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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty |
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added:
AnnotateRNAz.py rnazAnnotate.xml test-data/Annotation.bed test-data/IRE.aln test-data/miRNA.maf test-data/notsorandom.aln test-data/randomize.aln test-data/snoRNA.aln test-data/tRNA.aln test-data/tRNA.aln.window test-data/tRNA.maf test-data/tRNA.maf.window test-data/tRNA.rnaz test-data/tRNA.rnaz.clustered test-data/tRNA.rnaz.clustered.annotated.bed test-data/tRNA.rnaz.clustered.annotated.rnaz test-data/tRNA_selected.aln test-data/unknown.aln test-data/unknown.aln.window test-data/unknown.rnaz test-data/unknown.rnaz.clustered test-data/unknown.rnaz.clustered.annotated.bed test-data/unknown.rnaz.clustered.annotated.rnaz |
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| diff -r 000000000000 -r e123d5c6f489 AnnotateRNAz.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/AnnotateRNAz.py Wed Jan 30 04:12:06 2019 -0500 |
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| @@ -0,0 +1,205 @@ +# AnnotateRnaz.py --- +# +# Filename: AnnotateRnaz.py +# Description: +# Author: Joerg Fallmann +# Maintainer: +# Created: Sat Jan 26 12:45:25 2019 (+0100) +# Version: +# Package-Requires: () +# Last-Updated: Tue Jan 29 13:52:57 2019 (+0100) +# By: Joerg Fallmann +# Update #: 188 +# URL: +# Doc URL: +# Keywords: +# Compatibility: +# +# + +# Commentary: +# This script is a replacement for rnazAnnotate.pl +# rnazAnnotate can not handle the output from version 2 adequatly +# This script uses the bedtools API to fast intersect an annotation Bed +# with output from RNAz + +# Change Log: +# +# +# +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or (at +# your option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>. +# +# + +# Code: + +#!/usr/bin/env python3 + +import sys +import glob +import argparse +from io import StringIO +import gzip +import traceback as tb +import pybedtools +import re +import tempfile + +def parseargs(): + parser = argparse.ArgumentParser(description='Intersect RNAz output with Annotation from BED') + parser.add_argument("-b", "--bed", type=str, help='Annotation BED file') + parser.add_argument("-i", "--input", type=str, help='RNAz output') + parser.add_argument("-o", "--bedout", type=str, help='Annotation BED output') + parser.add_argument("-r", "--rnazout", type=str, help='Annotation rnaz output') + return parser.parse_args() + +def annotate(bed, input, bedout, rnazout): + try: + + pybedtools.set_tempdir('.') # Make sure we do not write somewhere we are not supposed to + anno = pybedtools.BedTool(bed) + rnaz=readrnaz(input) + tmpbed = pybedtools.BedTool(rnaztobed(rnaz), from_string=True) + + intersection = tmpbed.intersect(anno,wa=True,wb=True,s=True) # intersect strand specific, keep all info on a and b files + + bedtornaz(intersection, rnaz, bedout, rnazout) + + return 1 + + except Exception as err: + exc_type, exc_value, exc_tb = sys.exc_info() + tbe = tb.TracebackException( + exc_type, exc_value, exc_tb, + ) + print(''.join(tbe.format()),file=sys.stderr) + +def readin(file): + try: + if '.gz' in file: + f = gzip.open(file,'rt') + else: + f = open(file,'rt') + return f + + except Exception as err: + exc_type, exc_value, exc_tb = sys.exc_info() + tbe = tb.TracebackException( + exc_type, exc_value, exc_tb, + ) + print(''.join(tbe.format()),file=sys.stderr) + +def readrnaz(rnaz): + try: + toparse = readin(rnaz) + tointersect = {} + header = [] + for line in toparse: + if '#' in line[0]: + tointersect['header']=line.strip() + line = re.sub('^#','',line) + cont = line.strip().split('\t') + foi = cont.index('seqID') # need to find which column contains seqID + sf = cont.index('start') # need to find which column contains start + ef = cont.index('end') # need to find which column contains end + if 'strand' in cont:# need to find which column contains strand + df = cont.index('strand') + else: + df = None + else: + content = line.strip().split('\t') + newid=re.split('\.|\,|\s|\\|\/|\_', content[foi])[1] # I can only hope that we have species.chromosome.whatever as annotation in aln or maf, if not this is hardly parseable + if df: + longid = '_'.join([newid, content[sf], content[ef], 'RNAzresult', '0', content[df]]) + tointersect[longid] = content + else: + longid = '_'.join([newid, content[sf], content[ef], 'RNAzresult', '0', '+']) + tointersect[longid] = content + longid = '_'.join([newid, content[sf], content[ef], 'RNAzresult', '0', '-']) + tointersect[longid] = content + + return tointersect + + except Exception as err: + exc_type, exc_value, exc_tb = sys.exc_info() + tbe = tb.TracebackException( + exc_type, exc_value, exc_tb, + ) + print(''.join(tbe.format()),file=sys.stderr) + + +def rnaztobed(rnaz): + try: + tmpbed = [] + for key in rnaz: + if key != 'header': + tmpbed.append('\t'.join(key.split('_'))) + + return '\n'.join(tmpbed) + + except Exception as err: + exc_type, exc_value, exc_tb = sys.exc_info() + tbe = tb.TracebackException( + exc_type, exc_value, exc_tb, + ) + print(''.join(tbe.format()),file=sys.stderr) + +def bedtornaz(bed, rnaz, bedout, rnazout): + try: + b = open(bedout,'w') + r = open(rnazout,'w') + + annotatedbed=[] + annotatedrnaz=[] + annotatedrnaz.append(str.join('\t',[rnaz['header'],'Annotation'])) + for line in open(bed.fn): + out = line.strip().split("\t") + annotatedbed.append(str.join('\t',out[0:3]+out[9:10]+out[4:6])) + key = str.join('_',out[0:6]) + annotatedrnaz.append(str.join('\t',rnaz[key]+out[9:10])) + + print(str.join('\n', annotatedbed),file=b) + print(str.join('\n', annotatedrnaz),file=r) + + except Exception as err: + exc_type, exc_value, exc_tb = sys.exc_info() + tbe = tb.TracebackException( + exc_type, exc_value, exc_tb, + ) + print(''.join(tbe.format()),file=sys.stderr) + + +def closefile(file): + try: + file.close() + + except Exception as err: + exc_type, exc_value, exc_tb = sys.exc_info() + tbe = tb.TracebackException( + exc_type, exc_value, exc_tb, + ) + print(''.join(tbe.format()),file=sys.stderr) + + + + +#################### +#### MAIN #### +#################### +if __name__ == '__main__': + args=parseargs() + annotate(args.bed, args.input, args.bedout, args.rnazout) +###################################################################### +# AnnotateRnaz.py ends here |
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| diff -r 000000000000 -r e123d5c6f489 rnazAnnotate.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnazAnnotate.xml Wed Jan 30 04:12:06 2019 -0500 |
