# HG changeset patch
# User bjoern-gruening
# Date 1326292485 18000
# Node ID e11e303c39a4c3d74f716790526b50019d6fed0f
Uploaded
diff -r 000000000000 -r e11e303c39a4 glimmer3/gbk2orf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer3/gbk2orf.xml Wed Jan 11 09:34:45 2012 -0500
@@ -0,0 +1,208 @@
+
+ from a GenBank file
+
+ gbk_to_orf.py -g $inputfile -a $aminoAcidOutput -n $orfOutput
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+Read a GenBank file and export fasta formatted amino acid and CDS files.
+
+
+-----
+
+**Example**
+ * input::
+
+ Genebankfile
+
+ LOCUS BA000030 9025608 bp DNA linear BCT 21-DEC-2007
+ DEFINITION Streptomyces avermitilis MA-4680 DNA, complete genome.
+ ACCESSION BA000030 AP005021-AP005050
+ VERSION BA000030.3 GI:148878541
+ DBLINK Project: 189
+ KEYWORDS .
+ SOURCE Streptomyces avermitilis MA-4680
+ ORGANISM Streptomyces avermitilis MA-4680
+ Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales;
+ Streptomycineae; Streptomycetaceae; Streptomyces.
+ REFERENCE 1
+ AUTHORS Omura,S., Ikeda,H., Ishikawa,J., Hanamoto,A., Takahashi,C.,
+ Shinose,M., Takahashi,Y., Horikawa,H., Nakazawa,H., Osonoe,T.,
+ Kikuchi,H., Shiba,T., Sakaki,Y. and Hattori,M.
+ TITLE Genome sequence of an industrial microorganism Streptomyces
+ avermitilis: deducing the ability of producing secondary
+ metabolites
+ JOURNAL Proc. Natl. Acad. Sci. U.S.A. 98 (21), 12215-12220 (2001)
+ PUBMED 11572948
+ REFERENCE 2
+ AUTHORS Ikeda,H., Ishikawa,J., Hanamoto,A., Shinose,M., Kikuchi,H.,
+ Shiba,T., Sakaki,Y., Hattori,M. and Omura,S.
+ TITLE Complete genome sequence and comparative analysis of the industrial
+ microorganism Streptomyces avermitilis
+ JOURNAL Nat. Biotechnol. 21 (5), 526-531 (2003)
+ PUBMED 12692562
+ REFERENCE 3 (bases 1 to 9025608)
+ AUTHORS Omura,S., Ikeda,H., Ishikawa,J., Hanamoto,A., Takahashi,C.,
+ Shinose,M., Takahashi,Y., Horikawa,H., Nakazawa,H., Osonoe,T.,
+ Kushida,N., Shiba,T., Sakaki,Y. and Hattori,M.
+ TITLE Direct Submission
+ JOURNAL Submitted (29-MAR-2002) Contact:S Omura Kitasato University,
+ Kitasato Institute for Life Sciences; 1-15-1 Kitasato, Sagamihara,
+ Kanagawa 228-8555, Japan URL
+ :http://avermitilis.ls.kitasato-u.ac.jp/
+ COMMENT On Jun 15, 2007 this sequence version replaced gi:57546753.
+ This work was done in collaboration with Haruo Ikeda(*1), Jun
+ Ishikawa(*2), Akiharu Hanamoto(*3), Chigusa Takahashi(*3), Mayumi
+ Shinose(*3), Hiroshi Horikawa(*4), Hidekazu Nakazawa(*4), Tomomi
+ Osonoe(*4), Norihiro Kushida(*4), Hisashi Kikuchi(*4), Tadayoshi
+ Shiba(*5), Yoshiyuki Sakaki(*6,*7), Masahira Hattori(*1,*7)
+ and Satoshi Omura(*1,*3).
+ Final finishing process and all annotation were done by H. Ikeda
+ and J. Ishikawa.
+ *1 Kitasato Institute for Life Sciences, Kitasato University *2
+ National Institute of Infectious Diseases
+ *3 The Kitasato Institute
+ *4 National Institute of Technology and Evaluation *5 School of
+ Science, Kitasato University
+ *6 Institute of Medical Science, University of Tokyo *7 RIKEN,
+ Genomic Sciences Center
+ All the annotated genes identified are available from following
+ urls.
+ http://avermitilis.ls.kitasato-u.ac.jp.
