| Previous changeset 2:434332033e82 (2018-04-13) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit 3abc213e109bb564de7dee75d71d90eb1bf78c7e |
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modified:
processMAF.sh rnacode.xml test-data/rnacode_result1.tabular test-data/rnacode_result2.gtf |
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added:
test-data/eps.eps test-data/eps.tar.gz test-data/hss-0.eps test-data/hss-1.eps |
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| diff -r 434332033e82 -r d49b9759e294 processMAF.sh --- a/processMAF.sh Fri Apr 13 07:40:08 2018 -0400 +++ b/processMAF.sh Thu Nov 15 01:24:06 2018 -0500 |
| [ |
| @@ -133,7 +133,7 @@ last=0 if [[ ! -z "$tabular" ]]; then - echo -e "HSS #\tFrame\tLength\tFrom\tTo\tName\tStart\tEnd\tScore\tP" >> ${outfile:-/dev/stdout} + echo -e "HSS #\tStrand\tFrame\tLength\tFrom\tTo\tName\tStart\tEnd\tScore\tP" >> ${outfile:-/dev/stdout} fi tmpif=$(mktemp -p '.') @@ -151,8 +151,7 @@ if [[ "$line" =~ ^# ]]; then echo -n > ${tmpif} elif [[ "$line" =~ ^$ ]]; then - run_rnacode ${args[@]} ${tmpif} - # >> ${outfile:-/dev/stdout} + run_rnacode ${args[@]} ${tmpif} >> ${outfile:-/dev/stdout} echo -n > ${tmpif} else if [[ -z $ref && "$line" =~ ^s ]]; then @@ -167,8 +166,7 @@ done < ${file:-/dev/stdin} # if there is something left -> process it if [[ "`cat ${tmpif} | wc -l`" -gt "0" ]]; then - run_rnacode ${args[@]} ${tmpif} - # >> ${outfile:-/dev/stdout} + run_rnacode ${args[@]} ${tmpif} >> ${outfile:-/dev/stdout} fi if [[ ! -z "$eps" ]]; then |
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| diff -r 434332033e82 -r d49b9759e294 rnacode.xml --- a/rnacode.xml Fri Apr 13 07:40:08 2018 -0400 +++ b/rnacode.xml Thu Nov 15 01:24:06 2018 -0500 |
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| @@ -1,7 +1,8 @@ -<tool id="rbc_rnacode" name="RNAcode" version="0.3.1"> +<tool id="rbc_rnacode" name="RNAcode" version="0.3.2"> <description>Analyze the protein coding potential in MSA.</description> <requirements> <requirement type="package" version="0.3">rnacode</requirement> + <requirement type="package" version="9.22">ghostscript</requirement> </requirements> <version_command>RNAcode --version</version_command> <command detect_errors="exit_code"> @@ -52,11 +53,22 @@ #elif $outputFormat.value == '--gtf' --outfile $outFileGTF #end if - + + ## add missing header + #if $cond_breakmaf.select_breakmaf != 'breakmaf' and $outputFormat.value == '--tabular': + && sed -i -e "1 i\HSS #\tStrand\tFrame\tLength\tFrom\tTo\tName\tStart\tEnd\tScore\tP" $outFileDefault #end if + + #if $cond_generateEPS.generateEPS == 'create' + #if $cond_generateEPS.imgoutfmt == 'zipeps' + && tar -czf '$out_eps_zip' eps + #else if $cond_generateEPS.imgoutfmt == 'eps' + && gs -sDEVICE=eps2write -dNOPAUSE -dBATCH -dSAFER -sOutputFile='$out_eps_mp' `ls -v eps/*.eps` + #end if + #end if ]]> </command> <inputs> - <param name="alignment" type="data" format="clustal,maf" label="Multiple Alignment" help="Alignment needs to be formatted in ClustalW or MAF format"/> + <param name="alignment" type="data" format="maf" label="Multiple Alignment" help="Alignment needs to be formatted in ClustalW or MAF format"/> <conditional name="cond_breakmaf"> <param name="select_breakmaf" type="select" label="Break long alignment blocks" help="If your alignments contain blocks of long genomic regions it is usually not reasonable to score these long regions as a whole."