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| @@ -0,0 +1,59 @@ +<tool id="rnaz_annotate" name="Annotate RNAz" version="2.1"> + <requirements> + <requirement type="package" version="2.1">rnaz</requirement> + <requirement type="package" version="3.6.7">python</requirement> + <requirement type="package" version="0.8.0">pybedtools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python3 '$__tool_directory__/AnnotateRNAz.py' + --bed '$bed' + --input '$input' + --bedout '$output1' + --rnazout '$output2' + ]]></command> + <inputs> + <param format="txt" name="input" type="data" label="RNAz output to annotate" /> + <param type="data" name="bed" format="bed" label="Bed file with annotation" /> + </inputs> + <outputs> + <data name="output1" format="bed" /> + <data name="output2" format="txt" /> + </outputs> + <tests> + <test> + <param name="input" value="unknown.rnaz.clustered"/> + <param name="bed" value="Annotation.bed"/> + <output name="output1" file="unknown.rnaz.clustered.annotated.bed"/> + <output name="output2" file="unknown.rnaz.clustered.annotated.rnaz"/> + </test> + <test> + <param name="input" value="tRNA.rnaz.clustered"/> + <param name="bed" value="Annotation.bed"/> + <output name="output1" file="tRNA.rnaz.clustered.annotated.bed"/> + <output name="output2" file="tRNA.rnaz.clustered.annotated.rnaz"/> + </test> + </tests> + <help><![CDATA[ + + Annotated rnaz hits with an annotation BED file, + replaces rnazAnnotate.pl and rnazIndex.pl. + Best used after clustering of RNAz hits. + + usage: AnnotateRNAz.py [-h] [-b BED] [-i INPUT] [-o BEDOUT] [-r RNAZOUT] + + Intersect RNAz output with Annotation from BED + + optional arguments: + -h, --help show this help message and exit + -b BED, --bed BED Annotation BED file + -i INPUT, --input INPUT (RNAz output) + -o BEDOUT, --bedout BEDOUT (Annotated BED output) + -r RNAZOUT, --rnazout RNAZOUT (Annotated rnaz-format output) + ]]> + </help> + + <citations> + <citation type="doi">10.1142/9789814295291_0009</citation> + </citations> + +</tool> |
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| diff -r 000000000000 -r e123d5c6f489 test-data/Annotation.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Annotation.bed Wed Jan 30 04:12:06 2019 -0500 |
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| @@ -0,0 +1,3 @@ +chr1 10 500 WhoKnows 0 + +chr1 90 900 WhoKnows2 0 - +chr4 1352400 1352700 tRNAContainer 0 + |
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| diff -r 000000000000 -r e123d5c6f489 test-data/IRE.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/IRE.aln Wed Jan 30 04:12:06 2019 -0500 |
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| @@ -0,0 +1,17 @@ +CLUSTAL W(1.81) multiple sequence alignment + +393758_ENSMUSG00000025993_MOUSE_9754_9818/1-65 TAAGGCTTTGGCTTTCCAACTTCAGCTACAGTGTTAGCTAAGTTTGGAAAGAAGACAAAA +393758_SINFRUG00000122977_FUGU_3358_3422/1-65 TAAAAGCATTTCTTTCCAACTTCAGCTACAGTGTTAGCTAAGTTTGGAGGGGAGGAAAAC +393758_ENSRNOG00000003872_RAT_9703_9767/1-65 TAAGGCTTTAGCTTTCCAACTTCAGCTACAGTGTTAGCTAAGTTTGGAAAGAAGACATAA +393758_ENSDARG00000000241_ZEBRAFISH_9812_9874/1-65 -AAGGTTATTTCTCTCCGACTTCAGCTACAGTGATAGCTAAGTTTGGAGAGGAGAGAAGG + ** * ** *** *************** ************** * ** * + + +393758_ENSMUSG00000025993_MOUSE_9754_9818/1-65 AGAAG +393758_SINFRUG00000122977_FUGU_3358_3422/1-65 GGGAG +393758_ENSRNOG00000003872_RAT_9703_9767/1-65 AGAAG +393758_ENSDARG00000000241_ZEBRAFISH_9812_9874/1-65 GAGA- + * + + +// |
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| diff -r 000000000000 -r e123d5c6f489 test-data/miRNA.maf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/miRNA.maf Wed Jan 30 04:12:06 2019 -0500 |
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| @@ -0,0 +1,15 @@ +##maf version=1 +a score=0 +s hg16.chr11 64433968 110 - 134482954 GCCGAGACCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCGTCTCCCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC +s panTro1.chr9 65642342 110 - 136640551 GCCGAGACCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCGTCTCCCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC +s baboon.1 349423 110 - 497844 GCTGAGACCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCGTCTCCCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC +s rheMac1.SCAFFOLD120618 41607 110 - 48031 GCTGAGACCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCGTCTCCCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC +s marmoset.1 290457 110 - 415896 GCCGAGACCGAGTGCACAAGGCTCTGACCTATGAGTTGACAGCCAGTGCTCTGGTCTCCCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC +s galago.1 408904 110 - 511463 GCCAAGACCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCATCTCCCCTCTGGCTGCCAATTACATAGGTCACAGGTATGTTCGCCTCAATGCCAGC +s rn3.chr1 58923176 110 + 268121971 GTCAAGATGGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTACTCTGATCTCGCCTCTGGCTGCCAGTTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC +s mm6.chr19 54573156 110 + 60626890 GCCAAGATGGCGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTACTCTTTTCTCTCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCACCTCAATGCCAGC +s canFam1.chr18 3536304 110 + 66173745 GCTGAGATCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCATCTCTCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC +s rfbat.1 111329 110 - 223543 GCCGAGACCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCGTGTCCCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC +s tenrec.32 717 110 - 2965 GCCCAGACCGAGTGCACAAGTCTCTGACCTATGAATTGACAGCCAGTGCCTTGGGCTCCCCTCTGGCTGCCAATACCATAGGTCACAGGTATGTTTGCCTCCATGCCAGC +s danRer2.chr10 14345337 107 + 36600514 GGTTAAGTCTAGGACACAGGGTGATGACCTATGAATTGACAGCCAGTGTTTGCAGT--CCAGCTGCCTGTCAGTTCTGTAGGCCACTGCCCTGTTTATCCTACTAAACA- + |
| b |
| diff -r 000000000000 -r e123d5c6f489 test-data/notsorandom.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/notsorandom.aln Wed Jan 30 04:12:06 2019 -0500 |
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| @@ -0,0 +1,13 @@ +CLUSTAL W(1.81) multiple sequence alignment + + +hg17.chr1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +panTro1.chr1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +canFam1.chr9 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +mm5.chr2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +rn3.chr3 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +galGal2.chr17 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +fr1.chrUn AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +danRer1.chr11 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + + |
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| diff -r 000000000000 -r e123d5c6f489 test-data/randomize.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/randomize.aln Wed Jan 30 04:12:06 2019 -0500 |
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| @@ -0,0 +1,12 @@ +CLUSTAL W (1.83) multiple sequence alignment + + +hg17.chr1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +panTro1.chr1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +canFam1.chr9 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +mm5.chr2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +rn3.chr3 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +galGal2.chr17 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +fr1.chrUn AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +danRer1.chr11 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + ************************************************************ \ No newline at end of file |
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| diff -r 000000000000 -r e123d5c6f489 test-data/snoRNA.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snoRNA.aln Wed Jan 30 04:12:06 2019 -0500 |
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| @@ -0,0 +1,36 @@ +CLUSTAL W(1.81) multiple sequence alignment + + +470004_ENSG00000182512_HUMAN_8267_8506/1-243 GTACCCTCGAGCACACCAGACTTGCAGAAAAAGCATACTCCAGAGGAAGCTGAGGCATGC +470004_ENSMUSG00000021102_MOUSE_8376_8616/1-243 GTACCCTAGAGCACACCAGACTTGCAGAGAAAGCAGACAACAGAGGAAGCTGAGGCATGC +470004_SINFRUG00000145950_FUGU_5916_6140/1-243 --------GGGCACAACAAGGTTGC--AGAAAGCAT-C-CCAAAGGATGAAAAGGCGTGA +470004_ENSRNOG00000004206_RAT_8331_8570/1-243 -TACCCTCGAGCACACCAGACTTGCAGAAAAAGCATACTCCAGAGGAAGCTGAGGCATGC + * ***** ** **** * ****** * ** **** * **** ** + + +470004_ENSG00000182512_HUMAN_8267_8506/1-243 CTGCTCGAGAGCCAGCTGTTCCATGTGCAATTTTCCTCTGATAGTTTCTGGTCACTGTTG +470004_ENSMUSG00000021102_MOUSE_8376_8616/1-243 CTGCTCGAGAGGCAGCAGGCCCATGTGCAATTTTCCTCTGATAGGGCCTGGGTACTGTTG +470004_SINFRUG00000145950_FUGU_5916_6140/1-243 CTTCCAGAGGTCTGGGAATTCCACGTGCGATGTT-CTTTGA-A---CAAACACCTGCTTT +470004_ENSRNOG00000004206_RAT_8331_8570/1-243 CTGCTCGAGAGCCAGCGGTTCCATGTGCAATTTTCCTCTGATAAATCCTGGGTACTGTTG + ** * *** * *** **** ** ** ** *** * ** + + +470004_ENSG00000182512_HUMAN_8267_8506/1-243 CCACGGTGATAATGACTGGGCTATGTCATTATCTATCCGCCAACAGTAAGAGAAGCTTTG +470004_ENSMUSG00000021102_MOUSE_8376_8616/1-243 CCACGGTGATAATGGCTGTGCCGTGTCATTGTCGATCCACCAACAGTCAGAGAAGCTTGG +470004_SINFRUG00000145950_FUGU_5916_6140/1-243 CCACGGTGGCGATGGCCTTGTTCTGTAGCCATCGCATTTCTTGAGGCAGGTAGAAAAAAA +470004_ENSRNOG00000004206_RAT_8331_8570/1-243 CCACGGTGATAATGACTGTGCCGTGTCATTGTCGATCCACCAACAGTCAGAGAAGCTTTG + ******** *** * * *** ** * * * * + + +470004_ENSG00000182512_HUMAN_8267_8506/1-243 CAGTCGAGATATTGTTT--AGCAGATGGAGTGTTTTCTGTTGAACACTAAGTACTGCCAC +470004_ENSMUSG00000021102_MOUSE_8376_8616/1-243 CAGTCAAGATATTGTTT--AGCAGACGGAGCGGTTTCTGTTGGACACTAAGTACTGCCAC +470004_SINFRUG00000145950_FUGU_5916_6140/1-243 CAG-CATGATATTGTTTGAAGCGGGGAGAGCTGTTCCCGTCAGACACTGTCCGCTGTCAC +470004_ENSRNOG00000004206_RAT_8331_8570/1-243 CAGTCAAGATATTGTTT--AGCAGACGGAGCGGTTTCTGTTGGACACTAAGTGCTGCTAC + *** * ********** *** * *** ** * ** ***** *** ** + + +470004_ENSG00000182512_HUMAN_8267_8506/1-243 AA- +470004_ENSMUSG00000021102_MOUSE_8376_8616/1-243 AAA +470004_SINFRUG00000145950_FUGU_5916_6140/1-243 AGC +470004_ENSRNOG00000004206_RAT_8331_8570/1-243 AAG + * |
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| diff -r 000000000000 -r e123d5c6f489 test-data/tRNA.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.aln Wed Jan 30 04:12:06 2019 -0500 |
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| @@ -0,0 +1,14 @@ +CLUSTAL W (1.83) multiple sequence alignment + + +sacCer1 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC +sacBay GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC +sacKlu GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGCTAGGGGTTCGAGC +sacCas GCTTCAGTAGCTCAGTCGGAAGAGCGTCAGTCTCATAATCTGAAGGTCGAGAGTTCGAAC + ** * * ** ** **** ** **** * *** ***** **** * ****** * + +sacCer1 CCCCTACAGGGCT +sacBay CCCCTACAGGGCT +sacKlu CCCCTACAGGGCT +sacCas CTCCCCTGGAGCA + * ** * ** |
| b |
| diff -r 000000000000 -r e123d5c6f489 test-data/tRNA.aln.window --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.aln.window Wed Jan 30 04:12:06 2019 -0500 |
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| @@ -0,0 +1,30 @@ +CLUSTAL W(1.81) multiple sequence alignment + + +sacCer1/0-73 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC +sacBay/0-73 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC +sacKlu/0-73 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGCTAGGGGTTCGAGC +sacCas/0-73 GCTTCAGTAGCTCAGTCGGAAGAGCGTCAGTCTCATAATCTGAAGGTCGAGAGTTCGAAC + + +sacCer1/0-73 CCCCTACAGGGCT +sacBay/0-73 CCCCTACAGGGCT +sacKlu/0-73 CCCCTACAGGGCT +sacCas/0-73 CTCCCCTGGAGCA + + +CLUSTAL W(1.81) multiple sequence alignment + + +sacCer1_rev/0-73 AGCCCTGTAGGGGGCTCGAACCCCTAACCTTATGATTAAGAGTCATACGCGCTACCGATT +sacBay_rev/0-73 AGCCCTGTAGGGGGCTCGAACCCCTAACCTTATGATTAAGAGTCATACGCGCTACCGATT +sacKlu_rev/0-73 AGCCCTGTAGGGGGCTCGAACCCCTAGCCTTATGATTAAGAGTCATACGCGCTACCGATT +sacCas_rev/0-73 TGCTCCAGGGGAGGTTCGAACTCTCGACCTTCAGATTATGAGACTGACGCTCTTCCGACT + + +sacCer1_rev/0-73 GCGCCAACAAGGC +sacBay_rev/0-73 GCGCCAACAAGGC +sacKlu_rev/0-73 GCGCCAACAAGGC +sacCas_rev/0-73 GAGCTACTGAAGC + + |
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| diff -r 000000000000 -r e123d5c6f489 test-data/tRNA.maf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.maf Wed Jan 30 04:12:06 2019 -0500 |
| b |
| @@ -0,0 +1,6 @@ +##maf version=1 +a score=119673.000000 +s sacCer1.chr4 1352453 73 - 1531914 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGCCCCCTACAGGGCT +s sacBay.contig_465 14962 73 - 57401 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGCCCCCTACAGGGCT +s sacKlu.Contig1694 137 73 + 4878 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGCTAGGGGTTCGAGCCCCCTACAGGGCT +s sacCas.Contig128 258 73 + 663 GCTTCAGTAGCTCAGTCGGAAGAGCGTCAGTCTCATAATCTGAAGGTCGAGAGTTCGAACCTCCCCTGGAGCA |
| b |
| diff -r 000000000000 -r e123d5c6f489 test-data/tRNA.maf.window --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.maf.window Wed Jan 30 04:12:06 2019 -0500 |
| b |
