| Previous changeset 6:7f9cf152cf8f (2020-04-16) Next changeset 8:c836a05bd6a3 (2020-05-29) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440" |
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modified:
chira_merge.xml macros.xml test-data/alignments.bed test-data/annotation.gtf test-data/chimeras test-data/ref1.fasta test-data/ref2.fasta |
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| diff -r 7f9cf152cf8f -r 35f433d0bd7f chira_merge.xml --- a/chira_merge.xml Thu Apr 16 13:23:11 2020 -0400 +++ b/chira_merge.xml Thu May 07 03:35:27 2020 -0400 |
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| @@ -20,6 +20,11 @@ #else: -ao '$merge.alignment_overlap' #end if + #if str($reference.ref_type) == "split": + -f1 '$reference.ref_fasta1' + -f2 '$reference.ref_fasta2' + #end if + $chimeric_only -o ./ ]]></command> @@ -59,6 +64,22 @@ help="scale stddev for a single read"/> </when> </conditional> + <conditional name="reference"> + <param name="ref_type" type="select" label="Did you use single or split reference for alignment?"> + <option value="single">Single reference</option> + <option value="split">Split reference</option> + </param> + <when value="split"> + <param format="fasta" name="ref_fasta1" type="data" label="Reference FASTA file" + help="Reference fasta file"/> + <param format="fasta" name="ref_fasta2" type="data" label="Second reference FASTA file" + help="Second reference fasta file."/> + </when> + <when value="single"> + <!-- no need to provide a fasta file --> + </when> + </conditional> + <param name="chimeric_only" type="boolean" truevalue="-c" falsevalue="" checked="false" /> </inputs> <outputs> <data format="bed" name="segments_bed" from_work_dir="segments.bed" label="ChiRA aligned read segments on ${on_string}"/> @@ -70,15 +91,18 @@ <test expect_num_outputs="2"> <param name="alignments" value="alignments.bed"/> <param name="choice" value="no" /> + <param name="ref_type" value="split"/> + <param name="ref_fasta1" value="ref1.fasta"/> + <param name="ref_fasta2" value="ref2.fasta"/> <output name="segments_bed" > <assert_contents> - <has_text_matching expression="ENSMUST00000160533\t69\t82\t34\|1\|2,ENSMUST00000160533,69,82,\+,42S13M\t1\t\+" /> + <has_text_matching expression="ENSMUST00000146006\t6703\t6718\t10\|2\|3,ENSMUST00000146006,6703,6718,\+,24S15M16S\t1\t\+" /> </assert_contents> </output> <output name="merged_bed" > <assert_contents> <has_text_matching expression="ENSMUST00000182010\t408\t477\t\+" /> - <has_text_matching expression="mmu-miR-106a-3p\t4\t15\t\+" /> + <has_text_matching expression="mmu-miR-9-5p\t0\t23\t\+" /> </assert_contents> </output> </test> @@ -87,15 +111,19 @@ <param name="alignments" value="alignments.bed" /> <param name="choice" value="yes" /> <param name="gtf" value="annotation.gtf" /> + <param name="ref_type" value="split"/> + <param name="ref_fasta1" value="ref1.fasta"/> + <param name="ref_fasta2" value="ref2.fasta"/> <output name="segments_bed" > <assert_contents> - <has_text_matching expression="5\t137142331\t137142344\t34\|1\|2,ENSMUST00000160533,69,82,\+,42S13M\t1\t-" /> + <has_text_matching