> <option value="keepmaf" selected="true">Process original alignment</option> @@ -85,13 +97,18 @@ </when> </conditional> <conditional name="cond_generateEPS"> - <param name="generateEPS" type="select" label="Create colored plots in EPS format" help="The generated plots are resolution independent vector graphics that can be included in any graphics software. For each high scoring segment below a given cutoff (see --eps-cutoff) a file named hss-N.eps is created (N is the running number of the high scoring segment)"> - <option value="create" selected="true">Create Plots</option> - <option value="nocreate">Do not generate EPS plots</option> + <param name="generateEPS" type="select" label="Create plots" help="The generated plots are resolution independent vector graphics that can be included in any graphics software. For each high scoring segment below a given cutoff (see --eps-cutoff) a file named hss-N.eps is created (N is the running number of the high scoring segment)"> + <option value="create">Create Plots</option> + <option value="nocreate" selected="true">Do not generate EPS plots</option> </param> <when value="create"> <param argument="--eps_cutoff" name="eps_cutoff" type="float" optional="true" value="0.05" label="Create plots only for high scoring segments with p better than:" help=""/> - </when> + <param name="imgoutfmt" type="select" label="Output format" help="For larger numbers of high scoring segments output to a collection can be slow. Choose zipped or single page eps in this case."> + <option value="sepeps" selected="true">separate eps in collection</option> + <option value="zipeps">zipped eps</option> + <option value="eps">multi page eps</option> + </param> + </when> <when value="nocreate"/> </conditional> @@ -107,24 +124,43 @@ <data name="outFileGTF" format="gtf" label="${tool.name} on ${on_string}"> <filter>outputFormat == '--gtf'</filter> </data> - <collection name="output_eps" type="list" label="Plots for ${tool.name} on ${on_string}"> - <filter>cond_generateEPS['generateEPS'] == "create"</filter> + <collection name="output_eps" type="list" label="Plots for ${tool.name} on ${on_string} (plots)"> + <filter>cond_generateEPS['generateEPS'] == "create" and cond_generateEPS['imgoutfmt'] == "sepeps"</filter> <discover_datasets pattern="(?P<designation>.*)\.eps" directory="eps" ext="eps"/> </collection> + <data name="out_eps_zip" format="zip" label="${tool.name} on ${on_string} (plots)"> + <filter>cond_generateEPS['generateEPS'] == "create" and cond_generateEPS['imgoutfmt'] == "zipeps"</filter> + </data> + <data name="out_eps_mp" format="eps" label="${tool.name} on ${on_string} (plots)"> + <filter>cond_generateEPS['generateEPS'] == "create" and cond_generateEPS['imgoutfmt'] == "eps"</filter> + </data> </outputs> <tests> <test> <param name="alignment" value="coding.aln"/> - <param name="generateEPS" value="nocreate"/> <param name="outputFormat" value="--tabular"/> <output name="outFileDefault" ftype="tabular" file="rnacode_result1.tabular" compare="sim_size"/> + <conditional name="cond_generateEPS"> + <param name="generateEPS" value="create"/> + <param name="eps_cutoff" value="0.05"/> + <param name="imgoutfmt" value="sepeps" /> + </conditional> + <output_collection name="output_eps" type="list" count="2"> + <element name="hss-0" file="hss-0.eps" ftype="eps" compare="sim_size" delta="50000"/> + <element