Repository 'graphclust_preprocessing'
hg clone https://toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_preprocessing

Changeset 8:a04e93fdb40a (2017-05-24)
Previous changeset 7:07ad2d77f28a (2017-05-22) Next changeset 9:0690d59881b9 (2017-06-01)
Commit message:
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 9a3dc91fa984be18fabc0d968360634d787c9589
modified:
preprocessing.xml
splitSHAPE.py
added:
test-data/sample_3.fa
test-data/sample_3.react
test-data/sample_3_shape_data_split.react
b
diff -r 07ad2d77f28a -r a04e93fdb40a preprocessing.xml
--- a/preprocessing.xml Mon May 22 12:45:22 2017 -0400
+++ b/preprocessing.xml Wed May 24 09:57:18 2017 -0400
[
@@ -47,6 +47,15 @@
             <output name="data.names" file="FASTA/data.names"/>
             <output name="data.fasta.scan" file="FASTA/data.fasta.scan" />
         </test>
+
+        <test>
+            <param name="fastaFile" value="sample_3.fa"/>
+            <param name="SHAPEdata" value="sample_3.react"/>
+            <param name="max_length" value="100"/>
+            <param name="in_winShift" value="50"/>
+            <param name="min_seq_length" value="5"/>
+            <output name="shape_data_split" file="sample_3_shape_data_split.react" />
+        </test>        
     </tests>
     <help>
 <![CDATA[
b
diff -r 07ad2d77f28a -r a04e93fdb40a splitSHAPE.py
--- a/splitSHAPE.py Mon May 22 12:45:22 2017 -0400
+++ b/splitSHAPE.py Wed May 24 09:57:18 2017 -0400
[
@@ -56,8 +56,8 @@
     for j in react_val[int(chunks[1])-1:int(chunks[2])]:
         id_s = int(j.split()[0])
 
-        if id_s > win_size:
-            id_s = id_s - int(chunks[1])
+
+        id_s = id_s - int(chunks[1]) + 1
         toWrite += str(id_s) + '\t' + j.split()[1] + "\n"
 