expression="2\t31033086\t31033109\t38\|2\|2,ENSMUST00000113555,1676,1699,\+,32S23M\t1\t-" /> + <has_text_matching expression="7\t83738820\t83738843\t38\|2\|1,mmu-miR-9-5p,0,23,\+,5S23M27S\t1\t\+" /> </assert_contents> </output> <output name="merged_bed" > <assert_contents> - <has_text_matching expression="17\t39846957\t39847016\t\+" /> - <has_text_matching expression="5\t137142331\t137142344\t-" /> + <has_text_matching expression="2\t31033086\t31033109\t-" /> + <has_text_matching expression="7\t83738820\t83738843\t\+" /> </assert_contents> </output> </test> @@ -106,14 +134,39 @@ <param name="gtf" value="annotation.gtf" /> <param name="mode" value="blockbuster" /> <param name="min_cluster_height" value="5" /> + <param name="ref_type" value="split"/> + <param name="ref_fasta1" value="ref1.fasta"/> + <param name="ref_fasta2" value="ref2.fasta"/> <output name="segments_bed" > <assert_contents> - <has_text_matching expression="5\t137142331\t137142344\t34\|1\|2,ENSMUST00000160533,69,82,\+,42S13M\t1\t-" /> + <has_text_matching expression="2\t31033086\t31033109\t38\|2\|2,ENSMUST00000113555,1676,1699,\+,32S23M\t1\t-" /> + <has_text_matching expression="7\t83738820\t83738843\t38\|2\|1,mmu-miR-9-5p,0,23,\+,5S23M27S\t1\t\+" /> </assert_contents> </output> <output name="merged_bed" > <assert_contents> - <has_text_matching expression="17\t39846957\t39847016\t\+" /> + <has_text_matching expression="7\t83738820\t83738843\t\+" /> + </assert_contents> + </output> + </test> + <!-- Test: Chimeric only without annotation --> + <test expect_num_outputs="2"> + <param name="alignments" value="alignments.bed"/> + <param name="choice" value="no" /> + <param name="ref_type" value="split"/> + <param name="ref_fasta1" value="ref1.fasta"/> + <param name="ref_fasta2" value="ref2.fasta"/> + <param name="chimeric_only" value="true"/> + <output name="segments_bed" > + <assert_contents> + <has_text_matching expression="mmu-miR-9-5p\t0\t23\t38\|2\|1,mmu-miR-9-5p,0,23,\+,5S23M27S\t1\t\+" /> + <has_text_matching expression="ENSMUST00000113555\t1676\t1699\t38\|2\|2,ENSMUST00000113555,1676,1699,\+,32S23M\t1\t\+" /> + </assert_contents> + </output> + <output name="merged_bed" > + <assert_contents> + <has_text_matching expression="ENSMUST00000113555\t1676\t1699\t\+" /> + <has_text_matching expression="mmu-miR-9-5p\t0\t23\t\+" /> </assert_contents> </output> </test> |
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| diff -r 7f9cf152cf8f -r 35f433d0bd7f macros.xml --- a/macros.xml Thu Apr 16 13:23:11 2020 -0400 +++ b/macros.xml Thu May 07 03:35:27 2020 -0400 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy</token> - <token name="@TOOL_VERSION@">1.1.5</token> + <token name="@TOOL_VERSION@">1.2.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">chira</requirement> |
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| diff -r 7f9cf152cf8f -r 35f433d0bd7f test-data/alignments.bed --- a/test-data/alignments.bed Thu Apr 16 13:23:11 2020 -0400 +++ b/test-data/alignments.bed Thu May 07 03:35:27 2020 -0400 |