+ FEATURES Location/Qualifiers
+ source 1..9025608
+ /organism="Streptomyces avermitilis MA-4680"
+ /mol_type="genomic DNA"
+ /strain="MA-4680"
+ /db_xref="taxon:227882"
+ /note="This strain is also named as strain: ATCC 31267,
+ NCIMB 12804 or NRRL 8165."
+ gene complement(1380..1811)
+ /locus_tag="SAV_1"
+ CDS complement(1380..1811)
+ /locus_tag="SAV_1"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="BAC67710.1"
+ /db_xref="GI:29603637"
+ /translation="MTAEWYVLVEEDTRETKRADGVELRLHRWKLAATQHIAGDQEQA
+ AAAAEDAALNYMPGVLARHARPGDEPARHAFLTQDGAWLVLLRQRHRECHIRVTTARL
+ MHTQEEKEAPPKSFKEKLRSALDGPQPPEPAGRPWKPGSET"
+
+
+* output::
+
+ - aminoAcidOutput
+ >SAV_1
+ MTAEWYVLVEEDTRETKRADGVELRLHRWKLAATQHIAGDQEQAAAAAEDAALNYMPGVL
+ ARHARPGDEPARHAFLTQDGAWLVLLRQRHRECHIRVTTARLMHTQEEKEAPPKSFKEKL
+ RSALDGPQPPEPAGRPWKPGSET
+ >SAV_2
+ VPPQGARGTIVSATGSGKTSMAAASTLNCFPEGRILVTVPTLDLLAQTAQAWRAVGHHSP
+ MIAVCSLENDPVLNERT
+ >SAV_3
+ MDWNFPDDDIFFCGGCGDDDTPDPRVPRQDKALCVRCDRVERQVRRYRITVPRRNAIMRF
+ QRDVCALCQEGPPTDHCPDAVSFWHIDHDHRCCPPGGSCGRCVRGLLCLPCNATRLPAYE
+ RLPNVLRDSPRFNTYLNSPPARHPEARPTARDHAGPRDASSYLIDAFFTAADHPEGNALS
+ S
+ >SAV_4
+ VALTPGGTRVTQWQDRQAIGDMHERRVAAALRARGWTVQPCGQGTYPPAVREALRRTRSA
+ LRHFPDLIAARGADLITIDAKDRMPSTDTDRYAVSADTVTAGLFFTAAHAPTPLYYVFGD
+ LKVLTPAEVVHYTAHALRHRSGAFHLVRTEQAHCFDDVFGSAGAAAAA
+ >SAV_5
+ MMLLMAAYVDPRFRPTLWPGTPVPTPELMPLRGARADGEWIVWTPQVRSRSHTVPVPEDF
+ YLREFMEVDPEDLDAVAALMGAYGHLGGSINTGSWDVDVYERLKELTEREHPRAPFALHG
+ ELATLFMREAQAAITTWLALRREGGLDALIEPEVSEEELAQWQASNADLEEAWPRDLDHL
+ RELSLEIRISNLVSELNAALKPFSIGIGGLGDRYPTILAVAFLQLYNHLAEDATIRECAN
+ ETCRRHFVRQRGRAAYGQNRTSGIKYCTRECARAQAQREHRRRRKQQTTTLQQPPAPGPQ
+ SHDTSEPTAEGR
+ >SAV_6
+ MISLREHQVEANARIRAWAGFPTRSPVPAQGLRGTVVSATGSGKTITAAWAARECFRGGR
+ ILVMVPTLDLLVQTAQAWRRVGHNGPMVAACSLEKDEVLEQLGVRTTTNPIQLALWAGHG
+ PVVVFATYASLVDREDPEDVTGRAKVRGPLEAALAGGQRLYGQTMDGFDLAVVDEAHSTT
+ GDLGRPWAAIHDNSRIPADFRLYLTATPRILASPRPQKGADGRELEIATMASDPDGPYGE
+ WLFELGLSEAVERGILAGFEIDVLEIRDPSPALGESEEAQRGRRLALLQTALLEHAAARN
+ LRTVMTFHQRVEEAAAFAQTMPQTAARLYEAEVSAEALVDAGALPESSIGAEFYELEAGR
+ HVPPDRVWAAWLCGDHLVAERREVLRQFADGLDAGNKRVHRAFLASVRVLGEGVDIVGER
+ GVEAICFADTRGSQVEIVQNIGRALRPNPDGTNKTARIIVPVFLQPGENPTDMVASASFA
+ PLVTVLQGLRSHSERLVEQLASRALTSGQRHVHVKRDEDGRIIGTTTEGEGGQHESEGAV
+ ESALLHFSTPRDATTIAAFLRTRVYRPESLVWLEGYQALLRWRKKNHITGLYAVPYDTET
+ EAGVTKAFPLGRWVHQQRRTYRAGELDPHRTTLLDEAGMVWEPGDEAWENKLAALRSFHR
+ AHGHLAPRRDAVWGDADSELVPVGEHMANLRRKDGLGKNPQRAATRATQLAAIDPDWNCP
+ WPLDWQRHYRVLADLATDEPHSRLPDIQPGVQFEGDDLGKWLQRQRRSWAELSEEQQQRL
+ TALGVTPAEPPTPTPSAKGGGKAAAFQRGLAALAQWIQREGAHKVVPRGHVEAVVIDGQE
+ HQHKLGVWISNTKTRRDKLTHDQRTALAALGVEWA
+ ....
+
+ - orfs
+
+ >SAV_1
+ ATGACCGCCGAGTGGTACGTCCTCGTCGAAGAGGACACACGAGAGACCAAGCGCGCCGAC
+ GGCGTTGAACTCAGATTGCACCGCTGGAAACTGGCGGCCACTCAGCACATCGCAGGAGAT
+ CAGGAACAGGCCGCCGCCGCGGCCGAGGATGCGGCCCTGAACTACATGCCGGGAGTGCTC
+ GCTCGGCATGCCCGACCGGGAGACGAACCGGCCCGGCATGCTTTCCTCACCCAGGACGGG
+ GCCTGGCTGGTGCTCCTCAGGCAGCGGCACCGCGAGTGTCACATACGGGTGACCACTGCC
+ CGGCTCATGCATACACAGGAAGAGAAGGAGGCCCCGCCGAAAAGCTTCAAGGAGAAACTC
+ CGCAGCGCCCTGGATGGTCCTCAGCCGCCCGAACCGGCTGGTAGGCCATGGAAGCCGGGC
+ AGCGAAACCTGA
+ >SAV_2
+ GTGCCCCCTCAGGGAGCCCGTGGCACGATCGTGTCAGCTACCGGGTCCGGCAAAACGAGC
+ ATGGCCGCCGCGAGCACGCTGAACTGCTTCCCCGAAGGCCGGATCCTCGTGACCGTGCCG
+ ACCCTGGACCTGCTCGCACAGACCGCCCAGGCGTGGCGGGCAGTCGGCCACCACTCCCCC
+ ATGATCGCGGTGTGCTCGCTGGAGAACGACCCAGTGCTGAACGAGCGGACCTGA
+ >SAV_3
+ ATGGACTGGAACTTCCCCGACGACGACATCTTCTTCTGCGGCGGGTGCGGCGACGACGAC
+ ACCCCCGACCCGCGGGTCCCGCGTCAGGACAAGGCCCTGTGCGTCCGCTGCGACAGAGTC
+ GAACGGCAGGTCCGCCGATACCGGATCACCGTGCCGCGGAGGAACGCGATCATGCGCTTC
+ CAGCGCGACGTCTGCGCCCTGTGCCAGGAAGGCCCGCCGACCGACCACTGCCCCGATGCC
+ GTCAGCTTCTGGCACATCGACCACGACCACCGCTGCTGCCCTCCCGGCGGCTCATGCGGG
+ CGGTGCGTCCGCGGCCTCCTGTGCCTGCCCTGCAACGCCACCCGCCTGCCCGCCTACGAA
+ CGCCTCCCCAACGTCCTCCGCGACAGCCCTCGCTTCAACACCTACCTCAACAGCCCACCC
+ GCCCGGCACCCCGAAGCCCGCCCCACCGCCAGGGACCATGCAGGCCCCCGCGACGCATCC
+ AGCTACCTCATCGACGCCTTTTTCACCGCCGCGGACCATCCCGAGGGGAACGCCCTCAGC
+ TCCTGA
+ >SAV_4
+ GTGGCACTTACCCCAGGGGGAACCCGAGTGACGCAGTGGCAGGACCGCCAGGCGATAGGC
+ GACATGCACGAACGTCGGGTGGCGGCCGCGCTGCGCGCCCGCGGCTGGACCGTCCAGCCC
+ TGCGGACAGGGCACCTACCCGCCCGCCGTACGGGAAGCCCTGCGCCGGACCCGCTCCGCC
+ CTGCGGCACTTCCCCGACCTCATCGCCGCCCGCGGCGCCGACCTGATCACCATCGACGCC
+ AAGGACCGCATGCCCAGCACCGACACCGACCGCTACGCCGTCAGCGCCGACACCGTGACC
+ GCCGGCCTCTTTTTCACCGCGGCCCACGCTCCGACTCCGCTGTACTACGTCTTCGGCGAC
+ CTGAAGGTCCTCACGCCGGCGGAGGTGGTCCACTACACCGCTCACGCCTTGCGCCACCGC
+ AGCGGTGCCTTCCACCTCGTACGCACGGAGCAAGCACACTGCTTCGACGACGTCTTCGGA
+ TCGGCTGGCGCAGCAGCTGCGGCATGA
+ >SAV_5
+ ATGATGCTCCTCATGGCGGCATACGTTGACCCACGCTTTCGTCCTACGCTATGGCCTGGA
+ ACGCCCGTGCCGACACCGGAGTTGATGCCTCTTCGCGGAGCGCGGGCCGACGGTGAATGG
