGGCG\n+ATCGAGCGGAAAATTCTTGCGCCTTTCGAGATTGATGTTTTGGAGATTACCGATCCTGAG\n+CCGGAATTGATGGAAGGAATGGACCGGGAGGCGCGGCGTGGGCGGCGGCTCGCCCTGCTC\n+CAGACTGCGTTGCTGGAGCACGCGGCCGAGCACAATCTGCGCACCGTGATGACGTTCCAT\n+CAGCGGGTGGAGGAGGCGGCGGCTTTCGCGGAGAAAATGCCGGAGACAGCGGCGGAGCTT\n+TACCGGAATGAGGTGTCGGCGGAGGATCTTGCCCTAGCCGAGGAGCTCCCGGCCTCCGAG\n+GTGGGCGGGGGCTTCTACGAGCTGGAGCCGGGGCGGCATGTGCGGCCGGAGCGGGTGTGG\n+TCGCGGTGGCTGTACGGAGAGCACCCGGTGGCCGAACGCCGTGCGGTGCTGCGGGAGTTC\n+GCGAACGGGATGGACTCGGCAGGGGTGCGGGTGCACCGCGCGTTCCTCGCCTCCGTCCGC\n+GTGCTCGGCGAGGGCGTCGACATCGTCGGGGAGCGCGGGGTCGAGGCGATCTGCTTCGCC\n+GACGCGCGCGGGTCCCAGGTCGAGATCGTGCAGAACATCGGCAGGGCGCTGCGCCCGAAC\n+CCGGACGGGCAGACGAAGACGGCGCGGATCATCGTGCCCGTCTTCTTGGAGGCCGACGAG\n+GACGGGGAGGGGATGGTCGCGAGCGAGGCGTACCGGCCGCTCGTGGCCGTGCTCCAGGGG\n+CTGCGCTCGCACTCCGAGCACCTGGTCGAGAAGCTGATGCTCCGGGCCCGGGTGCGGGCC\n+GAGAGCGCGAGCGCGCGCAGCGCGGAGGAGGCCGGTGCGGGGCCCGCGCGGGTCCTGTCC\n+GACTCCGGGACCTCTTCCCCCGCCTCCCAGGCCTCCGGGGACGTCGAAGGCGAGAACGAG\n+GACGACGTCGAGGCGGGCGCGGACGGCGCTGAGGCGGGCGCGGACGGCGCTGAGGAGTCG\n+GAGTCGGTGTTGTTGCGGTTCTCGACGCCGCGCTCGGCGTCGACCATCGCGGCCTTCCTG\n+CGGACGCGGGTGTACCAGCCGGAGTCGACGGTGTGGCTGGAGGGCTACGAGGCGCTGCGC\n+GCCTGGCGGGCCGAGCAAGGGGTGCGCGGCTTGTGCGCGGTCCCGTACGACGCCGAGGTC\n+GCCGCGGGGGCCTCGCGGCGGTACCCGGTCGGGCGGTGGACCACCGCGCAACGCCGCGCC\n+CGCCGCGAGGGCACCCTCAGCGCACACCGCATCGACCTGCTCGACGCGGAGGGCATGGTG\n+TGGGAGCCGCGCGAAGAGGAGTGGGAGCGCACGCTCGCCGGGCTTCGCTCCTACCGGGCC\n+GCGTACGGGCACCTCGCCCCCCGCCGGCGCGAAACCTGGGGCGAAGACGAGGGTGAGGAC\n+GTCGTACGCGTCGGGGACCTGATGGCGAACCTCCGCCGCAAGGACGGACTCGGGCGGGAC\n+GCGGAGCGGGCCGCCGCGCGCGCGGCCCAGCTGAGGGCCGTCGATGCGGACTGGGACTGC\n+CCCTGGCCGCTGGACTGGCAGCGCTGCTGTCGGCAGCTCGCGCTCCTGGCCGCCGACGAA\n+CCCGACGGACGCGCGCCCCGGATCGCGCGCGGGGTGCGCATCGACGGGGACGACCTCGGC\n+GCGTGGGTCGCGCGGCAGCAGGAACCGCGGGTGTGGGCGAAGCTCAGCACCGAGCAGCGG\n+GCGCGACTCGAAGCGCTCGGGCTCCGGCCTACCGAGACGGCCCCACGGCGGGGTGTGGAG\n+GGCACGGGGGCGGCGGGGAGCGGGAAGCGGACGGCGGCGGCGCGAACGGCCTTCCAGCGC\n+GGCCTCGCGGCGCTCGCGCAGTGGGTCGAGCGGGAAGGCGCGGAGAAACCCGTACCCCGC\n+AAACACACCGAGACCGTGAGCGTGGACGGTGAGGACGTCGACGTACGCCTCGGCGTGTGG\n+GTCTCGAACGTGAAGAGCCGCTTCGACGGGATGGGCGAGGACGAGCGCGGCCAGCTCACC\n+GCGCTCGGAGTGCCCTGGGCGGTGTAG\n' |
| b |
| diff -r 000000000000 -r 841357e0acbf test-data/streptomyces_Tu6071_genomic.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streptomyces_Tu6071_genomic.fasta Sat Jul 06 10:09:30 2013 -0400 |
| b |