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| b'@@ -1,337 +1,337 @@\n-mmu-miR-124-3p\t0\t20\t3|2,mmu-miR-124-3p,0,20,+,5S20M30S\t1\t+\n-ENSMUST00000182884\t6023\t6051\t28|3,ENSMUST00000182884,6023,6051,+,27S28M\t1\t+\n-ENSMUST00000182010\t428\t477\t36|10,ENSMUST00000182010,428,477,+,5S49M1S\t1\t+\n-ENSMUST00000113560\t1969\t1992\t38|2,ENSMUST00000113560,1969,1992,+,32S23M\t1\t+\n+ENSMUST00000049393\t5443\t5458\t10|2,ENSMUST00000049393,5443,5458,+,16S15M24S\t1\t+\n+ENSMUST00000099265\t1630\t1645\t10|2,ENSMUST00000099265,1630,1645,+,10S15M30S\t1\t+\n+ENSMUST00000105900\t7194\t7209\t10|2,ENSMUST00000105900,7194,7209,+,24S15M16S\t1\t+\n+ENSMUST00000105902\t8013\t8028\t10|2,ENSMUST00000105902,8013,8028,+,24S15M16S\t1\t+\n+ENSMUST00000111813\t56\t73\t10|2,ENSMUST00000111813,56,73,+,38S17M\t1\t+\n+ENSMUST00000140487\t2875\t2890\t10|2,ENSMUST00000140487,2875,2890,+,23S15M17S\t1\t+\n+ENSMUST00000146006\t6703\t6718\t10|2,ENSMUST00000146006,6703,6718,+,24S15M16S\t1\t+\n+ENSMUST00000165055\t615\t630\t10|2,ENSMUST00000165055,615,630,+,12S15M28S\t1\t+\n+ENSMUST00000168430\t291\t306\t10|2,ENSMUST00000168430,291,306,+,12S15M28S\t1\t+\n+mmu-miR-188-3p\t1\t11\t10|2,mmu-miR-188-3p,1,11,+,22S10M23S\t1\t+\n+mmu-miR-7651-3p\t9\t19\t10|2,mmu-miR-7651-3p,9,19,+,16S10M29S\t1\t+\n+ENSMUST00000028829\t496\t511\t11|1,ENSMUST00000028829,496,511,+,29S15M11S\t1\t+\n+ENSMUST00000039796\t1502\t1517\t11|1,ENSMUST00000039796,1502,1517,+,33S15M7S\t1\t+\n+ENSMUST00000100301\t1765\t1780\t11|1,ENSMUST00000100301,1765,1780,+,35S15M5S\t1\t+\n+ENSMUST00000110901\t232\t247\t11|1,ENSMUST00000110901,232,247,+,29S15M11S\t1\t+\n+ENSMUST00000118936\t1387\t1402\t11|1,ENSMUST00000118936,1387,1402,+,33S15M7S\t1\t+\n+ENSMUST00000172109\t1499\t1514\t11|1,ENSMUST00000172109,1499,1514,+,35S15M5S\t1\t+\n+ENSMUST00000181221\t1499\t1514\t11|1,ENSMUST00000181221,1499,1514,+,35S15M5S\t1\t+\n+ENSMUST00000181455\t1765\t1780\t11|1,ENSMUST00000181455,1765,1780,+,35S15M5S\t1\t+\n mmu-miR-9-5p\t0\t23\t11|1,mmu-miR-9-5p,0,23,+,5S23M27S\t1\t+\n-mmu-miR-9-5p\t0\t23\t38|2,mmu-miR-9-5p,0,23,+,5S23M27S\t1\t+\n-ENSMUST00000138581\t1621\t1644\t38|2,ENSMUST00000138581,1621,1644,+,32S23M\t1\t+\n-ENSMUST00000182010\t419\t468\t34|1,ENSMUST00000182010,419,468,+,5S49M1S\t1\t+\n-ENSMUST00000047061\t2204\t2232\t28|3,ENSMUST00000047061,2204,2232,+,27S28M\t1\t+\n-ENSMUST00000100207\t1580\t1603\t38|2,ENSMUST00000100207,1580,1603,+,32S23M\t1\t+\n-ENSMUST00000172109\t1499\t1514\t11|1,ENSMUST00000172109,1499,1514,+,35S15M5S\t1\t+\n-ENSMUST00000182795\t2429\t2457\t28|3,ENSMUST00000182795,2429,2457,+,27S28M\t1\t+\n-ENSMUST00000075326\t1661\t1684\t38|2,ENSMUST00000075326,1661,1684,+,32S23M\t1\t+\n-ENSMUST00000106215\t953\t1003\t21|3,ENSMUST00000106215,953,1003,+,5S50M\t1\t+\n-ENSMUST00000182439\t2218\t2246\t28|3,ENSMUST00000182439,2218,2246,+,27S28M\t1\t+\n-ENSMUST00000185502\t4240\t4290\t7|1,ENSMUST00000185502,4240,4290,+,5S50M\t1\t+\n-ENSMUST00000166060\t435\t467\t19|2,ENSMUST00000166060,435,467,+,26S12M3D17M\t1\t+\n+ENSMUST00000182010\t409\t445\t12|3,ENSMUST00000182010,409,445,+,5S36M14S\t1\t+\n+ENSMUST00000182010\t409\t459\t12|3,ENSMUST00000182010,409,459,+,5S50M\t1\t+\n+ENSMUST00000182010\t446\t459\t12|3,ENSMUST00000182010,446,459,+,42S13M\t1\t+\n+mmu-miR-22-3p\t8\t18\t12|3,mmu-miR-