| @@ -0,0 +1,12 @@ +a score=0 +s sacCer1.chr4 1352453 73 - 1531914 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGCCCCCTACAGGGCT +s sacBay.contig_465 14962 73 - 57401 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGCCCCCTACAGGGCT +s sacKlu.Contig1694 137 73 + 4878 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGCTAGGGGTTCGAGCCCCCTACAGGGCT +s sacCas.Contig128 258 73 + 663 GCTTCAGTAGCTCAGTCGGAAGAGCGTCAGTCTCATAATCTGAAGGTCGAGAGTTCGAACCTCCCCTGGAGCA + +a score=0 +s sacCer1.chr4 1352453 73 + 1531914 AGCCCTGTAGGGGGCTCGAACCCCTAACCTTATGATTAAGAGTCATACGCGCTACCGATTGCGCCAACAAGGC +s sacBay.contig_465 14962 73 + 57401 AGCCCTGTAGGGGGCTCGAACCCCTAACCTTATGATTAAGAGTCATACGCGCTACCGATTGCGCCAACAAGGC +s sacKlu.Contig1694 137 73 - 4878 AGCCCTGTAGGGGGCTCGAACCCCTAGCCTTATGATTAAGAGTCATACGCGCTACCGATTGCGCCAACAAGGC +s sacCas.Contig128 258 73 - 663 TGCTCCAGGGGAGGTTCGAACTCTCGACCTTCAGATTATGAGACTGACGCTCTTCCGACTGAGCTACTGAAGC + |
| b |
| diff -r 000000000000 -r e123d5c6f489 test-data/tRNA.rnaz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.rnaz Wed Jan 30 04:12:06 2019 -0500 |
| b |
| @@ -0,0 +1,156 @@ + +############################ RNAz 2.1 ############################## + + Sequences: 4 + Columns: 73 + Reading direction: forward + Mean pairwise identity: 80.82 + Shannon entropy: 0.31118 + G+C content: 0.54795 + Mean single sequence MFE: -27.20 + Consensus MFE: -26.50 + Energy contribution: -23.63 + Covariance contribution: -2.87 + Combinations/Pair: 1.43 + Mean z-score: -1.82 + Structure conservation index: 0.97 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: 2.15 + SVM RNA-class probability: 0.984068 + Prediction: RNA + +###################################################################### + +>sacCer1.chr4 1352453 73 - 1531914 +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R) +>sacBay.contig_465 14962 73 - 57401 +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R) +>sacKlu.Contig1694 137 73 + 4878 +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((.(((((........)))).(((((.......)))))......(((((....)))))).))))))). ( -27.20, z-score = -1.34, R) +>sacCas.Contig128 258 73 + 663 +GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAACCUCCCCUGGAGCA +(((((((..((((........)))).((((.........))))((((((......)).))))...))))))). ( -23.20, z-score = -1.22, R) +>consensus +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-26.50 = -23.63 + -2.87) + +############################ RNAz 2.1 ############################## + + Sequences: 4 + Columns: 73 + Reading direction: reverse + Mean pairwise identity: 80.82 + Shannon entropy: 0.31118 + G+C content: 0.54795 + Mean single sequence MFE: -24.15 + Consensus MFE: -26.66 + Energy contribution: -23.35 + Covariance contribution: -3.31 + Combinations/Pair: 1.48 + Mean z-score: -1.79 + Structure conservation index: 1.10 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: 2.58 + SVM RNA-class probability: 0.992927 + Prediction: RNA + +###################################################################### + +>sacCer1.chr4 1352453 73 + 1531914 +AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC +.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R) +>sacBay.contig_465 14962 73 + 57401 +AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC +.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R) +>sacKlu.Contig1694 137 73 - 4878 +AGCCCUGUAGGGGGCUCGAACCCCUAGCCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC +.......((((((.......))))))((((((((((.....)))))..((((........))))....))))) ( -25.20, z-score = -1.87, R) +>sacCas.Contig128 258 73 - 663 +UGCUCCAGGGGAGGUUCGAACUCUCGACCUUCAGAUUAUGAGACUGACGCUCUUCCGACUGAGCUACUGAAGC +.(((.(((.((((((.(((....)))))))))................((((........))))..))).))) ( -22.00, z-score = -0.83, R) +>consensus +AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC +.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) (-26.66 = -23.35 + -3.31) + +############################ RNAz 2.1 ############################## + + Sequences: 4 + Columns: 73 + Reading direction: forward + Mean pairwise identity: 80.82 + Shannon entropy: 0.31118 + G+C content: 0.54795 + Mean single sequence MFE: -24.15 + Consensus MFE: -26.66 + Energy contribution: -23.35 + Covariance contribution: -3.31 + Combinations/Pair: 1.48 + Mean z-score: -1.79 + Structure conservation index: 1.10 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: 2.58 + SVM RNA-class probability: 0.992927 + Prediction: RNA + +###################################################################### + +>sacCer1.chr4 1352453 73 + 1531914 +AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC +.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R) +>sacBay.contig_465 14962 73 + 57401 +AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC +.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R) +>sacKlu.Contig1694 137 73 - 4878 +AGCCCUGUAGGGGGCUCGAACCCCUAGCCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC +.......((((((.......))))))((((((((((.....)))))..((((........))))....))))) ( -25.20, z-score = -1.87, R) +>sacCas.Contig128 258 73 - 663 +UGCUCCAGGGGAGGUUCGAACUCUCGACCUUCAGAUUAUGAGACUGACGCUCUUCCGACUGAGCUACUGAAGC +.(((.(((.((((((.(((....)))))))))................((((........))))..))).))) ( -22.00, z-score = -0.83, R) +>consensus +AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC +.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) (-26.66 = -23.35 + -3.31) + +############################ RNAz 2.1 ############################## + + Sequences: 4 + Columns: 73 + Reading direction: reverse + Mean pairwise identity: 80.82 + Shannon entropy: 0.31118 + G+C content: 0.54795 + Mean single sequence MFE: -27.20 + Consensus MFE: -26.50 + Energy contribution: -23.63 + Covariance contribution: -2.87 + Combinations/Pair: 1.43 + Mean z-score: -1.82 + Structure conservation index: 0.97 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: 2.15 + SVM RNA-class probability: 0.984068 + Prediction: RNA + +###################################################################### + +>sacCer1.chr4 1352453 73 - 1531914 +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R) +>sacBay.contig_465 14962 73 - 57401 +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R) +>sacKlu.Contig1694 137 73 + 4878 +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((.(((((........)))).(((((.......)))))......(((((....)))))).))))))). ( -27.20, z-score = -1.34, R) +>sacCas.Contig128 258 73 + 663 +GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAACCUCCCCUGGAGCA +(((((((..((((........)))).((((.........))))((((((......)).))))...))))))). ( -23.20, z-score = -1.22, R) +>consensus +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-26.50 = -23.63 + -2.87) |
| b |