name="hss-1" file="hss-1.eps" ftype="eps" compare="sim_size" delta="50000"/> + </output_collection> <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented --> </test> <test> <param name="alignment" value="coding.aln"/> - <param name="generateEPS" value="nocreate"/> + <conditional name="cond_generateEPS"> + <param name="generateEPS" value="create"/> + <param name="eps_cutoff" value="0.05"/> + <param name="imgoutfmt" value="zipeps" /> + </conditional> <param name="outputFormat" value="--tabular"/> <output name="outFileDefault" ftype="tabular" file="rnacode_result1.tabular" compare="sim_size"/> + <output name="out_eps_zip" ftype="zip" file="eps.tar.gz" compare="sim_size" delta="50000"/> <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented --> </test> <test> @@ -132,9 +168,14 @@ <conditional name="cond_breakmaf"> <param name="select_breakmaf" value="breakmaf"/> </conditional> - <param name="generateEPS" value="nocreate"/> + <conditional name="cond_generateEPS"> + <param name="generateEPS" value="create"/> + <param name="eps_cutoff" value="0.05"/> + <param name="imgoutfmt" value="eps" /> + </conditional> <param name="outputFormat" value="--gtf"/> <output name="outFileGTF" ftype="gtf" file="rnacode_result2.gtf" compare="sim_size"/> + <output name="out_eps_mp" ftype="eps" file="eps.eps" compare="sim_size" delta="50000"/> <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented --> </test> <test> |
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| diff -r 434332033e82 -r d49b9759e294 test-data/eps.eps --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/eps.eps Thu Nov 15 01:24:06 2018 -0500 |
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| b"@@ -0,0 +1,33175 @@\n+%!PS-Adobe-3.0 EPSF-3.0\n+%%BoundingBox: 0 6 584 377\n+%%HiResBoundingBox: 0.00 6.50 583.60 377.00\n+%%Creator: GPL Ghostscript 922 (eps2write)\n+%%LanguageLevel: 2\n+%%CreationDate: D:20180621162352+02'00'\n+%%Pages: 2\n+%%EndComments\n+%%BeginProlog\n+/DSC_OPDFREAD true def\n+/SetPageSize false def\n+/EPS2Write true def\n+currentdict/DSC_OPDFREAD known{\n+currentdict/DSC_OPDFREAD get\n+}{\n+false\n+}ifelse\n+10 dict begin\n+/DSC_OPDFREAD exch def\n+/this currentdict def\n+/y 720 def\n+/ebuf 200 string def\n+/prnt{\n+36//this/y get moveto//ebuf cvs show\n+//this/y 2 copy get 12 sub put\n+}bind def\n+/newline{\n+36//this/y get moveto\n+//this/y 2 copy get 12 sub put\n+}bind def\n+errordict/handleerror\n+{systemdict begin\n+$error begin\n+newerror\n+{(%%[ Error handled by opdfread.ps : )print errorname//ebuf cvs print(; OffendingCommand: )\n+print/command load//ebuf cvs print( ]%%)= flush\n+/newerror false store vmstatus pop pop 0 ne\n+{grestoreall\n+}if\n+errorname(VMerror)ne\n+{showpage\n+}if\n+initgraphics\n+0 720 moveto\n+errorname(VMerror)eq\n+{//this/ehsave known\n+{clear//this/ehsave get restore 2 vmreclaim\n+}if\n+vmstatus exch pop exch pop\n+}\n+/Courier 12 selectfont\n+{\n+(ERROR: )//prnt exec errorname//prnt exec\n+(OFFENDING COMMAND: )//prnt exec\n+/command load//prnt exec\n+$error/ostack known{\n+(%%[STACK:)=\n+(STACK:)//prnt exec\n+$error/ostack get aload length{\n+//newline exec\n+dup mark eq{\n+(-mark-)dup = show\n+}{\n+dup type/nametype eq{\n+dup xcheck not{\n+(/)show\n+(/)print\n+}if\n+}if\n+dup =//ebuf cvs show\n+}ifelse\n+}repeat\n+}if\n+}ifelse\n+(%%]%)=\n+//systemdict/showpage get exec\n+quit\n+}if\n+end\n+end\n+}bind readonly put\n+end\n+50 dict begin\n+/DefaultSwitch\n+{\n+dup where{\n+pop pop\n+}{\n+false def\n+}ifelse\n+}bind def\n+/=string 