22-3p,8,18,+,10M45S\t1\t+\n+mmu-miR-335-3p\t1\t10\t12|3,mmu-miR-335-3p,1,10,+,12S9M34S\t1\t+\n+ENSMUST00000006311\t2407\t2420\t13|8,ENSMUST00000006311,2407,2420,+,13M42S\t1\t+\n+ENSMUST00000099628\t995\t1008\t13|8,ENSMUST00000099628,995,1008,+,13M42S\t1\t+\n+ENSMUST00000106220\t383\t396\t13|8,ENSMUST00000106220,383,396,+,13M42S\t1\t+\n+ENSMUST00000147228\t572\t585\t13|8,ENSMUST00000147228,572,585,+,13M42S\t1\t+\n+ENSMUST00000182010\t0\t46\t13|8,ENSMUST00000182010,0,46,+,9S46M\t1\t+\n+mmu-miR-106a-3p\t6\t15\t13|8,mmu-miR-106a-3p,6,15,+,21S9M25S\t1\t+\n+mmu-miR-1943-3p\t2\t11\t13|8,mmu-miR-1943-3p,2,11,+,20S9M26S\t1\t+\n+mmu-miR-7677-5p\t14\t25\t13|8,mmu-miR-7677-5p,14,25,+,26S11M18S\t1\t+\n+ENSMUST00000041591\t326\t377\t1|3,ENSMUST00000041591,326,377,+,4S51M\t1\t+\n+ENSMUST00000167541\t285\t336\t1|3,ENSMUST00000167541,285,336,+,4S51M\t1\t+\n+ENSMUST00000171545\t470\t521\t1|3,ENSMUST00000171545,470,521,+,4S51M\t1\t+\n+ENSMUST00000173516\t342\t393\t1|3,ENSMUST00000173516,342,393,+,4S51M\t1\t+\n+mmu-miR-7046-5p\t8\t19\t1|3,mmu-miR-7046-5p,8,19,+,11S11M33S\t1\t+\n+ENSMUST00000075012\t856\t906\t14|1,ENSMUST'..b',1902,+,39S15M1S\t1\t+\n-ENSMUST00000137408\t2183\t2198\t26|1,ENSMUST00000137408,2183,2198,+,39S15M1S\t1\t+\n-ENSMUST00000189036\t14\t25\t20|1,ENSMUST00000189036,14,25,+,41S11M2S\t1\t+\n-ENSMUST00000000254\t463\t474\t20|1,ENSMUST00000000254,463,474,+,41S11M2S\t1\t+\n-ENSMUST00000138762\t6784\t6795\t20|1,ENSMUST00000138762,6784,6795,+,43S11M\t1\t+\n-ENSMUST00000129785\t2240\t2251\t20|1,ENSMUST00000129785,2240,2251,+,42S11M1S\t1\t+\n-ENSMUST00000166429\t2767\t2778\t20|1,ENSMUST00000166429,2767,2778,+,41S11M2S\t1\t+\n-ENSMUST00000136610\t265\t276\t20|1,ENSMUST00000136610,265,276,+,42S11M1S\t1\t+\n-ENSMUST00000131422\t2324\t2335\t20|1,ENSMUST00000131422,2324,2335,+,42S11M1S\t1\t+\n-ENSMUST00000142388\t401\t412\t20|1,ENSMUST00000142388,401,412,+,41S11M2S\t1\t+\n-ENSMUST00000075789\t241\t252\t20|1,ENSMUST00000075789,241,252,+,41S11M2S\t1\t+\n-ENSMUST00000053969\t2571\t2582\t20|1,ENSMUST00000053969,2571,2582,+,41S11M2S\t1\t+\n-ENSMUST00000030826\t1172\t1183\t20|1,ENSMUST00000030826,1172,1183,+,42S11M1S\t1\t+\n-ENSMUST00000113169\t7470\t7481\t20|1,ENSMUST00000113169,7470,7481,+,43S11M\t1\t+\n-ENSMUST00000149694\t433\t444\t20|1,ENSMUST00000149694,433,444,+,43S11M\t1\t+\n-ENSMUST00000081569\t891\t902\t20|1,ENSMUST00000081569,891,902,+,43S11M\t1\t+\n-ENSMUST00000073639\t2840\t2851\t20|1,ENSMUST00000073639,2840,2851,+,43S11M\t1\t+\n-ENSMUST00000127216\t2946\t2957\t20|1,ENSMUST00000127216,2946,2957,+,42S11M1S\t1\t+\n-ENSMUST00000087085\t1296\t1307\t20|1,ENSMUST00000087085,1296,1307,+,43S11M\t1\t+\n-ENSMUST00000088373\t8054\t8065\t20|1,ENSMUST00000088373,8054,8065,+,43S11M\t1\t+\n-ENSMUST00000129865\t905\t916\t20|1,ENSMUST00000129865,905,916,+,43S11M\t1\t+\n-ENSMUST00000147228\t572\t585\t13|8,ENSMUST00000147228,572,585,+,13M42S\t1\t+\n-ENSMUST00000106220\t383\t396\t13|8,ENSMUST00000106220,383,396,+,13M42S\t1\t+\n-ENSMUST00000006311\t2407\t2420\t13|8,ENSMUST00000006311,2407,2420,+,13M42S\t1\t+\n-ENSMUST00000099628\t995\t1008\t13|8,ENSMUST00000099628,995,1008,+,13M42S\t1\t+\n-ENSMUST00000114132