| diff -r 000000000000 -r e123d5c6f489 test-data/tRNA.rnaz.clustered --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.rnaz.clustered Wed Jan 30 04:12:06 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +# locusID seqID start end maxN maxIdentity maxP minZ +locus1 sacCer1.chr4 1352453 1352526 4 80.82 0.992927 -1.82 |
| b |
| diff -r 000000000000 -r e123d5c6f489 test-data/tRNA.rnaz.clustered.annotated.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.rnaz.clustered.annotated.bed Wed Jan 30 04:12:06 2019 -0500 |
| b |
| @@ -0,0 +1,1 @@ +chr4 1352453 1352526 tRNAContainer 0 + |
| b |
| diff -r 000000000000 -r e123d5c6f489 test-data/tRNA.rnaz.clustered.annotated.rnaz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.rnaz.clustered.annotated.rnaz Wed Jan 30 04:12:06 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +# locusID seqID start end maxN maxIdentity maxP minZ Annotation +locus1 sacCer1.chr4 1352453 1352526 4 80.82 0.992927 -1.82 tRNAContainer |
| b |
| diff -r 000000000000 -r e123d5c6f489 test-data/tRNA_selected.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_selected.aln Wed Jan 30 04:12:06 2019 -0500 |
| b |
| @@ -0,0 +1,9 @@ +CLUSTAL W(1.81) multiple sequence alignment + + +sacCer1 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC + + +sacCer1 CCCCTACAGGGCT + + |
| b |
| diff -r 000000000000 -r e123d5c6f489 test-data/unknown.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.aln Wed Jan 30 04:12:06 2019 -0500 |
| b |
| @@ -0,0 +1,72 @@ +CLUSTAL W (1.83) multiple sequence alignment + + +hg17.chr1 TACAGCAGCTGCTATTGCTTATGGCCTGGATAAGAGGGAGGGGGAGAAGAACATCCTGGT +panTro1.chr1 TACAGCAGCTGCTATTGCTTATGGCCTGGATAAGAGGGAGGGGGAGAAGAACATCCTTGT +canFam1.chr9 TACAGCAGCTGCTATTGCTTACGGCTTGGATAAGAGGGAAGGGGAGAAGAATATCCTGGT +mm5.chr2 TACAGCAGCTGCTATTGCATATGGCCTGGATAAGAGAGAGGGAGAGAAGAACATCCTTGT +rn3.chr3 AACAGCAGCTGCTATTGCATATGGCCTGGATAAGAGAGAGGGAGAGAAGAACATCCTCGT +galGal2.chr17 AACTGCTGCTGCAATTGCATACGGATTGGACAAGAGAGAGGGTGAAAAGAACATCCTTGT +fr1.chrUn AACCGCTGCTGCCATTGCTTATGGTCTGGACAAAAAGGACGGCGAGAAGAACATCCTCGT +danRer1.chr11 TACGGCGGCTGCCATTGCATACGGTCTGGACAAGAGGGACGGAGAGAAAAACATCCTGGT + ** ** ***** ***** ** ** **** ** * ** ** ** ** ** ***** ** + +hg17.chr1 GTTTGACCTGGGTGGTGGAACCTTTGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT +panTro1.chr1 GTTTGACCTGGGTGGTGGAACCTTCGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT +canFam1.chr9 GTTTGACCTGGGTGGTGGAACTTTTGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT +mm5.chr2 GTTTGACCTGGGTGGCGGCACCTTCGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT +rn3.chr3 GTTTGACCTGGGTGGTGGAACCTTCGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT +galGal2.chr17 ATTTGACCTGGGTGGTGGAACTTTTGATGTCTCCCTCCTGACAATTGACAACGGAGTCTT +fr1.chrUn GTTCGATCTCGGTGGCGGCACCTTCGACGTGTCTCTGCTCACCATTGACAACGGTGTGTT +danRer1.chr11 GTTCGATCTGGGTGGTGGCACCTTTGACGTGTCTCTGCTGACCATCGATAACGGCGTGTT + ** ** ** ***** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** + +hg17.chr1 CAAAGTTGTGGCCACTAATGGAGATACTTATCTGGGTGGAGAAGACTTTGACCAGCGTGT +panTro1.chr1 CAAAGTTGTGGTCACTAATGGAGATACTCATCTGGGTGGAAAAGACTTTGACCAGCATGT +canFam1.chr9 TGAAGTTGTGGCTACTAATGGAGATACTCACCTGGGTGGAGAAGACTTTGACCAACGTGT +mm5.chr2 TGAAGTGGTGGCCACTAATGGAGATACTCACCTGGGTGGGGAAGACTTTGATCAGCGGGT +rn3.chr3 TGAAGTGGTGGCCACTAATGGAGACACTCATCTGGGTGGGGAAGACTTTGATCAGCGGGT +galGal2.chr17 TGAAGTTGTGGCTACAAATGGTGACACACACCTGGGTGGAGAAGACTTTGACCAGCGTGT +fr1.chrUn TGAAGTGGTGGCCACCAATGGTGACACTCACCTTGGAGGTGAAGACTTTGATCAGCGCGT +danRer1.chr11 TGAAGTGGTGGCCACAAACGGAGACACTCACCTGGGCGGAGAAGACTTCGACCAGCGCGT + **** **** ** ** ** ** ** * ** ** ** ******* ** ** * ** + +hg17.chr1 CATGGAACACTTCATCAAACTGTACAAAAAGAAGACTGGCAAAGATGTCAGGAAAGACAA +panTro1.chr1 CATGGAACACTTCATCAAACTGTACAAAAAGAAGACTGGCAAAGATGTCGGGAAAGACAA +canFam1.chr9 CATGGAACACTTCATCAAACTCTACAAAAAGAAGACTGGCAAAGATGTTAGGAAAGACAA +mm5.chr2 CATGGAACACTTCATCAAGTTGTACAAAAAGAAAACTGGTAAAGATGTTAGGAAAGACAA +rn3.chr3 CATGGAGCACTTCATCAAGCTGTACAAAAAGAAGACTGGGAAAGATGTCAGAAAGGACAA +galGal2.chr17 TATGGAGCACTTCATCAAACTCTACAAGAAGAAAACAGGAAAAGATGTCAGGAAGGATAA +fr1.chrUn CATGGAACACTTCATCAAGCTATACAAGAAGAAGACTGGCAAAGACGTGCGCAAAGACAA +danRer1.chr11 CATGGAGCACTTCATCAAGCTGTACAAGAAGAAGACGGGCAAAGATGTGCGCAAAGACAA + ***** *********** * ***** ***** ** ** ***** ** * ** ** ** + +hg17.chr1 TAGAGCTGTGCAGAAACTCTGGCGCAAGGTAGAAAAGGCCAAACGGGCCCTGTCTTCTCA +panTro1.chr1 TAGAGCTGTGCAGAAACTCTGGCGCAAGGTAGAAAAGGCCAAACGGGCCCTGTCTTCTCA +canFam1.chr9 CAGAGCTGTGCAGAAACTCCGGCGGGAGGTAGAAAAAGCCAAACGGGCCCTGTCTTCTCA +mm5.chr2 CAGAGCTGTGCAGAAACTCCGGCGTGAGGTAGAAAAGGCTAAGAGAGCCTTGTCTTCTCA +rn3.chr3 CAGAGCTGTGCAGAAACTCCGGCGTGAGGTAGAAAAGGCCAAGAGAGCCCTGTCTTCTCA +galGal2.chr17 CAGAGCTGTACAGAAACTAAGACGGGAAGTAGAGAAAGCGAAGCGGGCCCTGTCATCCCA +fr1.chrUn CCGTGCTGTCCAGAAGCTGCGTCGTGAGGTTGAGAAGGCAAAGAGGGCCCTGTCTGCCCA +danRer1.chr11 CCGCGCCGTGCAGAAGCTGCGCAGAGAGGTGGAGAAGGCTAAGAGAGCCCTGTCTGCCCA + * ** ** ***** ** * * * ** ** ** ** ** * *** **** * ** + +hg17.chr1 ACATCAAGCAAGCAGTAATTGAAATTGAGTCCTTCTATGAAGGAGAAGACTTTTCTGAGA +panTro1.chr1 ACATCAAGCAAGCAGTAATTGAAATTGAGTCCTTCTATGAAGGAGAAGACTTTTCTGAGA +canFam1.chr9 ACATCAAGCAAG----AATTGAAATTGAGTCCTTCTATGAAGGAGAAGACTTCTCTGAGA +mm5.chr2 GCATCAAGCAAG----GATTGAAATTGAGTCCTTCTTCGAAGGAGAAGACTTCTCAGAGA +rn3.chr3 GCATCAAGCGAG----GATTGAAATTGAGTCCTTCTTCGAAGGAGAAGACTTCTCAGAGA +galGal2.chr17 GCACCAAGCTAG----AATTGAAATAGAATCCTTTTTTGAAGGAGAGGATTTCTCTGAGA +fr1.chrUn GCACCAGGCCCG----CATTGAGATCGAGTCTTTCTTTGAGGGAGAAGATTTCTCCGAGA +danRer1.chr11 GCATCAGGCCCG----CATCGAGATCGAGTCCTTCTTTGAGGGAGAAGATTTCTCTGAGA + ** ** ** * ** ** ** ** ** ** * ** ***** ** ** ** **** + +hg17.chr1 CCCTGACTCAGGCCAAATTTGAAGAGCTCAA +panTro1.chr1 CCCTGACTCAGGCCAAATTTGAAGAGCTCAA +canFam1.chr9 CTCTGACTCGGGCCAAATTTGAAGAGCTAAA +mm5.chr2 CCCTTACTCGGGCCAAATTTGAAGAGCTGAA +rn3.chr3 CCCTTACTCGGGCCAAATTTGAAGAGCTGAA +galGal2.chr17 CGCTTACTCGTGCCAAATTTGAAGAACTGAA +fr1.chrUn CACTGACCCGTGCCAAATTTGAAGAGCTTAA +danRer1.chr11 CTCTCACCAGAGCCAAGTTTGAAGAGCTCAA + * ** ** ***** ******** ** ** |
| b |
| diff -r 000000000000 -r e123d5c6f489 test-data/unknown.aln.window --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.aln.window Wed Jan 30 04:12:06 2019 -0500 |
| b |