+ ATCGTCTGGACCCCGCAGGTCCGCTCCCGCTCGCACACGGTCCCCGTGCCGGAGGACTTC
+ TACCTGCGCGAGTTCATGGAGGTCGACCCTGAGGACCTCGACGCCGTGGCCGCCCTGATG
+ GGCGCCTACGGACACCTCGGCGGGAGCATCAACACCGGAAGCTGGGACGTCGACGTCTAC
+ GAGCGCCTCAAGGAGCTCACGGAGCGCGAACACCCCCGCGCGCCGTTCGCCCTGCACGGC
+ GAACTGGCCACGCTGTTCATGAGGGAGGCGCAGGCGGCCATCACCACCTGGCTGGCCCTG
+ CGCCGCGAGGGCGGGCTCGACGCGCTCATCGAGCCCGAGGTGTCCGAGGAAGAACTGGCG
+ CAGTGGCAAGCGAGCAACGCTGATCTTGAGGAAGCGTGGCCGCGGGACCTGGACCACCTG
+ CGCGAACTCTCCCTGGAGATCAGGATCAGCAACCTCGTGAGCGAACTGAACGCCGCGCTG
+ AAGCCGTTCAGCATCGGCATCGGCGGCCTGGGCGACCGCTACCCCACCATCCTCGCTGTG
+ GCGTTCCTCCAGCTCTACAACCACCTCGCCGAGGACGCCACGATCCGCGAGTGCGCGAAC
+ GAGACCTGCCGCCGCCACTTCGTACGCCAGCGCGGCCGCGCCGCATACGGGCAGAACCGC
+ ACCAGCGGCATCAAGTACTGCACCCGCGAATGCGCCCGCGCCCAGGCCCAGCGCGAACAC
+ CGCCGGCGCCGCAAACAGCAGACCACGACCCTCCAGCAGCCGCCGGCGCCTGGTCCTCAG
+ TCTCACGACACCTCAGAGCCGACTGCCGAAGGGCGCTGA
+ .......
+
+
+
diff -r 000000000000 -r e11e303c39a4 glimmer3/gbk_to_orf.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer3/gbk_to_orf.py Wed Jan 11 09:34:45 2012 -0500
@@ -0,0 +1,61 @@
+#!/usr/bin/env python
+
+###################################################################
+##
+## gbk2orf.py by Errol Strain (estrain@gmail.com)
+##
+## Read a GenBank file and export fasta formatted amino acid and
+## CDS files
+##
+###################################################################
+
+import sys
+from optparse import OptionParser
+from Bio import SeqIO
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+
+## Command line usage
+usage = "usage: %prog -g input.gbk -a aa.fasta -n nuc.fasta"
+p = OptionParser(usage)
+p.add_option("-t","--translate", dest="transtabl",type="int",default=11,
+ help="Translation table used to translate coding regions (default=11)")
+p.add_option("-g","--genbank", dest="gb_file",help="GenBank input file")
+p.add_option("-a","--amino_acid", dest="aa_file",help="Fasta amino acid output")
+p.add_option("-n","--nucleotide", dest="orf_file",help="Fasta nucleotide output")
+(opts, args) = p.parse_args()
+## Do I need this next line?