\t3670\t3682\t23|1,ENSMUST00000114132,3670,3682,+,43S12M\t1\t+\n-ENSMUST00000028761\t3500\t3512\t23|1,ENSMUST00000028761,3500,3512,+,43S12M\t1\t+\n-ENSMUST00000029025\t3154\t3166\t23|1,ENSMUST00000029025,3154,3166,+,43S12M\t1\t+\n-ENSMUST00000055032\t3310\t3323\t31|10,ENSMUST00000055032,3310,3323,+,13M42S\t1\t+\n-ENSMUST00000168713\t538\t551\t31|10,ENSMUST00000168713,538,551,+,1S13M41S\t1\t+\n-ENSMUST00000187296\t2127\t2140\t31|10,ENSMUST00000187296,2127,2140,+,13M42S\t1\t+\n-ENSMUST00000167448\t329\t342\t31|10,ENSMUST00000167448,329,342,+,1S13M41S\t1\t+\n-ENSMUST00000043169\t442\t455\t31|10,ENSMUST00000043169,442,455,+,1S13M41S\t1\t+\n-ENSMUST00000045562\t3691\t3703\t5|12,ENSMUST00000045562,3691,3703,+,2S12M41S\t1\t+\n-ENSMUST00000179869\t1671\t1683\t5|12,ENSMUST00000179869,1671,1683,+,12M43S\t1\t+\n-ENSMUST00000182010\t408\t445\t22|1,ENSMUST00000182010,408,445,+,5S37M13S\t1\t+\n-ENSMUST00000182010\t409\t445\t12|3,ENSMUST00000182010,409,445,+,5S36M14S\t1\t+\n-ENSMUST00000182010\t419\t445\t34|1,ENSMUST00000182010,419,445,+,5S26M24S\t1\t+\n-ENSMUST00000182010\t424\t445\t35|9,ENSMUST00000182010,424,445,+,5S21M29S\t1\t+\n-ENSMUST00000182010\t426\t445\t15|2,ENSMUST00000182010,426,445,+,5S19M31S\t1\t+\n-ENSMUST00000182010\t428\t445\t36|10,ENSMUST00000182010,428,445,+,5S17M33S\t1\t+\n-ENSMUST00000182010\t430\t445\t30|4,ENSMUST00000182010,430,445,+,5S15M35S\t1\t+\n-ENSMUST00000182010\t446\t458\t22|1,ENSMUST00000182010,446,458,+,43S12M\t1\t+\n-ENSMUST00000182010\t446\t459\t12|3,ENSMUST00000182010,446,459,+,42S13M\t1\t+\n-ENSMUST00000182010\t446\t458\t34|1,ENSMUST00000182010,446,458,+,32S12M11S\t1\t+\n-ENSMUST00000182010\t446\t468\t35|9,ENSMUST00000182010,446,468,+,27S22M6S\t1\t+\n-ENSMUST00000182010\t446\t468\t15|2,ENSMUST00000182010,446,468,+,25S22M8S\t1\t+\n-ENSMUST00000182010\t446\t468\t36|10,ENSMUST00000182010,446,468,+,23S22M10S\t1\t+\n-ENSMUST00000182010\t446\t468\t30|4,ENSMUST00000182010,446,468,+,21S22M12S\t1\t+\n-ENSMUST00000064314\t967\t982\t23|1,ENSMUST00000064314,967,982,+,18S15M22S\t1\t+\n+mmu-miR-344c-5p\t8\t17\t9|1,mmu-miR-344c-5p,8,17,+,3S9M43S\t1\t+\n+mmu-miR-344d-1-5p\t8\t17\t9|1,mmu-miR-344d-1-5p,8,17,+,3S9M43S\t1\t+\n+mmu-miR-344d-2-5p\t8\t17\t9|1,mmu-miR-344d-2-5p,8,17,+,3S9M43S\t1\t+\n+mmu-miR-7046-5p\t9\t22\t9|1,mmu-miR-7046-5p,9,22,+,12S13M30S\t1\t+\n' |
| b |
| diff -r 7f9cf152cf8f -r 35f433d0bd7f test-data/annotation.gtf --- a/test-data/annotation.gtf Thu Apr 16 13:23:11 2020 -0400 +++ b/test-data/annotation.gtf Thu May 07 03:35:27 2020 -0400 |
| b |
| b'@@ -56,3 +56,431 @@\n 17\tensembl_havana\tUTR\t27655588\t27655759\t.\t+\t.\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n 17\tensembl_havana\tUTR\t27701767\t27701887\t.\t+\t.\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n 17\tensembl_havana\tUTR\t27708536\t27711106\t.\t+\t.\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n+2\tensembl_havana\tgene\t31026206\t31142008\t.\t-\t.\tgene_id "ENSMUSG00000075415"; gene_version "9"; gene_name "Fnbp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding";\n+2\thavana\ttranscript\t31026206\t31141802\t.\t-\t.