| b'@@ -0,0 +1,152 @@\n+CLUSTAL W(1.81) multiple sequence alignment\n+\n+\n+hg17.chr1/0-120 TACAGCAGCTGCTATTGCTTATGGCCTGGATAAGAGGGAGGGGGAGAAGAACATCCTGGT\n+canFam1.chr9/0-120 TACAGCAGCTGCTATTGCTTACGGCTTGGATAAGAGGGAAGGGGAGAAGAATATCCTGGT\n+mm5.chr2/0-120 TACAGCAGCTGCTATTGCATATGGCCTGGATAAGAGAGAGGGAGAGAAGAACATCCTTGT\n+galGal2.chr17/0-120 AACTGCTGCTGCAATTGCATACGGATTGGACAAGAGAGAGGGTGAAAAGAACATCCTTGT\n+fr1.chrUn/0-120 AACCGCTGCTGCCATTGCTTATGGTCTGGACAAAAAGGACGGCGAGAAGAACATCCTCGT\n+danRer1.chr11/0-120 TACGGCGGCTGCCATTGCATACGGTCTGGACAAGAGGGACGGAGAGAAAAACATCCTGGT\n+\n+\n+hg17.chr1/0-120 GTTTGACCTGGGTGGTGGAACCTTTGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT\n+canFam1.chr9/0-120 GTTTGACCTGGGTGGTGGAACTTTTGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT\n+mm5.chr2/0-120 GTTTGACCTGGGTGGCGGCACCTTCGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT\n+galGal2.chr17/0-120 ATTTGACCTGGGTGGTGGAACTTTTGATGTCTCCCTCCTGACAATTGACAACGGAGTCTT\n+fr1.chrUn/0-120 GTTCGATCTCGGTGGCGGCACCTTCGACGTGTCTCTGCTCACCATTGACAACGGTGTGTT\n+danRer1.chr11/0-120 GTTCGATCTGGGTGGTGGCACCTTTGACGTGTCTCTGCTGACCATCGATAACGGCGTGTT\n+\n+\n+CLUSTAL W(1.81) multiple sequence alignment\n+\n+\n+hg17.chr1_rev/0-120 AAGACACCATTGTCAATGGTGAGAAGAGACACATCAAAGGTTCCACCACCCAGGTCAAAC\n+canFam1.chr9_rev/0-120 AAGACACCATTGTCAATGGTGAGAAGAGACACATCAAAAGTTCCACCACCCAGGTCAAAC\n+mm5.chr2_rev/0-120 AAGACACCATTGTCAATGGTGAGAAGAGACACATCGAAGGTGCCGCCACCCAGGTCAAAC\n+galGal2.chr17_rev/0-120 AAGACTCCGTTGTCAATTGTCAGGAGGGAGACATCAAAAGTTCCACCACCCAGGTCAAAT\n+fr1.chrUn_rev/0-120 AACACACCGTTGTCAATGGTGAGCAGAGACACGTCGAAGGTGCCGCCACCGAGATCGAAC\n+danRer1.chr11_rev/0-120 AACACGCCGTTATCGATGGTCAGCAGAGACACGTCAAAGGTGCCACCACCCAGATCGAAC\n+\n+\n+hg17.chr1_rev/0-120 ACCAGGATGTTCTTCTCCCCCTCCCTCTTATCCAGGCCATAAGCAATAGCAGCTGCTGTA\n+canFam1.chr9_rev/0-120 ACCAGGATATTCTTCTCCCCTTCCCTCTTATCCAAGCCGTAAGCAATAGCAGCTGCTGTA\n+mm5.chr2_rev/0-120 ACAAGGATGTTCTTCTCTCCCTCTCTCTTATCCAGGCCATATGCAATAGCAGCTGCTGTA\n+galGal2.chr17_rev/0-120 ACAAGGATGTTCTTTTCACCCTCTCTCTTGTCCAATCCGTATGCAATTGCAGCAGCAGTT\n+fr1.chrUn_rev/0-120 ACGAGGATGTTCTTCTCGCCGTCCTTTTTGTCCAGACCATAAGCAATGGCAGCAGCGGTT\n+danRer1.chr11_rev/0-120 ACCAGGATGTTTTTCTCTCCGTCCCTCTTGTCCAGACCGTATGCAATGGCAGCCGCCGTA\n+\n+\n+CLUSTAL W(1.81) multiple sequence alignment\n+\n+\n+hg17.chr1/120-240 CAAAGTTGTGGCCACTAATGGAGATACTTATCTGGGTGGAGAAGACTTTGACCAGCGTGT\n+panTro1.chr1/120-240 CAAAGTTGTGGTCACTAATGGAGATACTCATCTGGGTGGAAAAGACTTTGACCAGCATGT\n+rn3.chr3/120-240 TGAAGTGGTGGCCACTAATGGAGACACTCATCTGGGTGGGGAAGACTTTGATCAGCGGGT\n+galGal2.chr17/120-240 TGAAGTTGTGGCTACAAATGGTGACACACACCTGGGTGGAGAAGACTTTGACCAGCGTGT\n+fr1.chrUn/120-240 TGAAGTGGTGGCCACCAATGGTGACACTCACCTTGGAGGTGAAGACTTTGATCAGCGCGT\n+danRer1.chr11/120-240 TGAAGTGGTGGCCACAAACGGAGACACTCACCTGGGCGGAGAAGACTTCGACCAGCGCGT\n+\n+\n+hg17.chr1/120-240 CATGGAACACTTCATCAAACTGTACAAAAAGAAGACTGGCAAAGATGTCAGGAAAGACAA\n+panTro1.chr1/120-240 CATGGAACACTTCATCAAACTGTACAAAAAGAAGACTGGCAAAGATGTCGGGAAAGACAA\n+rn3.chr3/120-240 CATGGAGCACTTCATCAAGCTGTACAAAAAGAAGACTGGGAAAGATGTCAGAAAGGACAA\n+galGal2.chr17/120-240 TATGGAGCACTTCATCAAACTCTACAAGAAGAAAACAGGAAAAGATGTCAGGAAGGATAA\n+fr1.chrUn/120-240 CATGGAACACTTCATCAAGCTATACAAGAAGAAGACTGGCAAAGACGTGCGCAAAGACAA\n+danRer1.chr11/120-240 CATGGAGCACTTCATCAAGCTGTACAAGAAGAAGACGGGCAAAGATGTGCGCAAAGACAA\n+\n+\n+CLUSTAL W(1.81) multiple sequence alignment\n+\n+\n+hg17.chr1_rev/120-240 TTGTCTTTCCTGACATCTTTGCCAGTCTTCTTTTTGTACAGTTTGATGAAGTGTTCCATG\n+panTro1.chr1_rev/120-240 TTGTCTTTCCCGACATCTTTGCCAGTCTTCTTTTTGTACAGTTTGATGAAGTGTTCCATG\n+rn3.chr3_rev/120-240 TTGTCCTTTCTGACATCTTTCCCAGTCTTCTTTTTGTACAGCTTGATGAAGTGCTCCATG\n+galGal2.chr17_rev/120-240 TTATCCTTCCTGACATCTTTTCCTGTTTTCTTCTTGTAGAGTTTGATGAAGTGCTCCATA\n+fr1.chrUn_rev/120-240 TTGTCTTTGCGCACGTCTTTGCCAGTCTTCTTCTTGTATAGCTTGATGAAGTGTTCCATG\n+danRer1.chr11_rev/120-240 TTGTCTTTGCGCACATCTTTGCCCGTCTTCTTCTTGTACAGCTTGATGAAGTGCTCCATG'..b'/240-360 ACATCAAGCAAGCAGTAATTGAAATTGAGTCCTTCTATGAAGGAGAAGACTTTTCTGAGA\n+mm5.chr2/240-360 GCATCAAGCAAG----GATTGAAATTGAGTCCTTCTTCGAAGGAGAAGACTTCTCAGAGA\n+rn3.chr3/240-360 GCATCAAGCGAG----GATTGAAATTGAGTCCTTCTTCGAAGGAGAAGACTTCTCAGAGA\n+galGal2.chr17/240-360 GCACCAAGCTAG----AATTGAAATAGAATCCTTTTTTGAAGGAGAGGATTTCTCTGAGA\n+fr1.chrUn/240-360 GCACCAGGCCCG----CATTGAGATCGAGTCTTTCTTTGAGGGAGAAGATTTCTCCGAGA\n+danRer1.chr11/240-360 GCATCAGGCCCG----CATCGAGATCGAGTCCTTCTTTGAGGGAGAAGATTTCTCTGAGA\n+\n+\n+CLUSTAL W(1.81) multiple sequence alignment\n+\n+\n+hg17.chr1_rev/240-360 TCTCAGAAAAGTCTTCTCCTTCATAGAAGGACTCAATTTCAATTACTGCTTGCTTGATGT\n+mm5.chr2_rev/240-360 TCTCTGAGAAGTCTTCTCCTTCGAAGAAGGACTCAATTTCAATC----CTTGCTTGATGC\n+rn3.chr3_rev/240-360 TCTCTGAGAAGTCTTCTCCTTCGAAGAAGGACTCAATTTCAATC----CTCGCTTGATGC\n+galGal2.chr17_rev/240-360 TCTCAGAGAAATCCTCTCCTTCAAAAAAGGATTCTATTTCAATT----CTAGCTTGGTGC\n+fr1.chrUn_rev/240-360 TCTCGGAGAAATCTTCTCCCTCAAAGAAAGACTCGATCTCAATG----CGGGCCTGGTGC\n+danRer1.chr11_rev/240-360 TCTCAGAGAAATCTTCTCCCTCAAAGAAGGACTCGATCTCGATG----CGGGCCTGATGC\n+\n+\n+hg17.chr1_rev/240-360 TGAGAAGACAGGGCCCGTTTGGCCTTTTCTACCTTGCGCCAGAGTTTCTGCACAGCTCTA\n+mm5.chr2_rev/240-360 TGAGAAGACAAGGCTCTCTTAGCCTTTTCTACCTCACGCCGGAGTTTCTGCACAGCTCTG\n+rn3.chr3_rev/240-360 TGAGAAGACAGGGCTCTCTTGGCCTTTTCTACCTCACGCCGGAGTTTCTGCACAGCTCTG\n+galGal2.chr17_rev/240-360 TGGGATGACAGGGCCCGCTTCGCTTTCTCTACTTCCCGTCTTAGTTTCTGTACAGCTCTG\n+fr1.chrUn_rev/240-360 TGGGCAGACAGGGCCCTCTTTGCCTTCTCAACCTCACGACGCAGCTTCTGGACAGCACGG\n+danRer1.chr11_rev/240-360 TGGGCAGACAGGGCTCTCTTAGCCTTCTCCACCTCTCTGCGCAGCTTCTGCACGGCGCGG\n+\n+\n+CLUSTAL W(1.81) multiple sequence alignment\n+\n+\n+hg17.chr1/271-391 GAAAAGGCCAAACGGGCCCTGTCTTCTCAACATCAAGCAAGCAGTAATTGAAATTGAGTC\n+mm5.chr2/271-391 GAAAAGGCTAAGAGAGCCTTGTCTTCTCAGCATCAAGCAAG----GATTGAAATTGAGTC\n+rn3.chr3/271-391 GAAAAGGCCAAGAGAGCCCTGTCTTCTCAGCATCAAGCGAG----GATTGAAATTGAGTC\n+galGal2.chr17/271-391 GAGAAAGCGAAGCGGGCCCTGTCATCCCAGCACCAAGCTAG----AATTGAAATAGAATC\n+fr1.chrUn/271-391 GAGAAGGCAAAGAGGGCCCTGTCTGCCCAGCACCAGGCCCG----CATTGAGATCGAGTC\n+danRer1.chr11/271-391 GAGAAGGCTAAGAGAGCCCTGTCTGCCCAGCATCAGGCCCG----CATCGAGATCGAGTC\n+\n+\n+hg17.chr1/271-391 CTTCTATGAAGGAGAAGACTTTTCTGAGACCCTGACTCAGGCCAAATTTGAAGAGCTCAA\n+mm5.chr2/271-391 CTTCTTCGAAGGAGAAGACTTCTCAGAGACCCTTACTCGGGCCAAATTTGAAGAGCTGAA\n+rn3.chr3/271-391 CTTCTTCGAAGGAGAAGACTTCTCAGAGACCCTTACTCGGGCCAAATTTGAAGAGCTGAA\n+galGal2.chr17/271-391 CTTTTTTGAAGGAGAGGATTTCTCTGAGACGCTTACTCGTGCCAAATTTGAAGAACTGAA\n+fr1.chrUn/271-391 TTTCTTTGAGGGAGAAGATTTCTCCGAGACACTGACCCGTGCCAAATTTGAAGAGCTTAA\n+danRer1.chr11/271-391 CTTCTTTGAGGGAGAAGATTTCTCTGAGACTCTCACCAGAGCCAAGTTTGAAGAGCTCAA\n+\n+\n+CLUSTAL W(1.81) multiple sequence alignment\n+\n+\n+hg17.chr1_rev/271-391 TTGAGCTCTTCAAATTTGGCCTGAGTCAGGGTCTCAGAAAAGTCTTCTCCTTCATAGAAG\n+mm5.chr2_rev/271-391 TTCAGCTCTTCAAATTTGGCCCGAGTAAGGGTCTCTGAGAAGTCTTCTCCTTCGAAGAAG\n+rn3.chr3_rev/271-391 TTCAGCTCTTCAAATTTGGCCCGAGTAAGGGTCTCTGAGAAGTCTTCTCCTTCGAAGAAG\n+galGal2.chr17_rev/271-391 TTCAGTTCTTCAAATTTGGCACGAGTAAGCGTCTCAGAGAAATCCTCTCCTTCAAAAAAG\n+fr1.chrUn_rev/271-391 TTAAGCTCTTCAAATTTGGCACGGGTCAGTGTCTCGGAGAAATCTTCTCCCTCAAAGAAA\n+danRer1.chr11_rev/271-391 TTGAGCTCTTCAAACTTGGCTCTGGTGAGAGTCTCAGAGAAATCTTCTCCCTCAAAGAAG\n+\n+\n+hg17.chr1_rev/271-391 GACTCAATTTCAATTACTGCTTGCTTGATGTTGAGAAGACAGGGCCCGTTTGGCCTTTTC\n+mm5.chr2_rev/271-391 GACTCAATTTCAATC----CTTGCTTGATGCTGAGAAGACAAGGCTCTCTTAGCCTTTTC\n+rn3.chr3_rev/271-391 GACTCAATTTCAATC----CTCGCTTGATGCTGAGAAGACAGGGCTCTCTTGGCCTTTTC\n+galGal2.chr17_rev/271-391 GATTCTATTTCAATT----CTAGCTTGGTGCTGGGATGACAGGGCCCGCTTCGCTTTCTC\n+fr1.chrUn_rev/271-391 GACTCGATCTCAATG----CGGGCCTGGTGCTGGGCAGACAGGGCCCTCTTTGCCTTCTC\n+danRer1.chr11_rev/271-391 GACTCGATCTCGATG----CGGGCCTGATGCTGGGCAGACAGGGCTCTCTTAGCCTTCTC\n+\n+\n' |