+if not opts and not args : p.error("Use --help to see usage")
+if len(sys.argv)==1 : p.error("Use --help to see usage")
+
+## Lists to hold SeqRecords
+aalist = []
+nuclist = []
+
+## If the CDS does not have a locus tag the name will be assigned using the
+## order in which it was found
+feat_count=0
+
+## Iterate through genbank records in input file
+for gb_record in SeqIO.parse(open(opts.gb_file,"r"), "genbank") :
+ for (index, feature) in enumerate(gb_record.features) :
+ if feature.type=="CDS" :
+ feat_count = feat_count + 1
+ gene = feature.extract(gb_record.seq)
+ if "locus_tag" in feature.qualifiers :
+ value = feature.qualifiers["locus_tag"][0]
+ else :
+ value = "Index_" + str(feat_count)
+ nuclist.append(SeqRecord(Seq(str(gene)),id=value,name=value))
+ pro=Seq(str(gene.translate(table=opts.transtabl,to_stop=True)))
+ aalist.append(SeqRecord(pro,id=value,name=value))
+
+## Write out lists in fasta format
+aa_handle = open(opts.aa_file,"w")
+SeqIO.write(aalist,aa_handle,"fasta")
+aa_handle.close()
+orf_handle = open(opts.orf_file,"w")
+SeqIO.write(nuclist,orf_handle,"fasta")
+orf_handle.close()
+
diff -r 000000000000 -r e11e303c39a4 glimmer3/glimmer2gff.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer3/glimmer2gff.py Wed Jan 11 09:34:45 2012 -0500
@@ -0,0 +1,36 @@
+#!/usr/bin/env python
+
+"""
+Input: Glimmer3 prediction
+Output: GFF3 file
+Return a GFF3 file with the genes predicted by Glimmer3
+Bjoern Gruening
+
+Note: Its not a full-fledged GFF3 file, its a really simple one.
+
+"""
+
+import sys, re
+
+def __main__():
+ input_file = open(sys.argv[1], 'r')
+
+ print '##gff-version 3\n'
+ for line in input_file:
+ line = line.strip()
+ if line[0] == '>':
+ header = line[1:]
+ else:
+ (id, start, end, frame, score) = re.split('\s+', line)
+ if int(end) > int(start):
+ strand = '+'
+ else:
+ strand = '-'
+ (start, end) = (end, start)
+
+ rest = 'frame=%s;score=%s' % (frame, score)
+ print '\t'.join([header, 'glimmer_prediction', 'predicted_gene', start, end, '.', strand, '.', rest])
+
+
+if __name__ == "__main__" :
+ __main__()
diff -r 000000000000 -r e11e303c39a4 glimmer3/glimmer2gff.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer3/glimmer2gff.xml Wed Jan 11 09:34:45 2012 -0500
@@ -0,0 +1,60 @@
+
+ Converts Glimmer Files to GFF Files
+ glimmer2gff.py $input > $output
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+Converts a Glimmer3 output File to an GFF Annotation File::
+
+**Example**
+
+Input::
+ >contig00097 sbe.0.234
+ orf00003 2869 497 -2 5.60
+ orf00005 3894 2875 -1 7.05
+ orf00007 4242 4826 +3 8.04
+ orf00010 4846 5403 +1 8.57
+ orf00012 6858 5413 -1 10.87
+ orf00013 6857 7594 +2 3.61
+ orf00014 7751 9232 +2 11.34
+ orf00015 9374 10357 +2 10.66
+ orf00017 10603 11196 +1 13.39
+ orf00021 11303 11911 +2 8.81
+ orf00025 14791 12050 -2 13.51
+ orf00026 15216 16199 +3 6.37
+ orf00028 16333 16935 +1 8.86
+
+
+Output:
+ contig00097 sbe.0.234 glimmer gene 497 2869 . - . -2 5.60
+ contig00097 sbe.0.234 glimmer gene 2875 3894 . - . -1 7.05
+ contig00097 sbe.0.234 glimmer gene 4242 4826 . + . +3 8.04
+ contig00097 sbe.0.234 glimmer gene 4846 5403 . + . +1 8.57
+ contig00097 sbe.0.234 glimmer gene 5413 6858 . - . -1 10.87
+ contig00097 sbe.0.234 glimmer gene 6857 7594 . + . +2 3.61
+ contig00097 sbe.0.234 glimmer gene 7751 9232 . + . +2 11.34
+ contig00097 sbe.0.234 glimmer gene 9374 10357 . + . +2 10.66
+ contig00097 sbe.0.234 glimmer gene 10603 11196 . + . +1 13.39
+ contig00097 sbe.0.234 glimmer gene 11303 11911 . + . +2 8.81
+ contig00097 sbe.0.234 glimmer gene 12050 14791 . - . -2 13.51
+ contig00097 sbe.0.234 glimmer gene 15216 16199 . + . +3 6.37
+ contig00097 sbe.0.234 glimmer gene 16333 16935 . + . +1 8.86
+
+
+-----
+
+
+
+
diff -r 000000000000 -r e11e303c39a4 glimmer3/glimmer3-build-icm-wrapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer3/glimmer3-build-icm-wrapper.xml Wed Jan 11 09:34:45 2012 -0500
@@ -0,0 +1,74 @@
+
+ glimmer3-build-icm
+ tigr-glimmer build-icm -r $output < $inputfile
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+ This program constructs an interpolated context model (ICM) from an input set of sequences.