256 string def\n+/=only{\n+//=string cvs print\n+}bind def\n+/HexDigits(0123456789ABCDEF)readonly def\n+/PrintHex\n+{8{\n+dup -28 bitshift 15 and//HexDigits exch 1 getinterval//=only exec\n+4 bitshift\n+}repeat\n+pop\n+}bind def\n+/PDFR_DEBUG DefaultSwitch\n+/PDFR_DUMP DefaultSwitch\n+/PDFR_STREAM DefaultSwitch\n+/TTFDEBUG DefaultSwitch\n+/RotatePages DefaultSwitch\n+/FitPages DefaultSwitch\n+/CenterPages DefaultSwitch\n+/SetPageSize DefaultSwitch\n+/error\n+{\n+counttomark 1 sub -1 0{\n+index dup type/arraytype eq{==}{=only}ifelse\n+}for\n+()=\n+cleartomark\n+....Undefined\n+}bind def\n+//SetPageSize{\n+//RotatePages//FitPages or//CenterPages or{\n+mark(/RotatePages, /FitPages and CenterPages are not allowed with /SetPageSize)//error exec\n+}if\n+}\n+{\n+//FitPages//CenterPages and{\n+mark(CenterPages is not allowed with /FitPages)//error exec\n+}if\n+}\n+ifelse\n+/knownget\n+{\n+2 copy known{\n+get true\n+}{\n+pop pop false\n+}ifelse\n+}bind def\n+/IsUpper\n+{dup(A)0 get ge exch(Z)0 get le and\n+}bind def\n+/cpa2g{\n+dup length array\n+0 1 2 index length 1 sub{\n+dup 3 index exch get cp2g\n+3 copy put pop pop\n+}for\n+exch pop\n+}bind def\n+/cpd2g{\n+dup length dict exch{\n+cp2g 2 index 3 1 roll put\n+}forall\n+}bind def\n+/cps2g{\n+dup length string copy\n+}bind def\n+/cp2gprocs\n+<</arraytype//cpa2g/dicttype//cpd2g/packedarraytype//cpa2g/stringtype//cps2g >>\n+def\n+/cp2g{\n+dup gcheck not{\n+dup//cp2gprocs 1 index type\n+2 copy known{\n+get currentglobal 3 1 roll true setglobal exec exch setglobal\n+1 index wcheck not{readonly}if\n+1 index xcheck{cvx}if\n+exch pop\n+}{\n+pop pop\n+}ifelse\n+}if\n+}bind def\n+/BlockBuffer 65535 string def\n+/PDFReader currentdict def\n+/ObjectRegistryMaxLength 50000 def\n+/ObjectRegistry 10 dict def\n+ObjectRegistry\n+begin\n+0 ObjectRegistryMaxLength dict def\n+end\n+/CurrentObject null def\n+/DoneDocumentStructure false def\n+/GraphicState 20 dict begin\n+/InitialTextMatrix matrix def\n+/InitialMatrix matrix currentmatrix def\n+currentdict end def\n+/TempMatrix matrix def\n+/GraphicStateStack 20 array def\n+/GraphicStateStackPointer 0 def\n+/InitialTextMatrixStack 20 array def\n+/InitialTextMatrixStackPointer 0 def\n+/PDFColorSpaces 50 dict def\n+/InstalledFonts 50 dict def\n+/MacRomanEncodingInverse null def\n+currentglobal false setglobal\n+userdict/PDFR_InitialGS gstate put\n+userdict/PDFR_Patter"..b'Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2460 545 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 246 56 Tm\n+(C)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2340 460 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 234 47.5 Tm\n+(G)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2400 460 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 240 47.5 Tm\n+(C)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2460 460 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 246 47.5 Tm\n+(C)Tj\n+ET\n+Q\n+0.767578 0.939453 0.751953 RG\n+0.767578 0.939453 0.751953 rg\n+2340 375 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R8 10 Tf\n+1 0 0 1 234 39 Tm\n+(G)Tj\n+ET\n+Q\n+0.767578 0.939453 0.751953 RG\n+0.767578 0.939453 0.751953 rg\n+2400 375 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R8 10 Tf\n+1 0 0 1 240 39 Tm\n+(C)Tj\n+ET\n+Q\n+0.767578 0.939453 0.751953 RG\n+0.767578 0.939453 0.751953 rg\n+2460 375 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R8 10 Tf\n+1 0 0 1 246 39 