\tgene_id "ENSMUSG00000075415"; gene_version "9"; transcript_id "ENSMUST00000073879"; transcript_version "7"; gene_name "Fnbp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Fnbp1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";\n+2\thavana\texon\t31141779\t31141802\t.\t-\t.\tgene_id "ENSMUSG00000075415"; gene_version "9"; transcript_id "ENSMUST00000073879"; transcript_version "7"; exon_number "1"; gene_name "Fnbp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Fnbp1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSMUSE00000696139"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";\n+2\thavana\tCDS\t31141779\t31141802\t.\t-\t0\tgene_id "ENSMUSG00000075415"; gene_version "9"; transcript_id "ENSMUST00000073879"; transcript_version "7"; exon_number "1"; gene_name "Fnbp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Fnbp1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSMUSP00000109188"; protein_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";\n+2\thavana\tstart_codon\t31141800\t31141802\t.\t-\t0\tgene_id "ENSMUSG00000075415"; gene_version "9"; transcript_id "ENSMUST00000073879"; transcript_version "7"; exon_number "1"; gene_name "Fnbp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Fnbp1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";\n+2\thavana\texon\t31105242\t31105357\t.\t-\t.\tgene_id "ENSMUSG00000075415"; gene_version "9"; transcript_id "ENSMUST00000073879"; transcript_version "7"; exon_number "2"; gene_name "Fnbp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Fnbp1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSMUSE00001040547"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";\n+2\thavana\tCDS\t31105242\t31105357\t.\t-\t0\tgene_id "ENSMUSG00000075415"; gene_version "9"; transcript_id "ENSMUST00000073879"; transcript_version "7"; exon_number "2"; gene_name "Fnbp1"; gene_source "ensembl_havana"; gene_biotype "protein_co'..b'bp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Fnbp1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSMUSE00001274115"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3";\n+2\thavana\tCDS\t31082974\t31083078\t.\t-\t0\tgene_id "ENSMUSG00000075415"; gene_version "9"; transcript_id "ENSMUST00000149196"; transcript_version "1"; exon_number "6"; gene_name "Fnbp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Fnbp1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSMUSP00000121282"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3";\n+2\thavana\texon\t31058944\t31059017\t.\t-\t.\tgene_id "ENSMUSG00000075415"; gene_version "9"; transcript_id "ENSMUST00000149196"; transcript_version "1"; exon_number "7"; gene_name "Fnbp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Fnbp1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSMUSE00000788616"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3";\n+2\thavana\tCDS\t31058944\t31059017\t.\t-\t0\tgene_id "ENSMUSG00000075415"; gene_version "9"; transcript_id "ENSMUST00000149196"; transcript_version "1"; exon_number "7"; gene_name "Fnbp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Fnbp1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSMUSP00000121282"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3";\n+2\thavana\tUTR\t31116288\t31116312\t.