+
+-----
+
+**Glimmer Overview**
+
+::
+
+************** ************** ************** **************
+* * * * * * * *
+* long-orfs * ===> * Extract * ===> * build-icm * ===> * glimmer3 *
+* * * * * * * *
+************** ************** ************** **************
+
+-----
+
+**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).
+
+
+
+
+
diff -r 000000000000 -r e11e303c39a4 glimmer3/glimmer3-extract-wrapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer3/glimmer3-extract-wrapper.xml Wed Jan 11 09:34:45 2012 -0500
@@ -0,0 +1,119 @@
+
diff -r 000000000000 -r e11e303c39a4 glimmer3/glimmer3-long-orfs-wrapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer3/glimmer3-long-orfs-wrapper.xml Wed Jan 11 09:34:45 2012 -0500
@@ -0,0 +1,117 @@
+
+ identify long, non-overlapping orfs(open reading frames)
+ tigr-glimmer long-orfs -n -t $cutoff $inputfile $output 2> /dev/null
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+ This program identifies long, non-overlapping open reading frames (orfs) in a DNA sequence file.
+ These orfs are very likely to contain genes, and can be used as a set of training sequences
+ More specifically, among all orfs longer than a minimum length , those that do not overlap any others are output. The start codon used for
+ each orf is the first possible one. The program, by default, automatically determines the
+ value that maximizes the number of orfs that are output. With the -t option, the initial
+ set of candidate orfs also can be filtered using entropy distance, which generally produces
+ a larger, more accurate training set, particularly for high-GC-content genomes.
+
+
+
+-----
+
+**Glimmer Overview**
+
+::
+
+************** ************** ************** **************
+* * * * * * * *
+* long-orfs * ===> * Extract * ===> * build-icm * ===> * glimmer3 *
+* * * * * * * *
+************** ************** ************** **************
+
+-----
+
+**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
+ .....
+
+ - Cutoff 1.5
+
+* output::
+
+ Sequence file = /home/mohammed/galaxy-central/database/files/000/dataset_34.dat
+ Excluded regions file = none
+ Circular genome = true
+ Initial minimum gene length = 90 bp
+ Determine optimal min gene length to maximize number of genes
+ Maximum overlap bases = 30
+ Start codons = atg,gtg,ttg
+ Stop codons = taa,tag,tga
+ Sequence length = 40222
+ Final minimum gene length = 97
+
+ Putative Genes:
+ 00001 40137 52 +2 0.892
+ 00002 1319 1095 -3 0.654
+ 00003 1555 1391 -2 0.793
+ 00004 1953 2066 +3 1.078
+ 00005 2045 2146 +2 0.919
+ 00006 4463 4759 +2 0.985
+ 00007 6785 6582 -3 1.033
+ 00008 6862 7020 +1 0.915
+ 00009 7300 7488 +1 0.900
+ 00010 7463 7570 +2 0.912
+ 00011 8399 8527 +2 1.044
+ 00012 10652 10545 -3 0.895
+ 00013 12170 12066 -3 1.108
+ 00014 13891 13748 -2 0.998
+ 00015 14157 14044 -1 1.026
+ 00016 15285 15410 +3 0.928
+ 00017 15829 15704 -2 0.949
+
+ ....
+
+-------
+
+**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).
+
+
+
+
+
diff -r 000000000000 -r e11e303c39a4 glimmer3/glimmer3-main-wrapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer3/glimmer3-main-wrapper.xml Wed Jan 11 09:34:45 2012 -0500
@@ -0,0 +1,146 @@
+
+ Predict ORFs in prokaryotic genomes (knowlegde-based)
+
+ tigr-glimmer glimmer3 -o$overlaplen -g$genlen -t$thresh $linear $seqInput $icmInput $prediction 2> /dev/null;
+ cp $prediction".predict" $prediction;
+ cp $prediction".detail" $detailed;
+ rm $prediction".predict";
+ rm $prediction".detail";
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+ This is the main program that makes gene preditions based on an interpolated context model (ICM).