| b |
| diff -r 000000000000 -r e123d5c6f489 test-data/unknown.rnaz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.rnaz Wed Jan 30 04:12:06 2019 -0500 |
| b |
| b'@@ -0,0 +1,720 @@\n+\n+############################ RNAz 2.1 ##############################\n+\n+ Sequences: 6\n+ Columns: 120\n+ Reading direction: forward\n+ Mean pairwise identity: 83.72\n+ Shannon entropy: 0.30516\n+ G+C content: 0.50000\n+ Mean single sequence MFE: -36.97\n+ Consensus MFE: -15.85\n+ Energy contribution: -15.72\n+ Covariance contribution: -0.13\n+ Combinations/Pair: 1.35\n+ Mean z-score: -0.44\n+ Structure conservation index: 0.43\n+ Background model: dinucleotide\n+ Decision model: sequence based alignment quality\n+ SVM decision value: -4.76\n+ SVM RNA-class probability: 0.000000\n+ Prediction: OTHER\n+\n+######################################################################\n+\n+>hg17.chr1/0-120\n+UACAGCAGCUGCUAUUGCUUAUGGCCUGGAUAAGAGGGAGGGGGAGAAGAACAUCCUGGUGUUUGACCUGGGUGGUGGAACCUUUGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU\n+.....(((..(((((.....)))))))).......((..((((((((...(((((..((.((((.(((.....))).))))))..))))).))))))))..))...((((....)))).. ( -39.90, z-score = -0.87, R)\n+>canFam1.chr9/0-120\n+UACAGCAGCUGCUAUUGCUUACGGCUUGGAUAAGAGGGAAGGGGAGAAGAAUAUCCUGGUGUUUGACCUGGGUGGUGGAACUUUUGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU\n+..((((....((....)).....)).)).......((..((((((((...(((((.....((((.(((.....))).))))....))))).))))))))..))...((((....)))).. ( -34.00, z-score = -0.16, R)\n+>mm5.chr2/0-120\n+UACAGCAGCUGCUAUUGCAUAUGGCCUGGAUAAGAGAGAGGGAGAGAAGAACAUCCUUGUGUUUGACCUGGGUGGCGGCACCUUCGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU\n+.....(((..(((((.....)))))))).......((((((((((((...(((((...(((((.(.((.....))))))))....))))).))))))))((((((.....)))))))))) ( -34.60, z-score = 0.44, R)\n+>galGal2.chr17/0-120\n+AACUGCUGCUGCAAUUGCAUACGGAUUGGACAAGAGAGAGGGUGAAAAGAACAUCCUUGUAUUUGACCUGGGUGGUGGAACUUUUGAUGUCUCCCUCCUGACAAUUGACAACGGAGUCUU\n+.(((.(((.((((((((((...(((..(((((.(((((((((((.......))))))....(((.(((.....))).))))))))..)))))...))))).)))))).)).))))))... ( -33.00, z-score = -0.79, R)\n+>fr1.chrUn/0-120\n+AACCGCUGCUGCCAUUGCUUAUGGUCUGGACAAAAAGGACGGCGAGAAGAACAUCCUCGUGUUCGAUCUCGGUGGCGGCACCUUCGACGUGUCUCUGCUCACCAUUGACAACGGUGUGUU\n+.((((((((..((...(((....((((.........)))))))((((.((((((....))))))..))))))..)))))..........((((..((.....))..))))..)))..... ( -39.10, z-score = -0.61, R)\n+>danRer1.chr11/0-120\n+UACGGCGGCUGCCAUUGCAUACGGUCUGGACAAGAGGGACGGAGAGAAAAACAUCCUGGUGUUCGAUCUGGGUGGUGGCACCUUUGACGUGUCUCUGCUGACCAUCGAUAACGGCGUGUU\n+((((.(((.((((((..(...(((..((((((...((((.(..........).))))..))))))..))).)..)))))))).((((.(.(((......)))).))))....).)))).. ( -41.20, z-score = -0.64, R)\n+>consensus\n+UACAGCAGCUGCUAUUGCAUACGGCCUGGACAAGAGGGAGGGAGAGAAGAACAUCCUGGUGUUUGACCUGGGUGGUGGAACCUUUGAUGUGUCUCUUCUCACCAUUGACAACGGUGUCUU\n+....(((.(..((((..(...(((..((((((...((((.(..........).))))..))))))..))).)..)))).....((((((((........))).)))))....).)))... (-15.85 = -15.72 + -0.13) \n+\n+############################ RNAz 2.1 ##############################\n+\n+ Sequences: 6\n+ Columns: 120\n+ Reading direction: reverse\n+ Mean pairwise identity: 83.72\n+ Shannon entropy: 0.30516\n+ G+C content: 0.50000\n+ Mean single sequence MFE: -30.48\n+ Consensus MFE: -16.68\n+ Energy contribution: -16.27\n+ Covariance contribution: -0.41\n+ Combinations/Pair: 1.38\n+ Mean z-score: -0.85\n+ Structure conservation index: 0.55\n+ Background model: dinucleotide\n+ Decision model: sequence based alignment quality\n+ SVM decision value: -2.64\n+ SVM RNA-class probability: 0.005929\n+ Prediction: OTHER\n+\n+######################################################################\n+\n+>hg17.chr1/0-120\n+AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAGGUUCCACCACCCAGGUCAAACACCAGGAUGUUCUUCUCCCCCUCCCUCUUAUCCAGGCCAUAAGCAAUAGCAGCUGCUGUA\n+..((((....)))).((((((((((((...(((((....(((..(((.....)))..))).....)))))))))))).........((.....))))))).....(((((....))))). ( -29.50, z-score = -1.08, R)\n+>canFam1.chr9/0-120\n+AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAAGUUCCACCACCCAGGUCAAACACCAGGAUAUUCUUCUCCCCUUCCCUCUUAUCCAAGCCGUAAGCAAUAGCAGCUGCUGUA\n+..((((....))))...((.((((((((....(((....(((..(((.....)))..))).....))).)))))))).))...............((.....)).(((((....))))). ( -24.60, z-sco'..b'((.....)))))).)) ( -34.40, z-score = 0.10, R)\n+>galGal2.chr17_rev/271-391\n+UUCAGUUCUUCAAAUUUGGCACGAGUAAGCGUCUCAGAGAAAUCCUCUCCUUCAAAAAAGGAUUCUAUUUCAAUU----CUAGCUUGGUGCUGGGAUGACAGGGCCCGCUUCGCUUUCUC\n+....((.((........)).))(((((((((.(((...(((((....(((((.....)))))....))))).(((----(((((.....))))))))....)))..))))).)))).... ( -27.00, z-score = 0.33, R)\n+>fr1.chrUn_rev/271-391\n+UUAAGCUCUUCAAAUUUGGCACGGGUCAGUGUCUCGGAGAAAUCUUCUCCCUCAAAGAAAGACUCGAUCUCAAUG----CGGGCCUGGUGCUGGGCAGACAGGGCCCUCUUUGCCUUCUC\n+.................((((((((((....(((.(((((.....))))).....)))..)))))).........----.((((((.((.((....)))).))))))....))))..... ( -34.20, z-score = 0.29, R)\n+>danRer1.chr11_rev/271-391\n+UUGAGCUCUUCAAACUUGGCUCUGGUGAGAGUCUCAGAGAAAUCUUCUCCCUCAAAGAAGGACUCGAUCUCGAUG----CGGGCCUGAUGCUGGGCAGACAGGGCUCUCUUAGCCUUCUC\n+..(((((..........))))).(((((((((((.(((....)))((((((....(..(((.((((((....)).----)))))))..)...))).)))..))))))))...)))..... ( -34.40, z-score = 1.40, R)\n+>consensus\n+UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCAGAGAAAUCUUCUCCUUCAAAGAAGGACUCAAUUUCAAUC____CUGGCUUGAUGCUGAGAAGACAGGGCCCUCUUAGCCUUCUC\n+...(((...(((.....(((((......)))))...((((((((((((.......)).))))))...))))..............))).))).....((.