| @@ -0,0 +1,20 @@ +>gi|333022496:2500-3701 Streptomyces sp. Tu6071 chromosome, whole genome shotgun sequence +CCGAGGAGGCGAAGACCGGCGCGCGCGCCGTGGCACCGTGATCCGCATGGGCGGCACCTCGACCAGAGCG +CCCGCATCGTGGTCCTCGCCAGGCGGCAGGCGCCTGACCCGGGCGGTCGCACGTGGAGGTCGCTCAGCTT +CCCGAGTGCGCGCGGATGCTTGGCGGCGGCCATCGGCGTTTTTAGTGGCTGCCCGATGTGGTGTCGGTGG +ACGGCTTGCCAGGGAGCCCGTCTGCGCCCGTAGCGTGCTCGGTGGCGGCCCAGGTGGCGAGAAGCCGCAG +GGTGTCGTGGTCGGGGGTGCCGGGGGCGGCGCTGTAGGCGGTCAGGGTCAGTCCCGGCTGAGCCGGTAGT +TCCATGGCGTCGAAGTCGAGGGCGAGGACGCCGACAGCGGGGTGGTGGAACGCTTTGCGGCCCGTGTGAT +GCAGGCGCACGTTGTGCCTGGCCCAAGCGGTGCGGAACTCATCGCTGCGGGTGACGAGCTCCCCGATCAG +TCCGGTCAGCCCGGTGTCATGCGGGGCTCGTCCGGCTTCGGTACGCAGGAGGGAGACGGTGGTGTTCACG +GCTTCCTCCCAGTGGGGGAAGAATTCGCGGCCTGTGGGGTCGAGGAACTGGAAGCGCGCGATGTTGACCG +GTTCGCGTGCGCCGGTGGCGTAGAGCGGGCTGTACAGGGCGCGGCCCAGGGGGTTGGTGGCCAGGACGTC +AAGGCGGCCGTTTCGGATGAAGGCCGGGCATTCGCCCATGGAGCGCAGGACGCGCAGCACGCTGTCGGGC +AGGGGGCCGCGGGCGCGCTTGGTGCGACGGGCGGGCCGGTGGGCGGCGGCGCGGGCCAGGTCGTACAGGT +GAGCGCGTTCGGCGTCGTCGAGCTGGAGAGCGTTCGCGAGCGCGTCAAGGACTTCTTCGGAGGCTCCGGC +GAGGTGGCCGCGCTCCAGGCGGACGTAGTAGTCGATGCTGACGCCGGCGAGCAGGGCGACTTCCTCGCGG +CGCAGGCCGGGCACGCGCCGGTTGCCGCCGTAGGCGGGCAGCCCGGCCTGCTGCGGGGTGATCCTGGCGC +GGCGGGAGCCAAGGAATTCGCGGATGTCGCTCGCGGTACTCATGCCTTCCACGCTAAGCCGGACGGCGCA +GACGTGGGGGGGCCTGTCAGTACCTGTAACAGCAAGCCCTTCTTCCCCTTCTTGACCTGGTGTTTCCTCG +AAGTCGCAGGCC + |
| b |
| diff -r 000000000000 -r 841357e0acbf test-data/streptomyces_Tu6071_plasmid_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streptomyces_Tu6071_plasmid_genes.fasta Sat Jul 06 10:09:30 2013 -0400 |
| [ |
| b'@@ -0,0 +1,1937 @@\n+>lcl|NZ_CM001166.1_gene_1 [locus_tag=STTU_p0001] [location=183..2918]\n+TTGGCTCGTCTGCCTCGTGAGGAGATTCAAATGTCTGTTTCCCGGGTTCCGCTGCGGAAACATCAGGTAG\n+AGCTTATGTCGGACCTCAGGAAATGGGTCCGGGTAGCCGCCCGGGAAAGCGCCCGCACGGAGCGTGGGGC\n+GCGGGCCACGGTGGTGTCCGCTACGGGTACGGGAAAGACGATCAGCGCGGCTGCTGCGGCGTTGGAGTTG\n+TTCCCTTCGGGGCGGGTTCTCGTGATGGTGCCGACGCTGGATCTGCTGGTGCAGACGGCGCAGTCGTGGC\n+GGGCGGTGGGGCACACGGCGCCGATGGTCGGGGTGTGCTCGCTGCCCAGGGATCTGCTCCTGGAGGAGCT\n+GCGGGTGCGGACGACGACCCACCCGATCCGGCTCGCGCTTTGGGCCGGATCGGGGCCGGTGGTCGTGCTG\n+GCGACGTACTCCTCGCTCGTGGGCGAGGACGGGCAGGGCGGACCCTTGGAGGCCGCTCTCGCCGGGGCTG\n+GCTTGTACGGGCAGCGGATGGATGGCTTCGACCTTGCGGTCGTGGACGAGGCGCACCGCACGGCGGGCAG\n+CGCGGAGAAGGCGTGGGCGGCGATCCACGACAACGCCCGTTTTCCGGCGGCGCACCGGCTGTACCTCACC\n+GCGACCCCGCGCGTCCTGGCCCCGGCCCGTCCCGCCAGGCACGAGGGCGAGGAGGGACGCGGGGAGGCGC\n+CGGCACTCGTGACGATGGCGAATGATCCGGCGGGCGAGTACGGGGCGTGGATTCACGAACTCGGTTTGTC\n+CGAGGCAATCGCGCGAAAAATCGTCGCGCCTTTTGAGATTGACGTTTTGGAGATTACTGATCCTGAGCCG\n+GAATTGATGGAGGGATTGGATCGGGAGGCGCGGCGTGGGCGGCGGCTTGCGTTGCTTCAGACCGGGCTTT\n+TGGAGCACGCGGCCGAGCATAATATTTGCACCATGATGACGCTTCATCAGCAGGTTGAGGAGGCGGCGGC\n+TTTCGCGGAGAAAATGCCGGAGACGGCGGCGGAGCTTTACCGGAATGAGGTGTCGGCGGAGGATTTTGCC\n+CTGGCCGAGGAGCTCCCGGCCTCCGAGGTGGGTGGGGGGTTCTACGAGCTGGAGCCGGGGCGTCATGTGC\n+CGCCGTCGCGGGTGTGGTCGCGGTGGCTGTATGGGGAGCATCCTGTGGCCGAACGGCGTTCTGTGCTGCG\n+GGAGTTCGCGAACGGGATGGACGCGGAGGGGCGGCGGGTGCACCGGGCGTTCCTCGCTTCCGTACGGGTC\n+CTGGGTGAGGGCGTCGACATCGTCGGGGAGCGCGGGGTCGAGGCGATCTGCTTTGCCGACGCACGCGGGT\n+CTCAGGTGGAGATCGTGCAGAACATCGGGCGCGCGTTGCGCCAGAACCCGGATGGGCGGGCGAAGACGGC\n+GCGGATCATCGTGCCGGTCTTCCTGCGGCCGGACGAGGACGGGGAGGGCATGGTGGCGTCGGAGGCGTAC\n+CGGCCGCTCGTCGCCGTACTCCAGGGCCTGCGCTCGCACGACGAGCACCTGGTCGAGAAACTCATGCTGC\n+GGGCGCGCGTACGGGCCGAGAGCGCGAGCGCGCGCAGCGCGGAGGAGGGCGGTGCGGGGCCCTCGCGGCT\n+CCTGTCGGACTCCGGGACGGCGGCTGCGGCCTCCGAGGGCGTCGAGGGCCAGGAGCAGGGCGAGGACGGC\n+GCCGAGGCGGAGTCGGTGCTGCTGCGGTTCTCCTCGCCGCGCGCGGCGTCGACGGTCGCGGCGTTCCTGC\n+GGACGCGGGTGTACCAGCCCGAGTCGCTGGTGTGGCTGGAGGGGTACGAGGCCCTGCGCGCCTGGCGGGC\n+CGAGCAAGGGGTGAGCGGGGTGTGCGCGGTCCCGTACGACGCCGAGGTCGCCGCGGGGGCCTCGCGGCGG\n+TACCCGGTCGGGCGGTGGACCGCCGCGCAACGCCGCGCCCGCCGCGAGGGCACCCTCAGCGCACACCGCG\n+TCGAGCTCCTCGACGCGGAGGGCATGGTGTGGGAGCCGCGCGAGGAGGAATGGGAGCGCACGCTCGCGGG\n+GCTTCGCTCCTACCGGACGGCGTACGGGCACCTCGCCCCCCACAGGCGCGAAACCTGGGGCGAAGACGAG\n+GGTGAGGACGTCGTACGCGTCGGGGACCTGATGGCGAACCTCCGCCGCAAGGACGGACTCGGGAAGGACG\n+CGAAGCGGGCCGCCGCGCGCGCCGCGCAGCTGAGGGCCGTCGATGCGGACTGGGACTGCCCGTGGCCGCT\n+GGACTGGCAGCGCTGCTGCCGGAAACTCGTGCTCCTGGCCGCGGACGAGCCCGGCGGGCGCCTGCCGGAG\n+ATCGCGCCCGGGGTCTGCCTGGACGGGGATGACCTCGGGGTGTGGGTCGCGCGGCAGCAGGAGCCGCGGG\n+TGTGGGCGCGGCTCAGCACCGAGCAGCGGGCGCGGCTCGAAGCGCTCGGGCTGCGGCCCACCGAAGCGGC\n+CCCGGGGCGGGGTGTGGAGGGCACGGGGGCGGCGGGGAGCATGAAGCGGACGGCGACGGCGCGAACGGCT\n+TTTCAGCGGGGTGTGGCGGCGCTCGCGCAGTGGGTCGAGCGGGAAGGCGCGGGGAAACCCGTACCCCGCA\n+AACACGTCGAGACCGTCAGCGTCGACGGCGAGGACGTCGACGTACGCCTCGGCGTATGGATCTCGAACAC\n+CAAGAGCCGGTACGACGGGCTGAGCGAGGACGAACGCGCGCAGCTCACCGCACTCGGAATGCCCTGGGCA\n+GGATGA\n+>lcl|NZ_CM001166.1_gene_2 [locus_tag=STTU_p0002] [location=complement(2995..3171)]\n+GTGCTCGCCGCCGTACGGGACACGATCGCCGAGACCGGCCAGGGACCGTCCGTACGGCAGATCCAGCGCG\n+TCACCGGGCTCGCGCTCGGCACCATCGCCCACCACCTGAAGGCGCTGGAGGAGAGCGGCCCCCTCGTCCG\n+TACGGGCCTGCACTGGCGCACCTGCCGCCTGGGCTGA\n+>lcl|NZ_CM001166.1_gene_3 [locus_tag=STTU_p0003] [location=complement(3195..3407)]\n+GTGACCGATGAACTGCTCCGCCTCGCCCAGGAGAGGCGTGCGACCTACCGCGACCTCACCCTCGGCGGCC\n+CCGCCCGCCCCCCGACACCTCTGCGCCGGGCACTGATCCGGCAGTCCGCCCGCCTGCTCGACGGCCCGCC\n+CACCACGGCCCGCCGGGCTCTGCTGTGCCGCCCGCCCACGCCCGCGTCCCCGCCCTCGCGGGGGACCAGG\n+TGA\n+>lcl|NZ_CM001166.1_gene_4 [locus_tag=STTU_p0004] [location=3510..3866]\n+GTGACCGATTTCCCCGACGATCTCCTCGCGGCTCAGCGCGACCTCACCGCCGTACGCGCCACCCTTTCCG\n+CCCGCCTCGCGGCGCTGCCGCCCTCGGCCGAGCCGATGCCCGCGTGGGAGCGGCCCGACGGCTACTGGGC\n+GGGCGCCCGTACGCACCCGGCCTCCCCGGGGTGGAGCGAGGAGGAGCGCGAGGAGGTCGCCGCGCTCCGC\n+GAGCGGGAGCGGGATCTGGCCGGGGTGATCGTGACGCACGAGCTGTGGGCGAGCGTGCCGGCCGGGGAGC\n+GGATGCGGGCCCGCGACGCACTCAAGCACGCCCACGAGGCCCCGGCCGCAGCCGGGGCGGCGGGGGCGCG\n+GGGCTGA\n+>lcl|NZ_CM001166.1_gene_5 [locus_tag=STTU_p0005] [location=complement(4344..560'..b'ATCTGCTCGCTGCCGCGGCCCCG\n+GCAGAGTACGATCCGGCCTCGCTCACCCCTGAGGAGAAGACCCACCTGTTGTCCGCCGCGGCCTGGCAGG\n+CAGAGGAGGGCGCCTACATGCACCAGCAGAACACCCGTCCCCTCACCCTCGCGCCCGCACTGAACGACTC\n+GCCCGCCGGACTGCTCTCCTGGATCCTCGAGAAGTACCGCGCGTGGACCGACTGCGGCGGCGACCTGTCC\n+ACCCGCTTCGGCGACGACTTCCTCCTCACCCAGGCATCGCTCTACTGGTTCACCGGCACGATCTCCACGT\n+CCTTCCGCCCGTACTACGAGTACGCGCACCAGCTCACCCGGCGCGTGCGGCGGGTCGACGTCCCCACCGC\n+CCTCGCCCTGTTCCCCGCAGACCTCGCCCAACCGCCCCGGAGCTGGGCCGAGCGCACCTACCACCTCACG\n+CGTTACACCCGTATGCCTCGCGGCGGCCACTTCGCCGCGCACGAGGAACCGGCCTTGCTTGCCGACGACA\n+TCACCGCGTTCTTCGGCGACCTCCGTTAG\n+>lcl|NZ_CM001166.1_gene_174 [locus_tag=STTU_p0174] [location=complement(143857..143970)]\n+GTGGATGGACTGCATGGGAGCCCACTTCATAAGAGGCTCGACGAACACTGCGCTGGCCGATTCGGGATCG\n+CACCACCGCTAACCGGGGAAATCACCACGAAGATCAACCACTGA\n+>lcl|NZ_CM001166.1_gene_175 [locus_tag=STTU_p0175] [location=complement(143981..144157)]\n+ATGCCCACCGAGACCCTGCCGCCCGAGGTGCGGAATTTCATCGACGATGCGCGGCGTCACCTGGCTTTCT\n+GCGCCGGGCTGCGCGCGGGCGAGGACCCGGCGTACGCGACCGTGCTCCTGGCCGCCGCCGAGCAGGGAGA\n+AGAAGTCCTCGCCCGGTACGAAGGCCGCGTAGCTTAG\n+>lcl|NZ_CM001166.1_gene_176 [locus_tag=STTU_p0176] [location=complement(144230..147016)]\n+TTGGCTTGTCTGCCTCGTGAGGAGTTTCAAATTTCTGTTTCTCGGGTTCCGTTGCGGAAACATCAGGTGG\n+AGCTTATGTCGGACCTCAGGAAATGGGTTCGGGTGGCTGCCCGGGAAAGCGCCCGTTCGGGGCGGGGGGC\n+GCGGGCGACGGTGGTGTCCGCTACGGGTACGGGGAAGACGATCAGCGCGGCTGTTGCGGCGTTGGAGTTG\n+TTCCCTTCGGGGCGGGTTCTCGTGATGGTGCCGACGCTGGATCTGCTGGTGCAGACGGCGCAGTCGTGGC\n+GGGCGGTGGGGCACACGGCGCCGATGGTCGGGGTGTGCTCGCTGCCCGGGGATCTGCTCCTGGAGGAGTT\n+GCGGGTGCGGACGACGACGCACCCGATCCGGCTCGCGCTGTGGGCCGGGCAGGGGCCTGTGGTCGTGCTG\n+GCGACGTACTCCTCGCTCGTGGGCGGGGACGGGCAGGGCGGGCCCCTGGAGGCCGCCCTGGCGGGCTCGG\n+GGTTGTACGGGCAGCGGATGGACGGCTTCGACCTCGCGGTCGTGGACGAGGCGCACCGTACGGCGGGCAG\n+CGCGGCGAAGCCCTGGGCCGCGATCCACGACAACGCCCGTATCCCGGCGGCGCACCGGCTCTACCTCACC\n+GCCACCCCGCGCGTCCTCGCGCCCGCCCGCCCCGACAGGGACGAGGACCAGGAGGAGGGCGGCGGGGAGG\n+CGCCGGCACTCGTGACGATGGCGAACGACCCGGAAGGCGAGTACGGGGCGTGGATTCACGAACTCGGGTT\n+GTCCGAGGCGATCGAGCGGAAAATTCTTGCGCCTTTCGAGATTGATGTTTTGGAGATTACCGATCCTGAG\n+CCGGAATTGATGGAAGGAATGGACCGGGAGGCGCGGCGTGGGCGGCGGCTCGCCCTGCTCCAGACTGCGT\n+TGCTGGAGCACGCGGCCGAGCACAATCTGCGCACCGTGATGACGTTCCATCAGCGGGTGGAGGAGGCGGC\n+GGCTTTCGCGGAGAAAATGCCGGAGACAGCGGCGGAGCTTTACCGGAATGAGGTGTCGGCGGAGGATCTT\n+GCCCTAGCCGAGGAGCTCCCGGCCTCCGAGGTGGGCGGGGGCTTCTACGAGCTGGAGCCGGGGCGGCATG\n+TGCGGCCGGAGCGGGTGTGGTCGCGGTGGCTGTACGGAGAGCACCCGGTGGCCGAACGCCGTGCGGTGCT\n+GCGGGAGTTCGCGAACGGGATGGACTCGGCAGGGGTGCGGGTGCACCGCGCGTTCCTCGCCTCCGTCCGC\n+GTGCTCGGCGAGGGCGTCGACATCGTCGGGGAGCGCGGGGTCGAGGCGATCTGCTTCGCCGACGCGCGCG\n+GGTCCCAGGTCGAGATCGTGCAGAACATCGGCAGGGCGCTGCGCCCGAACCCGGACGGGCAGACGAAGAC\n+GGCGCGGATCATCGTGCCCGTCTTCTTGGAGGCCGACGAGGACGGGGAGGGGATGGTCGCGAGCGAGGCG\n+TACCGGCCGCTCGTGGCCGTGCTCCAGGGGCTGCGCTCGCACTCCGAGCACCTGGTCGAGAAGCTGATGC\n+TCCGGGCCCGGGTGCGGGCCGAGAGCGCGAGCGCGCGCAGCGCGGAGGAGGCCGGTGCGGGGCCCGCGCG\n+GGTCCTGTCCGACTCCGGGACCTCTTCCCCCGCCTCCCAGGCCTCCGGGGACGTCGAAGGCGAGAACGAG\n+GACGACGTCGAGGCGGGCGCGGACGGCGCTGAGGCGGGCGCGGACGGCGCTGAGGAGTCGGAGTCGGTGT\n+TGTTGCGGTTCTCGACGCCGCGCTCGGCGTCGACCATCGCGGCCTTCCTGCGGACGCGGGTGTACCAGCC\n+GGAGTCGACGGTGTGGCTGGAGGGCTACGAGGCGCTGCGCGCCTGGCGGGCCGAGCAAGGGGTGCGCGGC\n+TTGTGCGCGGTCCCGTACGACGCCGAGGTCGCCGCGGGGGCCTCGCGGCGGTACCCGGTCGGGCGGTGGA\n+CCACCGCGCAACGCCGCGCCCGCCGCGAGGGCACCCTCAGCGCACACCGCATCGACCTGCTCGACGCGGA\n+GGGCATGGTGTGGGAGCCGCGCGAAGAGGAGTGGGAGCGCACGCTCGCCGGGCTTCGCTCCTACCGGGCC\n+GCGTACGGGCACCTCGCCCCCCGCCGGCGCGAAACCTGGGGCGAAGACGAGGGTGAGGACGTCGTACGCG\n+TCGGGGACCTGATGGCGAACCTCCGCCGCAAGGACGGACTCGGGCGGGACGCGGAGCGGGCCGCCGCGCG\n+CGCGGCCCAGCTGAGGGCCGTCGATGCGGACTGGGACTGCCCCTGGCCGCTGGACTGGCAGCGCTGCTGT\n+CGGCAGCTCGCGCTCCTGGCCGCCGACGAACCCGACGGACGCGCGCCCCGGATCGCGCGCGGGGTGCGCA\n+TCGACGGGGACGACCTCGGCGCGTGGGTCGCGCGGCAGCAGGAACCGCGGGTGTGGGCGAAGCTCAGCAC\n+CGAGCAGCGGGCGCGACTCGAAGCGCTCGGGCTCCGGCCTACCGAGACGGCCCCACGGCGGGGTGTGGAG\n+GGCACGGGGGCGGCGGGGAGCGGGAAGCGGACGGCGGCGGCGCGAACGGCCTTCCAGCGCGGCCTCGCGG\n+CGCTCGCGCAGTGGGTCGAGCGGGAAGGCGCGGAGAAACCCGTACCCCGCAAACACACCGAGACCGTGAG\n+CGTGGACGGTGAGGACGTCGACGTACGCCTCGGCGTGTGGGTCTCGAACGTGAAGAGCCGCTTCGACGGG\n+ATGGGCGAGGACGAGCGCGGCCAGCTCACCGCGCTCGGAGTGCCCTGGGCGGTGTAG\n+\n' |
| b |
| diff -r 000000000000 -r 841357e0acbf test-data/streptomyces_Tu6071_plasmid_genes.icm |
| b |
| Binary file test-data/streptomyces_Tu6071_plasmid_genes.icm has changed |
| b |
| diff -r 000000000000 -r 841357e0acbf test-data/streptomyces_Tue6071_plasmid_genomic.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streptomyces_Tue6071_plasmid_genomic.fasta Sat Jul 06 10:09:30 2013 -0400 |
| b |
| b'@@ -0,0 +1,2107 @@\n+>gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+GGCCCCGTACGAGGGGCGCGGCCCCGTACGAGGGGCGCGGCGGCGCGGGTTTCATCATACGCTGCATCAG\n+GTGCTGATGCACTGTGTAGACTTGGGGGAATTCGGTGACACCCTGCCGCGTGTAGCTCTTCCCTGATTCG\n+CCCTCAACGCAGCCCAATTGATGCATATGTTGAGTTGGGGATTTGGCTCGTCTGCCTCGTGAGGAGATTC\n+AAATGTCTGTTTCCCGGGTTCCGCTGCGGAAACATCAGGTAGAGCTTATGTCGGACCTCAGGAAATGGGT\n+CCGGGTAGCCGCCCGGGAAAGCGCCCGCACGGAGCGTGGGGCGCGGGCCACGGTGGTGTCCGCTACGGGT\n+ACGGGAAAGACGATCAGCGCGGCTGCTGCGGCGTTGGAGTTGTTCCCTTCGGGGCGGGTTCTCGTGATGG\n+TGCCGACGCTGGATCTGCTGGTGCAGACGGCGCAGTCGTGGCGGGCGGTGGGGCACACGGCGCCGATGGT\n+CGGGGTGTGCTCGCTGCCCAGGGATCTGCTCCTGGAGGAGCTGCGGGTGCGGACGACGACCCACCCGATC\n+CGGCTCGCGCTTTGGGCCGGATCGGGGCCGGTGGTCGTGCTGGCGACGTACTCCTCGCTCGTGGGCGAGG\n+ACGGGCAGGGCGGACCCTTGGAGGCCGCTCTCGCCGGGGCTGGCTTGTACGGGCAGCGGATGGATGGCTT\n+CGACCTTGCGGTCGTGGACGAGGCGCACCGCACGGCGGGCAGCGCGGAGAAGGCGTGGGCGGCGATCCAC\n+GACAACGCCCGTTTTCCGGCGGCGCACCGGCTGTACCTCACCGCGACCCCGCGCGTCCTGGCCCCGGCCC\n+GTCCCGCCAGGCACGAGGGCGAGGAGGGACGCGGGGAGGCGCCGGCACTCGTGACGATGGCGAATGATCC\n+GGCGGGCGAGTACGGGGCGTGGATTCACGAACTCGGTTTGTCCGAGGCAATCGCGCGAAAAATCGTCGCG\n+CCTTTTGAGATTGACGTTTTGGAGATTACTGATCCTGAGCCGGAATTGATGGAGGGATTGGATCGGGAGG\n+CGCGGCGTGGGCGGCGGCTTGCGTTGCTTCAGACCGGGCTTTTGGAGCACGCGGCCGAGCATAATATTTG\n+CACCATGATGACGCTTCATCAGCAGGTTGAGGAGGCGGCGGCTTTCGCGGAGAAAATGCCGGAGACGGCG\n+GCGGAGCTTTACCGGAATGAGGTGTCGGCGGAGGATTTTGCCCTGGCCGAGGAGCTCCCGGCCTCCGAGG\n+TGGGTGGGGGGTTCTACGAGCTGGAGCCGGGGCGTCATGTGCCGCCGTCGCGGGTGTGGTCGCGGTGGCT\n+GTATGGGGAGCATCCTGTGGCCGAACGGCGTTCTGTGCTGCGGGAGTTCGCGAACGGGATGGACGCGGAG\n+GGGCGGCGGGTGCACCGGGCGTTCCTCGCTTCCGTACGGGTCCTGGGTGAGGGCGTCGACATCGTCGGGG\n+AGCGCGGGGTCGAGGCGATCTGCTTTGCCGACGCACGCGGGTCTCAGGTGGAGATCGTGCAGAACATCGG\n+GCGCGCGTTGCGCCAGAACCCGGATGGGCGGGCGAAGACGGCGCGGATCATCGTGCCGGTCTTCCTGCGG\n+CCGGACGAGGACGGGGAGGGCATGGTGGCGTCGGAGGCGTACCGGCCGCTCGTCGCCGTACTCCAGGGCC\n+TGCGCTCGCACGACGAGCACCTGGTCGAGAAACTCATGCTGCGGGCGCGCGTACGGGCCGAGAGCGCGAG\n+CGCGCGCAGCGCGGAGGAGGGCGGTGCGGGGCCCTCGCGGCTCCTGTCGGACTCCGGGACGGCGGCTGCG\n+GCCTCCGAGGGCGTCGAGGGCCAGGAGCAGGGCGAGGACGGCGCCGAGGCGGAGTCGGTGCTGCTGCGGT\n+TCTCCTCGCCGCGCGCGGCGTCGACGGTCGCGGCGTTCCTGCGGACGCGGGTGTACCAGCCCGAGTCGCT\n+GGTGTGGCTGGAGGGGTACGAGGCCCTGCGCGCCTGGCGGGCCGAGCAAGGGGTGAGCGGGGTGTGCGCG\n+GTCCCGTACGACGCCGAGGTCGCCGCGGGGGCCTCGCGGCGGTACCCGGTCGGGCGGTGGACCGCCGCGC\n+AACGCCGCGCCCGCCGCGAGGGCACCCTCAGCGCACACCGCGTCGAGCTCCTCGACGCGGAGGGCATGGT\n+GTGGGAGCCGCGCGAGGAGGAATGGGAGCGCACGCTCGCGGGGCTTCGCTCCTACCGGACGGCGTACGGG\n+CACCTCGCCCCCCACAGGCGCGAAACCTGGGGCGAAGACGAGGGTGAGGACGTCGTACGCGTCGGGGACC\n+TGATGGCGAACCTCCGCCGCAAGGACGGACTCGGGAAGGACGCGAAGCGGGCCGCCGCGCGCGCCGCGCA\n+GCTGAGGGCCGTCGATGCGGACTGGGACTGCCCGTGGCCGCTGGACTGGCAGCGCTGCTGCCGGAAACTC\n+GTGCTCCTGGCCGCGGACGAGCCCGGCGGGCGCCTGCCGGAGATCGCGCCCGGGGTCTGCCTGGACGGGG\n+ATGACCTCGGGGTGTGGGTCGCGCGGCAGCAGGAGCCGCGGGTGTGGGCGCGGCTCAGCACCGAGCAGCG\n+GGCGCGGCTCGAAGCGCTCGGGCTGCGGCCCACCGAAGCGGCCCCGGGGCGGGGTGTGGAGGGCACGGGG\n+GCGGCGGGGAGCATGAAGCGGACGGCGACGGCGCGAACGGCTTTTCAGCGGGGTGTGGCGGCGCTCGCGC\n+AGTGGGTCGAGCGGGAAGGCGCGGGGAAACCCGTACCCCGCAAACACGTCGAGACCGTCAGCGTCGACGG\n+CGAGGACGTCGACGTACGCCTCGGCGTATGGATCTCGAACACCAAGAGCCGGTACGACGGGCTGAGCGAG\n+GACGAACGCGCGCAGCTCACCGCACTCGGAATGCCCTGGGCAGGATGACGAGCAGGCGGCGGATGCGACC\n+AGCGTAGGAGGGGCGGGGAGCGGCGGCAGCCGGACCGGGCCCGGCTGCCGCCGGTCAGCCCAGGCGGCAG\n+GTGCGCCAGTGCAGGCCCGTACGGACGAGGGGGCCGCTCTCCTCCAGCGCCTTCAGGTGGTGGGCGATGG\n+TGCCGAGCGCGAGCCCGGTGACGCGCTGGATCTGCCGTACGGACGGTCCCTGGCCGGTCTCGGCGATCGT\n+GTCCCGTACGGCGGCGAGCACGCGGTGGCGCCCGTCCCCCGCCGTCACCTGGTCCCCCGCGAGGGCGGGG\n+ACGCGGGCGTGGGCGGGCGGCACAGCAGAGCCCGGCGGGCCGTGGTGGGCGGGCCGTCGAGCAGGCGGGC\n+GGACTGCCGGATCAGTGCCCGGCGCAGAGGTGTCGGGGGGCGGGCGGGGCCGCCGAGGGTGAGGTCGCGG\n+TAGGTCGCACGCCTCTCCTGGGCGAGGCGGAGCAGTTCATCGGTCACCCCCACACTGGATCACGTGTTCG\n+ATTTTCTGGGCAACCGAACCCTCACAAAACGCCACATCACCACCGTGCGCGCGCTCTGGCCGGTCGTACT\n+CTCGCTGGTGTGACCGATTTCCCCGACGATCTCCTCGCGGCTCAGCGCGACCTCACCGCCGTACGCGCCA\n+CCCTTTCCGCCCGCCTCGCGGCGCTGCCGCCCTCGGCCGAGCCGATGCCCGCGTGGGAGCGGCCCGACGG\n+CTACTGGGCGGGCGCCCGTACGCACCCGGCCTCCCCGGGGTGGAGCGAGGAGGAGCGCGAGGAGGTCGCC\n+GCGCTCCGCGAGCGGGAGCGGGATCTGGCCGGGGTGATCGTGACGCACGAGCTGTGGG'..b'GAGTACGCGCACCAGCTCACCCGGCGCGTGCGGCGGGTC\n+GACGTCCCCACCGCCCTCGCCCTGTTCCCCGCAGACCTCGCCCAACCGCCCCGGAGCTGGGCCGAGCGCA\n+CCTACCACCTCACGCGTTACACCCGTATGCCTCGCGGCGGCCACTTCGCCGCGCACGAGGAACCGGCCTT\n+GCTTGCCGACGACATCACCGCGTTCTTCGGCGACCTCCGTTAGACCGCAGGCCCATGCGTGACTCTGTCG\n+GTGACGTCGGGAATGTCCGACGGGCGGCGGACCCGATGACCCTGGGGCCATTCCAGCCCCTGTGGGGTTC\n+GGGGAAGAGGCCCCCGAGATGTTCGGGTTTCCCCACCACTGATGCTGACTCATGTTTGCCCTGGCCAGTC\n+GACGTTTCAGTGGTTGATCTTCGTGGTGATTTCCCCGGTTAGCGGTGGTGCGATCCCGAATCGGCCAGCG\n+CAGTGTTCGTCGAGCCTCTTATGAAGTGGGCTCCCATGCAGTCCATCCACGTGGCAATCACTAAGCTACG\n+CGGCCTTCGTACCGGGCGAGGACTTCTTCTCCCTGCTCGGCGGCGGCCAGGAGCACGGTCGCGTACGCCG\n+GGTCCTCGCCCGCGCGCAGCCCGGCGCAGAAAGCCAGGTGACGCCGCGCATCGTCGATGAAATTCCGCAC\n+CTCGGGCGGCAGGGTCTCGGTGGGCATCGGCGTACGCGCCACCCCAGGCGGAGACGTCCCGCCGGGGGCG\n+GCGCGTACGGCGTGGACATCGACCACCACCTACACCGCCCAGGGCACTCCGAGCGCGGTGAGCTGGCCGC\n+GCTCGTCCTCGCCCATCCCGTCGAAGCGGCTCTTCACGTTCGAGACCCACACGCCGAGGCGTACGTCGAC\n+GTCCTCACCGTCCACGCTCACGGTCTCGGTGTGTTTGCGGGGTACGGGTTTCTCCGCGCCTTCCCGCTCG\n+ACCCACTGCGCGAGCGCCGCGAGGCCGCGCTGGAAGGCCGTTCGCGCCGCCGCCGTCCGCTTCCCGCTCC\n+CCGCCGCCCCCGTGCCCTCCACACCCCGCCGTGGGGCCGTCTCGGTAGGCCGGAGCCCGAGCGCTTCGAG\n+TCGCGCCCGCTGCTCGGTGCTGAGCTTCGCCCACACCCGCGGTTCCTGCTGCCGCGCGACCCACGCGCCG\n+AGGTCGTCCCCGTCGATGCGCACCCCGCGCGCGATCCGGGGCGCGCGTCCGTCGGGTTCGTCGGCGGCCA\n+GGAGCGCGAGCTGCCGACAGCAGCGCTGCCAGTCCAGCGGCCAGGGGCAGTCCCAGTCCGCATCGACGGC\n+CCTCAGCTGGGCCGCGCGCGCGGCGGCCCGCTCCGCGTCCCGCCCGAGTCCGTCCTTGCGGCGGAGGTTC\n+GCCATCAGGTCCCCGACGCGTACGACGTCCTCACCCTCGTCTTCGCCCCAGGTTTCGCGCCGGCGGGGGG\n+CGAGGTGCCCGTACGCGGCCCGGTAGGAGCGAAGCCCGGCGAGCGTGCGCTCCCACTCCTCTTCGCGCGG\n+CTCCCACACCATGCCCTCCGCGTCGAGCAGGTCGATGCGGTGTGCGCTGAGGGTGCCCTCGCGGCGGGCG\n+CGGCGTTGCGCGGTGGTCCACCGCCCGACCGGGTACCGCCGCGAGGCCCCCGCGGCGACCTCGGCGTCGT\n+ACGGGACCGCGCACAAGCCGCGCACCCCTTGCTCGGCCCGCCAGGCGCGCAGCGCCTCGTAGCCCTCCAG\n+CCACACCGTCGACTCCGGCTGGTACACCCGCGTCCGCAGGAAGGCCGCGATGGTCGACGCCGAGCGCGGC\n+GTCGAGAACCGCAACAACACCGACTCCGACTCCTCAGCGCCGTCCGCGCCCGCCTCAGCGCCGTCCGCGC\n+CCGCCTCGACGTCGTCCTCGTTCTCGCCTTCGACGTCCCCGGAGGCCTGGGAGGCGGGGGAAGAGGTCCC\n+GGAGTCGGACAGGACCCGCGCGGGCCCCGCACCGGCCTCCTCCGCGCTGCGCGCGCTCGCGCTCTCGGCC\n+CGCACCCGGGCCCGGAGCATCAGCTTCTCGACCAGGTGCTCGGAGTGCGAGCGCAGCCCCTGGAGCACGG\n+CCACGAGCGGCCGGTACGCCTCGCTCGCGACCATCCCCTCCCCGTCCTCGTCGGCCTCCAAGAAGACGGG\n+CACGATGATCCGCGCCGTCTTCGTCTGCCCGTCCGGGTTCGGGCGCAGCGCCCTGCCGATGTTCTGCACG\n+ATCTCGACCTGGGACCCGCGCGCGTCGGCGAAGCAGATCGCCTCGACCCCGCGCTCCCCGACGATGTCGA\n+CGCCCTCGCCGAGCACGCGGACGGAGGCGAGGAACGCGCGGTGCACCCGCACCCCTGCCGAGTCCATCCC\n+GTTCGCGAACTCCCGCAGCACCGCACGGCGTTCGGCCACCGGGTGCTCTCCGTACAGCCACCGCGACCAC\n+ACCCGCTCCGGCCGCACATGCCGCCCCGGCTCCAGCTCGTAGAAGCCCCCGCCCACCTCGGAGGCCGGGA\n+GCTCCTCGGCTAGGGCAAGATCCTCCGCCGACACCTCATTCCGGTAAAGCTCCGCCGCTGTCTCCGGCAT\n+TTTCTCCGCGAAAGCCGCCGCCTCCTCCACCCGCTGATGGAACGTCATCACGGTGCGCAGATTGTGCTCG\n+GCCGCGTGCTCCAGCAACGCAGTCTGGAGCAGGGCGAGCCGCCGCCCACGCCGCGCCTCCCGGTCCATTC\n+CTTCCATCAATTCCGGCTCAGGATCGGTAATCTCCAAAACATCAATCTCGAAAGGCGCAAGAATTTTCCG\n+CTCGATCGCCTCGGACAACCCGAGTTCGTGAATCCACGCCCCGTACTCGCCTTCCGGGTCGTTCGCCATC\n+GTCACGAGTGCCGGCGCCTCCCCGCCGCCCTCCTCCTGGTCCTCGTCCCTGTCGGGGCGGGCGGGCGCGA\n+GGACGCGCGGGGTGGCGGTGAGGTAGAGCCGGTGCGCCGCCGGGATACGGGCGTTGTCGTGGATCGCGGC\n+CCAGGGCTTCGCCGCGCTGCCCGCCGTACGGTGCGCCTCGTCCACGACCGCGAGGTCGAAGCCGTCCATC\n+CGCTGCCCGTACAACCCCGAGCCCGCCAGGGCGGCCTCCAGGGGCCCGCCCTGCCCGTCCCCGCCCACGA\n+GCGAGGAGTACGTCGCCAGCACGACCACAGGCCCCTGCCCGGCCCACAGCGCGAGCCGGATCGGGTGCGT\n+CGTCGTCCGCACCCGCAACTCCTCCAGGAGCAGATCCCCGGGCAGCGAGCACACCCCGACCATCGGCGCC\n+GTGTGCCCCACCGCCCGCCACGACTGCGCCGTCTGCACCAGCAGATCCAGCGTCGGCACCATCACGAGAA\n+CCCGCCCCGAAGGGAACAACTCCAACGCCGCAACAGCCGCGCTGATCGTCTTCCCCGTACCCGTAGCGGA\n+CACCACCGTCGCCCGCGCCCCCCGCCCCGAACGGGCGCTTTCCCGGGCAGCCACCCGAACCCATTTCCTG\n+AGGTCCGACATAAGCTCCACCTGATGTTTCCGCAACGGAACCCGAGAAACAGAAATTTGAAACTCCTCAC\n+GAGGCAGACAAGCCAAATCCCCAACTCAACATATGCATCAGTCACCCGCGTTGAGGGCAAGTCAGGGAAG\n+AGCTACACGCGACAGGGTGTTACCTAATTCCCCCAAGTCTACACAGTGCATCAGCACCTGATGCGGCGTA\n+TGATGAAACCCGCGCTCGTCGTACGGGGCCGCGCTCGTCGTACGGGGCCGCGCTCGTCGTACGGGGCCGC\n+GCTCGTCGTACGGGGCCGCGCTCGTCGTACGGGGCCGCGCTCGTCGTACGGGGCCGCGCTCGTCGTACGG\n+GGCCGCGCTCGTCGTACGGGGCCGCGCTCGTCGTACGGGGCCGCGCTCGTCGTACGGGGCCACGCTC\n+\n' |
| b |
| diff -r 000000000000 -r 841357e0acbf tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Jul 06 10:09:30 2013 -0400 |
| b |
| @@ -0,0 +1,30 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="biopython" version="1.61"> + <repository name="package_biopython_1_61" owner="biopython" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <set_environment version="1.0"> + <environment_variable action="set_to" name="GLIMMER_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> + <package name="glimmer" version="3.02b"> + <install version="1.0"> + <actions> + <action type="download_file">http://www.cbcb.umd.edu/software/glimmer/glimmer302b.tar.gz</action> + <action type="shell_command">tar xfvz glimmer302b.tar.gz</action> + <action type="shell_command">cd ./glimmer3.02/src && make</action> + + <action type="move_directory_files"> + <source_directory>./glimmer3.02/bin</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme>To compile glimmer you need a C compiler (usually gcc). +Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. +Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. +http://www.cbcb.umd.edu/software/glimmer/</readme> + </package> +</tool_dependency> |