+ The ICM can be generated either with a de novo prediction (see glimmer Overview) or with extracted CDS from related organisms.
+
+-----
+
+**TIP** To extract CDS from a GenBank file use the tool *Extract ORF from a GenBank file*.
+
+-----
+
+**Glimmer Overview**
+
+::
+
+************** ************** ************** **************
+* * * * * * * *
+* long-orfs * ===> * Extract * ===> * build-icm * ===> * glimmer3 *
+* * * * * * * *
+************** ************** ************** **************
+
+**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
+ .....
+
+
+ - interpolated context model (ICM) 92: glimmer3-build-icm on data 89
+ - maximum overlap length 50
+ - minimum gene length. 90
+ - threshold score 30
+ - linear True
+
+* output::
+
+ .predict file
+ >CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7.
+ orf00001 40137 52 +2 8.68
+ orf00004 603 34 -1 2.91
+ orf00006 1289 1095 -3 3.16
+ orf00007 1555 1391 -2 2.33
+ orf00008 1809 1576 -1 1.02
+ orf00010 1953 2066 +3 3.09
+ orf00011 2182 2304 +1 0.89
+ orf00013 2390 2521 +2 0.60
+ orf00018 2570 3073 +2 2.54
+ orf00020 3196 3747 +1 2.91
+ orf00022 3758 4000 +2 0.83
+ orf00023 4399 4157 -2 1.31
+ orf00025 4463 4759 +2 2.92
+ orf00026 4878 5111 +3 0.78
+ orf00027 5468 5166 -3 1.64
+ orf00029 5590 5832 +1 0.29
+ orf00032 6023 6226 +2 6.02
+ orf00033 6217 6336 +1 3.09
+ ........
+
+
+ .details file
+ >CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7.
+ Sequence length = 40222
+
+ ----- Start ----- --- Length ---- ------------- Scores -------------
+ ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 NC
+ 0001 +2 40137 40137 52 135 135 9.26 96 - 96 - - 3 - 0
+ 0002 +1 58 64 180 120 114 5.01 69 69 - - 30 - - 0
+ +3 300 309 422 120 111 -0.68 20 - - 20 38 - - 41
+ +3 423 432 545 120 111 1.29 21 - 51 21 13 - 8 5
+ 0003 +2 401 416 595 192 177 2.51 93 - 93 - 5 - - 1
+ 0004 -1 645 552 34 609 516 2.33 99 - - - 99 - - 0
+ +1 562 592 762 198 168 -2.54 1 1 - - - - - 98
+ +1 763 772 915 150 141 -1.34 1 1 - - - - 86 11
+ +3 837 846 1007 168 159 1.35 28 - 50 28 - - 17 3
+ 0005 -3 1073 977 654 417 321 0.52 84 - - - - - 84 15
+ 0006 -3 1373 1319 1095 276 222 3.80 99 - - - - - 99 0
+ 0007 -2 1585 1555 1391 192 162 2.70 98 - - - - 98 - 1
+ 0008 -1 1812 1809 1576 234 231 1.26 94 - - - 94 - - 5
+ 0009 +2 1721 1730 1945 222 213 0.68 80 - 80 - - - - 19
+ .....
+
+-------
+
+**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).
+
+
+
+
+
diff -r 000000000000 -r e11e303c39a4 glimmer3/glimmer_acgt_content.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer3/glimmer_acgt_content.xml Wed Jan 11 09:34:45 2012 -0500
@@ -0,0 +1,33 @@
+
+ ACGT-content of windows in each sequence.
+ tigr-glimmer window-acgt $p $output $input_fasta $input_win_len $input_win_skip
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+This tool calculates the ACGT-Content from a given Sequence, given a sliding window.
+
+-------
+
+**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).
+
+
+
+
diff -r 000000000000 -r e11e303c39a4 glimmer3/glimmer_orf_to_seq.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer3/glimmer_orf_to_seq.py Wed Jan 11 09:34:45 2012 -0500
@@ -0,0 +1,45 @@
+#!/usr/bin/env python
+"""
+Input: DNA Fasta File + Glimmer ORF File
+Output: ORF-sequence as FASTA file
+Author: Bjoern Gruening
+"""
+import sys, os
+import Bio.SeqIO
+from Bio.SeqRecord import SeqRecord as record
+
+def __main__():
+ if len(sys.argv) >= 4:
+ glimmerfile = open(sys.argv [1], "r")
+ sequence = open(sys.argv[2])
+ orf2seq = open(sys.argv [3], "w")
+ else:
+ print "Missing input values."