 with open("shape_data_split.react", 'w') as out:
b
diff -r 07ad2d77f28a -r a04e93fdb40a test-data/sample_3.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_3.fa Wed May 24 09:57:18 2017 -0400
b
@@ -0,0 +1,6 @@
+>SECIS_1 test
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+>6S_1 test1
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+>6S_2
+UUGUCCCUGCCGUGCUCGUGACUUGGCCAUACAUUCUCUGAACCUAUGUCUUACGGCAUAUGGGUUGCGGGAGUGUAGAGCUGGAGUGAUCGUCUACUCGUAGACGAACCCGAUGCUCUUCGGAUCGCGACCACCUUGAACCUCAGGGUUCGAGAUGCCGGCCUUGACGGCACAGGCGGGGCAUC
b
diff -r 07ad2d77f28a -r a04e93fdb40a test-data/sample_3.react
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_3.react Wed May 24 09:57:18 2017 -0400
b
@@ -0,0 +1,447 @@
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\ No newline at end of file
b
diff -r 07ad2d77f28a -r a04e93fdb40a test-data/sample_3_shape_data_split.react
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_3_shape_data_split.react Wed May 24 09:57:18 2017 -0400
b
b'@@ -0,0 +1,670 @@\n+>1 SEQ1#1#63#+\n+1\t0.0657466222\n+2\t0.1280448842\n+3\t0.2786665403\n+4\t0.1391216354\n+5\t0.0272299574\n+6\t0.1717063095\n+7\t0.488732281\n+8\t3.3015172695\n+9\t0.414494604\n+10\t0.1957445189\n+11\t0.4670328791\n+12\t0.1943420556\n+13\t0.2099109521\n+14\t0.5846784488\n+15\t0.1296563697\n+16\t0.0359267698\n+17\t0.0438238841\n+18\t1.6364597431\n+19\t1.72206594665E-17\n+20\t0.0099928394\n+21\t0.0475042774\n+22\t0.0065948845\n+23\t0.0574522715\n+24\t0.2126102485\n+25\t1.2006488448\n+26\t0.6040825271\n+27\t0.4114049219\n+28\t1.1514597937\n+29\t1.216707413\n+30\t0.0186005737\n+31\t0.0841609069\n+32\t0.086771667\n+33\t1.1672973211\n+34\t0.8144419625\n+35\t0.2583987716\n+36\t0.0182542709\n+37\t0.0875979754\n+38\t0.094456587\n+39\t0.5206337515\n+40\t0.000517531\n+41\t0.0253820905\n+42\t0.2076338063\n+43\t0.0087295599\n+44\t0.0129264641\n+45\t0.0127365182\n+46\t0.1193338151\n+47\t0.0186183812\n+48\t0.3581141112\n+49\t0.0941009884\n+50\t0.2050905673\n+51\t0.0209195644\n+52\t0.6030952711\n+53\t5.2129588113\n+54\t0.1747678483\n+55\t1.2231479801\n+56\t0.4978854319\n+57\t0.5711590135\n+58\t0.2793524314\n+59\t0.0037936012\n+60\t0.2158137729\n+61\t0.5646393912\n+62\t0.6229186627\n+63\t0.0193621982\n+>2 SEQ2#1#100#+\n+1\t0.1158690877\n+2\t0.0774028501\n+3\t0.2349947573\n+4\t1.72206594665E-17\n+5\t0.0926174169\n+6\t0.0505177415\n+7\t0.0457131819\n+8\t0.0194615986\n+9\t2.1495069267\n+10\t0.0409639397\n+11\t0.2185631969\n+12\t0.1776745985\n+13\t0.0086422926\n+14\t0.0241577615\n+15\t0.0092855631\n+16\t0.3453240509\n+17\t0.1535840586\n+18\t0.0180643958\n+19\t0.1188776616\n+20\t0.3091581196\n+21\t0.3748109806\n+22\t0.6187506508\n+23\t0.3511511383\n+24\t0.6512026704\n+25\t0.3096370415\n+26\t0.5283368492\n+27\t0.7500060952\n+28\t0.0352720444\n+29\t0.3776026196\n+30\t0.3489100484\n+31\t1.3035405919\n+32\t0.1023638167\n+33\t0.133082988\n+34\t0.0024118398\n+35\t0.0281166587\n+36\t0.2818828676\n+37\t0.1316060603\n+38\t0.1813992598\n+39\t0.0047490217\n+40\t0.0204058553\n+41\t0.0675891142\n+42\t0.045119933\n+43\t0.0266727645\n+44\t0.0673921107\n+45\t0.0085752561\n+46\t0.495476266\n+47\t0.8224799434\n+48\t0.5574272341\n+49\t0.2431151153\n+50\t0.256015696\n+51\t0.0386339787\n+52\t0.6618567864\n+53\t0.0707284393\n+54\t1.1215284869\n+55\t0.0463423016\n+56\t0.3338809513\n+57\t0.3987796157\n+58\t1.1046527917\n+59\t0.6156154318\n+60\t0.1179259769\n+61\t2.0333569471\n+62\t0.1224421595\n+63\t0.0266055429\n+64\t0.0298356423\n+65\t0.3004015135\n+66\t2.1966900004\n+67\t0.0222153137\n+68\t0.0095300422\n+69\t0.0503009918\n+70\t0.0418994997\n+71\t0.0384566069\n+72\t2.6211662666\n+73\t0.1704872628\n+74\t0.8386436572\n+75\t0.6961218859\n+76\t0.1995308419\n+77\t0.0552442152\n+78\t0.1937915065\n+79\t0.1239592493\n+80\t0.0782601391\n+81\t0.0138965117\n+82\t0.0231978646\n+83\t0.0150709773\n+84\t0.4084290821\n+85\t0.0792668417\n+86\t1.0630476211\n+87\t0.2524739666\n+88\t0.0229636507\n+89\t0.1153934877\n+90\t0.2693801005\n+91\t0.0071337145\n+92\t1.0279231796\n+93\t0.0574241281\n+94\t0.103312087\n+95\t0.2100864561\n+96\t0.0252070712\n+97\t0.6067864142\n+98\t0.0607860625\n+99\t0.5416948523\n+100\t0.7090251541\n+>3 SEQ2#51#150#+\n+1\t0.0386339787\n+2\t0.6618567864\n+3\t0.0707284393\n+4\t1.1215284869\n+5\t0.0463423016\n+6\t0.3338809513\n+7\t0.3987796157\n+8\t1.1046527917\n+9\t0.6156154318\n+10\t0.1179259769\n+11\t2.0333569471\n+12\t0.1224421595\n+13\t0.0266055429\n+14\t0.0298356423\n+15\t0.3004015135\n+16\t2.1966900004\n+17\t0.0222153137\n+18\t0.0095300422\n+19\t0.0503009918\n+20\t0.0418994997\n+21\t0.0384566069\n+22\t2.6211662666\n+23\t0.1704872628\n+24\t0.8386436572\n+25\t0.6961218859\n+26\t0.1995308419\n+27\t0.0552442152\n+28\t0.1937915065\n+29\t0.1239592493\n+30\t0.0782601391\n+31\t0.0138965117\n+32\t0.0231978646\n+33\t0.0150709773\n+34\t0.4084290821\n+35\t0.0792668417\n+36\t1.0630476211\n+37\t0.2524739666\n+38\t0.0229636507\n+39\t0.1153934877\n+40\t0.2693801005\n+41\t0.0071337145\n+42\t1.0279231796\n+43\t0.0574241281\n+44\t0.103312087\n+45\t0.2100864561\n+46\t0.0252070712\n+47\t0.6067864142\n+48\t0.0607860625\n+49\t0.5416948523\n+50\t0.7090251541\n+51\t2.0470096713\n+52\t0.0368697578\n+53\t0.1221648319\n+54\t0.0484836208\n+55\t0.7188621431\n+56\t0.2405585888\n+57\t0.1071170724\n+58\t0.6859305671\n+59\t0.0997679124\n+60\t0.0342400356\n+61\t0.0201635\n+62\t0.4527960874\n+63\t0.7018417748\n+64\t0.2561295384\n+65\t0.2788440973\n+66\t0.2437240042\n+67\t0.0984135237\n+68\t0.1146045041\n+69\t0.2116296362\n+70\t0.0360702095\n'..b'8878178\n+67\t0.0331980613\n+68\t0.2884058117\n+69\t0.1471099733\n+70\t0.0250835628\n+71\t0.0040433138\n+72\t2.1207460501\n+73\t0.7413016698\n+74\t0.2856087978\n+75\t0.1043896327\n+76\t2.5426831833\n+77\t0.024753755\n+78\t0.0197741979\n+79\t0.0256614712\n+80\t0.0931195919\n+81\t0.2341548619\n+82\t0.9442989\n+83\t0.6902004027\n+84\t0.2615426874\n+85\t0.1968596889\n+86\t0.1317761893\n+87\t0.3101105886\n+88\t0.3109082689\n+89\t0.6036478733\n+90\t0.1383132052\n+91\t1.72206594665E-17\n+92\t1.3701244222\n+93\t0.0259262955\n+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