Tm\n+(T)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2520 970 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R8 10 Tf\n+1 0 0 1 252 98.5 Tm\n+[(T)600(T)]TJ\n+/R6 10 Tf\n+6 8.5 Td\n+(C)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2580 970 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R8 10 Tf\n+1 0 0 1 258 98.5 Tm\n+[(G)600(G)]TJ\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2640 970 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R8 10 Tf\n+1 0 0 1 264 98.5 Tm\n+[(C)600(C)]TJ\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2520 885 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 252 90 Tm\n+(T)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2580 885 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 258 90 Tm\n+(G)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2640 885 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 264 90 Tm\n+(C)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2520 800 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 252 81.5 Tm\n+(T)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2580 800 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 258 81.5 Tm\n+(G)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2640 800 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 264 81.5 Tm\n+(C)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2520 715 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 252 73 Tm\n+(T)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2580 715 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 258 73 Tm\n+(G)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2640 715 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 264 73 Tm\n+(C)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2520 630 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 252 64.5 Tm\n+(T)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2580 630 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 258 64.5 Tm\n+(G)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2640 630 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 264 64.5 Tm\n+(C)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2520 545 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 252 56 Tm\n+(T)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2580 545 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 258 56 Tm\n+(G)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2640 545 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 264 56 Tm\n+(C)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2520 460 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 252 47.5 Tm\n+(T)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2580 460 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 258 47.5 Tm\n+(G)Tj\n+ET\n+Q\n+1 1 1 RG\n+1 1 1 rg\n+2640 460 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 264 47.5 Tm\n+(C)Tj\n+ET\n+Q\n+0.800781 G\n+0.800781 g\n+2520 375 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 252 39 Tm\n+(C)Tj\n+ET\n+Q\n+0.800781 G\n+0.800781 g\n+2580 375 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 258 39 Tm\n+(G)Tj\n+ET\n+Q\n+0.800781 G\n+0.800781 g\n+2640 375 60 85 re f\n+0 G\n+0 g\n+q\n+10 0 0 10 0 0 cm BT\n+/R6 10 Tf\n+1 0 0 1 264 39 Tm\n+(C)Tj\n+ET\n+Q\n+Q\n+\n+endstream\n+endobj\n+pagesave restore\n+%%PageTrailer\n+%%Trailer\n+end\n+%%EOF\n' |
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| diff -r 434332033e82 -r d49b9759e294 test-data/eps.tar.gz |