+ sys.exit()
+
+ fastafile = Bio.SeqIO.parse(sequence, "fasta")
+
+ sequences = {}
+ for entry in fastafile:
+ sequences[entry.description] = entry
+
+ for line in glimmerfile:
+ if line.startswith('>'):
+ print line[1:].strip()
+ 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:
+ new_line = record(entry.seq[orf_start-1 : orf_end], id = orf_name, description = entry.description).format("fasta") + "\n"
+ else:
+ new_line = record(entry.seq[orf_end-1 : orf_start].reverse_complement(), id = orf_name, description = entry.description).format("fasta") + "\n"
+ orf2seq.write(new_line)
+
+ orf2seq.close()
+ glimmerfile.close()
+
+if __name__ == "__main__" :
+ __main__()
diff -r 000000000000 -r e11e303c39a4 glimmer3/glimmer_orf_to_seq.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer3/glimmer_orf_to_seq.xml Wed Jan 11 09:34:45 2012 -0500
@@ -0,0 +1,26 @@
+
+ assigns ORF to its DNA sequence
+ glimmer_orf_to_seq.py $glimmer_orfs $input_fasta $output
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+
+This tool extract all gene sequences from a genome, which are predicted with Glimmer3.
+
+
+-----
+
+
+
diff -r 000000000000 -r e11e303c39a4 glimmer3/glimmer_predict.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer3/glimmer_predict.py Wed Jan 11 09:34:45 2012 -0500
@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+"""
+Input: DNA Fasta File
+Output: Tabular
+Return Tabular File with predicted ORF's
+Bjoern Gruening
+"""
+import sys, os
+import tempfile
+from random import Random
+import string
+import subprocess
+import shutil
+
+def __main__():
+
+ genome_seq_file = sys.argv[1]
+ outfile_path = sys.argv[2]
+ outfile_ext_path = sys.argv[3]
+
+
+ tag = ''.join(Random().sample(string.letters+string.digits, 12))
+ tempdir = tempfile.gettempdir()
+
+ #longorfs = os.path.join(tempdir, tag + ".longorf")
+ 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(["tigr-glimmer", "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(["tigr-glimmer", "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(["tigr-glimmer", "build-icm", "-r", "-"],
+ stdin=open(trainingset.name), stdout = icm,
+ stderr=subprocess.PIPE).communicate()
+
+ """
+ Run Glimmer3
+ """
+ b = subprocess.Popen(["tigr-glimmer", "glimmer3", glimmeropts,
+ genome_seq_file, icm.name, os.path.join(tempdir, tag)],
+ stdout = subprocess.PIPE, stderr=subprocess.PIPE).communicate()
+
+ #shutil.copyfileobj
+ shutil.copyfile( os.path.join(tempdir, tag + ".predict"), outfile_path )
+ shutil.copyfile( os.path.join(tempdir, tag + ".detail"), outfile_ext_path )
+
+
+
+if __name__ == "__main__" :
+ __main__()
diff -r 000000000000 -r e11e303c39a4 glimmer3/glimmer_predict.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer3/glimmer_predict.xml Wed Jan 11 09:34:45 2012 -0500
@@ -0,0 +1,69 @@
+
+ Predict ORFs in prokaryotic genomes (not knowlegde-based)
+ glimmer_predict.py $input $output $output_ext $o $g $t $l
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+This tool predicts open reading frames (orfs) from a given DNA Sequence. That tool is not knowlegde-based.
+If you want to use a trained Glimmer3 use the knowlegde-based version and insert/generate a training set.
+
+-----
+
+**Example**
+
+Suppose you have the following DNA formatted 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 this::
+
+ >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).
+
+
+
diff -r 000000000000 -r e11e303c39a4 readme.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.txt Wed Jan 11 09:34:45 2012 -0500
@@ -0,0 +1,73 @@
+Galaxy wrapper for RepeatMasker
+=====================================
+
+This wrapper is copyright 2012 by Björn Grüning.
+
+This is a wrapper for the command line tool of Glimmer3.
+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.
+
+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.
+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, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007).
+
+
+
+Installation
+============
+
+To install Glimmer3, 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:
+
+
+
+
+
+
+
+
+
+
+
+
+History
+=======
+
+v0.1 - Initial public release
+
+
+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.
+
diff -r 000000000000 -r e11e303c39a4 tool_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_conf.xml Wed Jan 11 09:34:45 2012 -0500
@@ -0,0 +1,17 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+