((((((.....)))))).)) (-22.01 = -20.72 + -1.30) \n+\n+############################ RNAz 2.1 ##############################\n+\n+ Sequences: 6\n+ Columns: 120\n+ Reading direction: reverse\n+ Mean pairwise identity: 82.22\n+ Shannon entropy: 0.33146\n+ G+C content: 0.47735\n+ Mean single sequence MFE: -32.55\n+ Consensus MFE: -18.57\n+ Energy contribution: -18.10\n+ Covariance contribution: -0.47\n+ Combinations/Pair: 1.42\n+ Mean z-score: -0.11\n+ Structure conservation index: 0.57\n+ Background model: dinucleotide\n+ Decision model: sequence based alignment quality\n+ SVM decision value: -3.82\n+ SVM RNA-class probability: 0.000001\n+ Prediction: OTHER\n+\n+######################################################################\n+\n+>hg17.chr1_rev/271-391\n+GAAAAGGCCAAACGGGCCCUGUCUUCUCAACAUCAAGCAAGCAGUAAUUGAAAUUGAGUCCUUCUAUGAAGGAGAAGACUUUUCUGAGACCCUGACUCAGGCCAAAUUUGAAGAGCUCAA\n+(((((((((.....))))..((((((((((..((((((.....))..))))..)))).((((((...)))))))))))))))))((((..((((...)))).((....)).....)))). ( -30.50, z-score = -0.31, R)\n+>mm5.chr2_rev/271-391\n+GAAAAGGCUAAGAGAGCCUUGUCUUCUCAGCAUCAAGCAAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA\n+((.((((((.....)))))).))...(((((........((----((((.......))))))((((((((.((((.....))))...(.(((......))).)...))))))))))))). ( -36.20, z-score = -0.98, R)\n+>rn3.chr3_rev/271-391\n+GAAAAGGCCAAGAGAGCCCUGUCUUCUCAGCAUCAAGCGAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA\n+.....((((..(((((....((((((((....(((((.(((----((((.......)))))))))).))..))))))))))))).(((.......))).))))................. ( -35.10, z-score = -0.51, R)\n+>galGal2.chr17_rev/271-391\n+GAGAAAGCGAAGCGGGCCCUGUCAUCCCAGCACCAAGCUAG----AAUUGAAAUAGAAUCCUUUUUUGAAGGAGAGGAUUUCUCUGAGACGCUUACUCGUGCCAAAUUUGAAGAACUGAA\n+(((.(((((.(((.((..(((......)))..))..)))..----..........(((((((((((....)))))))))))........))))).)))...................... ( -27.00, z-score = 0.10, R)\n+>fr1.chrUn_rev/271-391\n+GAGAAGGCAAAGAGGGCCCUGUCUGCCCAGCACCAGGCCCG----CAUUGAGAUCGAGUCUUUCUUUGAGGGAGAAGAUUUCUCCGAGACACUGACCCGUGCCAAAUUUGAAGAGCUUAA\n+.....((((....((((..((((((((........))).((----....((((((...(((..(.....)..))).))))))..)))))))..).))).))))................. ( -33.20, z-score = -0.02, R)\n+>danRer1.chr11_rev/271-391\n+GAGAAGGCUAAGAGAGCCCUGUCUGCCCAGCAUCAGGCCCG----CAUCGAGAUCGAGUCCUUCUUUGAGGGAGAAGAUUUCUCUGAGACUCUCACCAGAGCCAAGUUUGAAGAGCUCAA\n+((((.((((.....))))..(((((((........)))...----((..((((((...((((((...))))))...))))))..))))))))))....(((((.........).)))).. ( -33.30, z-score = 1.06, R)\n+>consensus\n+GAAAAGGCCAAGAGAGCCCUGUCUUCCCAGCAUCAAGCAAG____AAUUGAAAUUGAGUCCUUCUUUGAAGGAGAAGACUUCUCUGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA\n+.....((((....(((....((((((...((.....))....................((((((...))))))))))))..))).(((.......))).))))................. (-18.57 = -18.10 + -0.47) \n' |
| b |
| diff -r 000000000000 -r e123d5c6f489 test-data/unknown.rnaz.clustered --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.rnaz.clustered Wed Jan 30 04:12:06 2019 -0500 |
| b |
| @@ -0,0 +1,17 @@ +# windowID clusterID seqID start end strand N columns identity meanMFE consensusMFE energyTerm covarianceTerm combPerPair z SCI decValue P +GCwindow1 locus1 >hg17.chr1 0 120 + 6 120 83.72 -36.97 -15.85 -15.72 -0.13 1.35 -0.44 0.43 -4.76 0.000000 0.50000 +window2 locus1 >hg17.chr1 0 120 - 6 120 83.72 -30.48 -16.68 -16.27 -0.41 1.38 -0.85 0.55 -2.64 0.005929 0.50000 +window3 locus2 >hg17.chr1_rev 0 120 + 6 120 83.72 -30.48 -16.68 -16.27 -0.41 1.38 -0.85 0.55 -2.64 0.005929 0.50000 +window4 locus2 >hg17.chr1_rev 0 120 - 6 120 83.72 -36.97 -15.85 -15.72 -0.13 1.35 -0.44 0.43 -4.76 0.000000 0.50000 +window5 locus3 >hg17.chr1 120 240 + 6 120 85.83 -29.08 -17.18 -17.27 0.09 1.38 -0.03 0.59 -4.58 0.000000 0.46111 +window6 locus3 >hg17.chr1 120 240 - 6 120 85.83 -23.40 -9.31 -9.48 0.17 1.36 0.40 0.40 -7.30 0.000000 0.46111 +window7 locus4 >hg17.chr1_rev 120 240 + 6 120 85.83 -23.40 -9.31 -9.48 0.17 1.36 0.40 0.40 -7.30 0.000000 0.46111 +window8 locus4 >hg17.chr1_rev 120 240 - 6 120 85.83 -29.08 -17.18 -17.27 0.09 1.38 -0.03 0.59 -4.58 0.000000 0.46111 +window9 locus5 >hg17.chr1 240 360 + 6 120 80.00 -34.52 -15.70 -14.52 -1.19 1.43 0.11 0.45 -4.92 0.000000 0.50603 +window10 locus5 >hg17.chr1 240 360 - 6 120 80.00 -31.38 -17.15 -16.27 -0.88 1.50 0.17 0.55 -4.07 0.000000 0.50603 +window11 locus6 >hg17.chr1_rev 240 360 + 6 120 80.00 -31.38 -17.15 -16.27 -0.88 1.50 0.17 0.55 -4.07 0.000000 0.50603 +window12 locus6 >hg17.chr1_rev 240 360 - 6 120 80.00 -34.52 -15.70 -14.52 -1.19 1.43 0.11 0.45 -4.92 0.000000 0.50603 +window13 locus7 >hg17.chr1 271 391 + 6 120 82.22 -32.55 -18.57 -18.10 -0.47 1.42 -0.11 0.57 -3.82 0.000001 0.47735 +window14 locus7 >hg17.chr1 271 391 - 6 120 82.22 -33.18 -22.01 -20.72 -1.30 1.48 0.17 0.66 -3.58 0.000003 0.47735 +window15 locus8 >hg17.chr1_rev 271 391 + 6 120 82.22 -33.18 -22.01 -20.72 -1.30 1.48 0.17 0.66 -3.58 0.000003 0.47735 +window16 locus8 >hg17.chr1_rev 271 391 - 6 120 82.22 -32.55 -18.57 -18.10 -0.47 1.42 -0.11 0.57 -3.82 0.000001 0.47735 |
| b |
| diff -r 000000000000 -r e123d5c6f489 test-data/unknown.rnaz.clustered.annotated.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.rnaz.clustered.annotated.bed Wed Jan 30 04:12:06 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ +chr1 0 120 WhoKnows 0 + +chr1 0 120 WhoKnows2 0 - +chr1 120 240 WhoKnows 0 + +chr1 120 240 WhoKnows2 0 - +chr1 240 360 WhoKnows 0 + +chr1 240 360 WhoKnows2 0 - +chr1 271 391 WhoKnows 0 + +chr1 271 391 WhoKnows2 0 - |
| b |
| diff -r 000000000000 -r e123d5c6f489 test-data/unknown.rnaz.clustered.annotated.rnaz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.rnaz.clustered.annotated.rnaz Wed Jan 30 04:12:06 2019 -0500 |
| b |
| @@ -0,0 +1,9 @@ +# windowID clusterID seqID start end strand N columns identity meanMFE consensusMFE energyTerm covarianceTerm combPerPair z SCI decValue P Annotation +window3 locus2 >hg17.chr1_rev 0 120 + 6 120 83.72 -30.48 -16.68 -16.27 -0.41 1.38 -0.85 0.55 -2.64 0.005929 0.50000 WhoKnows +window4 locus2 >hg17.chr1_rev 0 120 - 6 120 83.72 -36.97 -15.85 -15.72 -0.13 1.35 -0.44 0.43 -4.76 0.000000 0.50000 WhoKnows2 +window7 locus4 >hg17.chr1_rev 120 240 + 6 120 85.83 -23.40 -9.31 -9.48 0.17 1.36 0.40 0.40 -7.30 0.000000 0.46111 WhoKnows +window8 locus4 >hg17.chr1_rev 120 240 - 6 120 85.83 -29.08 -17.18 -17.27 0.09 1.38 -0.03 0.59 -4.58 0.000000 0.46111 WhoKnows2 +window11 locus6 >hg17.chr1_rev 240 360 + 6 120 80.00 -31.38 -17.15 -16.27 -0.88 1.50 0.17 0.55 -4.07 0.000000 0.50603 WhoKnows +window12 locus6 >hg17.chr1_rev 240 360 - 6 120 80.00 -34.52 -15.70 -14.52 -1.19 1.43 0.11 0.45 -4.92 0.000000 0.50603 WhoKnows2 +window15 locus8 >hg17.chr1_rev 271 391 + 6 120 82.22 -33.18 -22.01 -20.72 -1.30 1.48 0.17 0.66 -3.58 0.000003 0.47735 WhoKnows +window16 locus8 >hg17.chr1_rev 271 391 - 6 120 82.22 -32.55 -18.57 -18.10 -0.47 1.42 -0.11 0.57 -3.82 0.000001 0.47735 WhoKnows2 |