\t-\t.\tgene_id "ENSMUSG00000075415"; gene_version "9"; transcript_id "ENSMUST00000149196"; transcript_version "1"; gene_name "Fnbp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Fnbp1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3";\n+2\thavana\ttranscript\t31096091\t31105450\t.\t-\t.\tgene_id "ENSMUSG00000075415"; gene_version "9"; transcript_id "ENSMUST00000136085"; transcript_version "1"; gene_name "Fnbp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Fnbp1-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; transcript_support_level "2";\n+2\thavana\texon\t31105242\t31105450\t.\t-\t.\tgene_id "ENSMUSG00000075415"; gene_version "9"; transcript_id "ENSMUST00000136085"; transcript_version "1"; exon_number "1"; gene_name "Fnbp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Fnbp1-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00000806059"; exon_version "1"; transcript_support_level "2";\n+2\thavana\texon\t31097094\t31097150\t.\t-\t.\tgene_id "ENSMUSG00000075415"; gene_version "9"; transcript_id "ENSMUST00000136085"; transcript_version "1"; exon_number "2"; gene_name "Fnbp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Fnbp1-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00001246254"; exon_version "1"; transcript_support_level "2";\n+2\thavana\texon\t31096091\t31096174\t.\t-\t.\tgene_id "ENSMUSG00000075415"; gene_version "9"; transcript_id "ENSMUST00000136085"; transcript_version "1"; exon_number "3"; gene_name "Fnbp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Fnbp1-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00000726303"; exon_version "1"; transcript_support_level "2";\n+13\t.\tmiRNA\t83738821\t83738843\t.\t+\t.\tID=MIMAT0000142;Alias=MIMAT0000142;Name=mmu-miR-9-5p;Derives_from=MI0000157\n+3\t.\tmiRNA\t88215613\t88215635\t.\t+\t.\tID=MIMAT0000142_1;Alias=MIMAT0000142;Name=mmu-miR-9-5p;Derives_from=MI0000720\n+7\t.\tmiRNA\t79505279\t79505301\t.\t+\t.\tID=MIMAT0000142_2;Alias=MIMAT0000142;Name=mmu-miR-9-5p;Derives_from=MI0000721\n' |
| b |
| diff -r 7f9cf152cf8f -r 35f433d0bd7f test-data/chimeras --- a/test-data/chimeras Thu Apr 16 13:23:11 2020 -0400 +++ b/test-data/chimeras Thu May 07 03:35:27 2020 -0400 |
| b |
| @@ -1,3 +1,3 @@ tagid txid1 txid2 geneid1 geneid2 symbol1 symbol2 region1 region2 tx_pos_start1 tx_pos_end1 tx_pos_strand1 length1 tx_pos_start2 tx_pos_end2 tx_pos_strand2 length2 read_info genomic_pos1 genomic_pos2 locus1 locus2 groupid1 groupid2 tpm1 tpm2 score1 score2 score sequences hybrid hybrid_pos mfe -4|1 ENSMUST00000136025 mmu-miR-6979-3p NA NA NA NA NA NA 32 46 + NA 2 12 + NA 2,15,30,39,54 ENSMUST00000136025:32:46:+ mmu-miR-6979-3p:2:12:+ ENSMUST00000136025:32:46:+ mmu-miR-6979-3p:2:12:+ 1 7 121100.0 165100.0 1.0 1.0 2.0 CAGGACUCUUGGCU&GUGUCUGUCU NA NA NA -3|2 mmu-miR-20a-5p ENSMUST00000136025 NA NA NA NA NA NA 0 23 + NA 132 142 + NA 6,28,35,44,55 mmu-miR-20a-5p:0:23:+ ENSMUST00000136025:132:142:+ mmu-miR-20a-5p:0:23:+ ENSMUST00000136025:132:142:+ 5 2 75660.0 165100.0 1.0 1.0 2.0 UAAAGUGCUUAUAGUGCAGGUAG&CUGCCUGCCU ((.