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| Binary file test-data/eps.tar.gz has changed |
| b |
| diff -r 434332033e82 -r d49b9759e294 test-data/hss-0.eps --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hss-0.eps Thu Nov 15 01:24:06 2018 -0500 |
| [ |
| b'@@ -0,0 +1,6005 @@\n+%!PS-Adobe-3.0 EPSF-3.0\n+%%BoundingBox: 0 0 744 377\n+%%EndComments\n+%Created by RNAcode; visit wash.github.com/rnacode\n+% draws box in color given by hue and saturation\n+/box { % x1 y1 x2 y2 hue saturation\n+ gsave\n+ dup 0.3 mul 1 exch sub sethsbcolor\n+ exch 3 index sub exch 2 index sub rectfill\n+ grestore\n+} def\n+% draws a box in current color\n+/box2 { % x1 y1 x2 y2\n+ exch 3 index sub exch 2 index sub rectfill\n+} def\n+/string { % (Text) x y\n+ 6 add\n+ moveto\n+ show\n+} def\n+0 377 translate\n+1 -1 scale\n+/Courier findfont\n+[10 0 0 -10 0 0] makefont setfont\n+0 setgray\n+(ec_K12.chr_fwd/3401506-3401703) 6.0 22.5 string\n+(58) 660.0 22.5 string\n+(ec_O157H7.chr_fwd/4138444-4138641) 6.0 31.0 string\n+(58) 660.0 31.0 string\n+(ec_APEC_O1.chr_fwd/3685781-3685978) 6.0 39.5 string\n+(58) 660.0 39.5 string\n+(ente638.chr_fwd/4000173-4000370) 6.0 48.0 string\n+(58) 660.0 48.0 string\n+(shigFlex_2A.chr_fwd/3391056-3391253) 6.0 56.5 string\n+(58) 660.0 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| b |
| diff -r 434332033e82 -r d49b9759e294 test-data/rnacode_result1.tabular --- a/test-data/rnacode_result1.tabular Fri Apr 13 07:40:08 2018 -0400 +++ b/test-data/rnacode_result1.tabular Thu Nov 15 01:24:06 2018 -0500 |
| b |
| @@ -1,7 +1,7 @@ -0 + 3 44 1 44 ec_K12.chr_fwd/3401506-3401703 3 134 39.108 2.206e-08 -1 - 3 32 12 43 ec_K12.chr_fwd/3401506-3401703 36 131 19.782 7.086e-04 -2 + 2 6 35 40 ec_K12.chr_fwd/3401506-3401703 104 121 2.738 0.999 +HSS # Strand Frame Length From To Name Start End Score P +0 + 3 44 1 44 ec_K12.chr_fwd/3401506-3401703 3 134 39.108 2.454e-10 +1 - 3 32 12 43 ec_K12.chr_fwd/3401506-3401703 36 131 19.782 9.920e-05 +2 + 2 6 35 40 ec_K12.chr_fwd/3401506-3401703 104 121 2.738 1.000 3 - 2 13 1 13 ec_K12.chr_fwd/3401506-3401703 2 40 2.426 1.000 4 - 3 5 6 10 ec_K12.chr_fwd/3401506-3401703 18 32 2.319 1.000 5 - 3 3 2 4 ec_K12.chr_fwd/3401506-3401703 6 14 1.736 1.000 -6 - 2 3 26 28 ec_K12.chr_fwd/3401506-3401703 77 85 1.344 1.000 |
| b |
| diff -r 434332033e82 -r d49b9759e294 test-data/rnacode_result2.gtf --- a/test-data/rnacode_result2.gtf Fri Apr 13 07:40:08 2018 -0400 +++ b/test-data/rnacode_result2.gtf Thu Nov 15 01:24:06 2018 -0500 |
| b |
| @@ -1,7 +1,6 @@ -chr RNAcode CDS 3401509 3401640 39.11|5.98e-10 + . gene_id "Gene0"; transcript_id "transcript 0"; -chr RNAcode CDS 3401574 3401669 19.78|1.33e-04 - . gene_id "Gene1"; transcript_id "transcript 0"; +chr RNAcode CDS 3401509 3401640 39.11|5.94e-10 + . gene_id "Gene0"; transcript_id "transcript 0"; +chr RNAcode CDS 3401574 3401669 19.78|1.36e-04 - . gene_id "Gene1"; transcript_id "transcript 0"; chr RNAcode CDS 3401610 3401627 2.74|9.99e-01 + . gene_id "Gene2"; transcript_id "transcript 0"; chr RNAcode CDS 3401665 3401703 2.43|1.00e+00 - . gene_id "Gene3"; transcript_id "transcript 0"; chr RNAcode CDS 3401673 3401687 2.32|1.00e+00 - . gene_id "Gene4"; transcript_id "transcript 0"; chr RNAcode CDS 3401691 3401699 1.74|1.00e+00 - . gene_id "Gene5"; transcript_id "transcript 0"; -chr RNAcode CDS 3401620 3401628 1.34|1.00e+00 - . gene_id "Gene6"; transcript_id "transcript 0"; |