((((((((&)))))))))) 13&1 -10.88 +4|1 mmu-miR-6979-3p ENSMUST00000136025 NA NA NA NA NA NA 2 12 + 21 32 46 + 188 30,39,2,15,54 mmu-miR-6979-3p:2:12:+ ENSMUST00000136025:32:46:+ mmu-miR-6979-3p:2:12:+ ENSMUST00000136025:32:46:+ 7 1 165100.0 121100.0 1.0 1.0 2.0 GUGUCUGUCU&CAGGACUCUUGGCU NA NA NA +3|2 mmu-miR-20a-5p ENSMUST00000136025 NA NA NA NA NA NA 0 23 + 23 132 142 + 188 6,28,35,44,55 mmu-miR-20a-5p:0:23:+ ENSMUST00000136025:132:142:+ mmu-miR-20a-5p:0:23:+ ENSMUST00000136025:132:142:+ 5 2 75660.0 165100.0 1.0 1.0 2.0 UAAAGUGCUUAUAGUGCAGGUAG&CUGCCUGCCU ((.((((((((&)))))))))) 13&1 -10.88 |
| b |
| diff -r 7f9cf152cf8f -r 35f433d0bd7f test-data/ref1.fasta --- a/test-data/ref1.fasta Thu Apr 16 13:23:11 2020 -0400 +++ b/test-data/ref1.fasta Thu May 07 03:35:27 2020 -0400 |
| b |
| @@ -6,3 +6,5 @@ TGTAAGGGGAGATGCAGGGAGC >mmu-miR-6979-3p TTGTGTCTGTCTGGCTCCCAG +>mmu-miR-9-5p +TCTTTGGTTATCTAGCTGTATGA |
| b |
| diff -r 7f9cf152cf8f -r 35f433d0bd7f test-data/ref2.fasta --- a/test-data/ref2.fasta Thu Apr 16 13:23:11 2020 -0400 +++ b/test-data/ref2.fasta Thu May 07 03:35:27 2020 -0400 |
| b |
| @@ -8,3 +8,5 @@ CAAAGGCAGTATCGTGGTGGATTATGATGTCATCCTGAAGGCCAAGTACACCCCAGGATTTGAAAACACATTAGATACCGTCGTCAAAAACCTGGAGACA >ENSMUST00000045896 GAGGCCAATGGTGGCGCCAACCCCTTCGAGGATGATGCCAAGGGAGTTCGTGTACGGGCACTCTATGACTACGACGGTCAGGAGCAGGATGAGCTCAGCT +>ENSMUST00000113555 +ATGAGCTGGGGCACTGAGCTCTGGGATCAGTTTGACAACTTGGAAAAACATACACAGTGGGGAATCGATATTCTTGAGAAATACATCAAGTTTGTCAAGGAGAGGACGGAGATTGAGCTCAGCTATGCCAAGCAACTCAGGAATCTTTCAAAGAAATACCAACCTAAGAAGAACTCGAAGGAAGAGGAGGAGTACAAGTACACGGCTTGCAAAGCCTTTCTTTCCACCCTGAATGAGATGAATGACTACGCCGGGCAGCACGAGGTCATCTCTGAGAACATGACGTCACAGATCACGGTGGACCTGATGCGCTACGTTCAGGAGCTGAAGCAGGAGAGGAAATCGAACTTCCATGATGGACGGAAGGCTCAGCAGCACATAGAAACGTGTTGGAAGCAACTGGAGTCAAGTAAGAGGAGGTTTGAGCGGGACTGTAAGGAAGCCGACCGGGCACAGCAGTACTTCGAGAAAATGGACGCTGACATCAACGTGACCAAGGCGGATGTGGAAAAGGCACGACAACAAGCTCAGATACGCCAGCAAATGGCAGAGGACAGCAAAGCAGATTACTCCTTAATCCTGCAGAGATTCAACCAGGAGCAATGGGAATACTACCATACCCACATCCCCAACATCTTCCAGAAAATACAAGAGATGGAGGAGAGGCGGATTGTGCGTATTGGGGAGTCCATGAAGACGTACGCAGAGGTGGACCGGCAGGTGATACCCATCATCGGGAAGTGCCTGGACGGGATAGTGAAGGCGGCCGAGTCTATCGACCAGAAAAACGACTCCCAGCTGGTCGTAGAAGCCTATAAGTCAGGATTCGAGCCTCCTGGAGACATTGAATTCGAAGATTACACACAGCCAATGAAACGCACAGTGTCAGACAACAGCCTTTCCAGCTCCAAAGAAGGCAAGCCTGAGCTCAGATTTGGCGGCAAGTCCAGAGGCAAGCTCTGGCCATTCATCAAGAAAAACAAGTCTCCCAAGCAGCCAAAGGAACCCCTCTCCCACCGCTTCAACGAGTTCATGACCTCCAAACCCAAAATCCACTGCTTCCGGAGCCTAAAGCGTGGGCTTTCTCTCAAGCTGGGTGTCACACCAGAAGACTTCAGCAACTTCCCACCTGAGCAGAGAAGGAAAAAACTACAACAGAAAGTTGACGATCTCAATAGAGAGATACAGAAGGAGACGGACCAGAGAGATGCCATCACCAAAATGAAAGATGTGTACCTAAAGAACCCTCAGATGGGAGACCCAGCCAGCCTGGACCAGAAGCTCACCGAAGTCACCCAGAACATAGAGAAACTGCGGCTGGAGGCTCAGAAGTTTGAGGCCTGGCTGGCTGAGGTAGAAGGCAGACTCCCAGCTCGGAGTGAGCAGGCACGCCGGCAGAGTGGACTGTATGATGGCCAGACACACCAGACGGTCACTAACTGTGCCCAGGACCGGGAGAGCCCAGATGGTAGTTACACAGAGGAGCAAAGCCAGGAGAGCGAGCACAAGGTCCTGGCCCCGGATTTCGACGATGAATTTGATGATGAGGAGCCGCTTCCAGCCATAGGGACCTGCAAGGCCCTCTACACATTTGAAGGTCAGAACGAAGGCACCATTTCCGTAGTTGAAGGAGAGACGCTGAGCGTGATTGAAGAGGACAAAGGCGATGGGTGGACTCGCATCCGCAGAAATGAAGACGAGGAGGGTTACGTCCCCACTTCCTACGTCGAAGTCTATTTAGACAAAAACGCCAAAGGTGCTAAGACTTATATTTAA |