| Previous changeset 2:bfe57d6e0c4c (2015-10-12) Next changeset 4:56e104999978 (2017-02-06) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 |
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modified:
macs2_callpeak.xml macs2_macros.xml macs2_predictd.xml test-data/callpeak_summits_part.bed test-data/predictd_on_ChIP_200K_and_Control_200K.pdf test-data/predictd_on_ChIP_200K_and_Control_200K.txt test-data/refinepeak_ChIP_and_summits.bed tool_dependencies.xml |
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added:
test-data/callpeak_part.tabular |
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removed:
test-data/callpeak_part.bed |
| b |
| diff -r bfe57d6e0c4c -r 6d4babad010f macs2_callpeak.xml --- a/macs2_callpeak.xml Mon Oct 12 11:24:39 2015 -0400 +++ b/macs2_callpeak.xml Wed Jan 27 15:23:25 2016 -0500 |
| [ |
| @@ -4,8 +4,7 @@ <import>macs2_macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="3.0.1">R_3_0_1</requirement> - <requirement type="package" version="4.1.0">gnu_awk</requirement> + <requirement type="package" version="3.1.2">R</requirement> <requirement type="set_environment">MACS2_SCRIPT_PATH</requirement> </expand> <expand macro="stdio" /> @@ -79,9 +78,9 @@ #end if 2> $temp_stderr) - #if 'peaks_bed' in str($outputs).split(','): + #if 'peaks_tabular' in str($outputs).split(','): && - awk '$2-=1' MACS2_peaks.xls | awk '!/^#/' | awk -v OFS='\t' '$1=$1' | tail -n+3 > "${ output_bed }" + cp MACS2_peaks.xls "${ output_tabular }" #end if ## run R to create pdf from model script @@ -152,7 +151,7 @@ </conditional> <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs" help="PDF only created when model is build"> - <option value="peaks_bed" selected="True">Peaks as BED file</option> + <option value="peaks_tabular" selected="True">Peaks as tabular file</option> <!--<option value="narrow">narrow Peaks</option>--> <option value="summits" selected="true">summits</option> <option value="bdg" selected="true">Scores in bedGraph files (--bdg)</option> @@ -202,8 +201,8 @@ </inputs> <outputs> <!--callpeaks output--> - <data name="output_bed" format="bed" label="${tool.name} on ${on_string} (Peaks in BED format)"> - <filter>'peaks_bed' in outputs</filter> + <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string} (Peaks in tabular format)"> + <filter>'peaks_tabular' in outputs</filter> </data> <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" label="${tool.name} on ${on_string} (broad Peaks)"> <filter> @@ -213,7 +212,7 @@ )) </filter> </data> - <data name="output_gappedpeaks" format="tabular" from_work_dir="MACS2_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)"> + <data name="output_gappedpeaks" format="bed" from_work_dir="MACS2_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)"> <filter> (( advanced_options['advanced_options_selector'] == "on" and @@ -221,7 +220,7 @@ )) </filter> </data> - <data name="output_narrowpeaks" format="tabular" from_work_dir="MACS2_peaks.narrowPeak" label="${tool.name} on ${on_string} (narrow Peaks)"> + <data name="output_narrowpeaks" format="bed" from_work_dir="MACS2_peaks.narrowPeak" label="${tool.name} on ${on_string} (narrow Peaks)"> <filter> ( advanced_options['advanced_options_selector'] == "off" or @@ -259,12 +258,12 @@ <param name="cutoff_options_selector" value="qvalue"/> <param name="qvalue" value="0.05"/> <param name="band_width" value="300"/> - <param name="outputs" value="peaks_bed,bdg"/> + <param name="outputs" value="peaks_tabular,bdg"/> <param name="effective_genome_size_options_selector" value="user_defined" /> <param name="gsize" value="3300000000" /> <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg"/> <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg"/> - <output name="output_bed" compare="contains" file="callpeak_part.bed"/> + <output name="output_tabular" compare="contains" file="callpeak_part.tabular"/> <output name="output_summits" compare="contains" file="callpeak_summits_part.bed"/> </test> <test> |
| b |
| diff -r bfe57d6e0c4c -r 6d4babad010f macs2_macros.xml --- a/macs2_macros.xml Mon Oct 12 11:24:39 2015 -0400 +++ b/macs2_macros.xml Wed Jan 27 15:23:25 2016 -0500 |
| b |
| @@ -1,14 +1,14 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.1.0">macs2</requirement> + <requirement type="package" version="2.1.0.20151222">macs2</requirement> <requirement type="package" version="1.7.1">numpy</requirement> <requirement type="package" version="0.12.0">scipy</requirement> <yield /> </requirements> </xml> - <token name="@VERSION_STRING@">2.1.0.20140616</token> + <token name="@VERSION_STRING@">2.1.0.20151222</token> <xml name="conditional_effective_genome_size"> <conditional name="effective_genome_size_options"> |
| b |
| diff -r bfe57d6e0c4c -r 6d4babad010f macs2_predictd.xml --- a/macs2_predictd.xml Mon Oct 12 11:24:39 2015 -0400 +++ b/macs2_predictd.xml Wed Jan 27 15:23:25 2016 -0500 |
| b |
| @@ -4,7 +4,7 @@ <import>macs2_macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="3.0.1">R_3_0_1</requirement> + <requirement type="package" version="3.1.2">R</requirement> <requirement type="package" version="4.1.0">gnu_awk</requirement> </expand> <expand macro="stdio" /> |
| b |
| diff -r bfe57d6e0c4c -r 6d4babad010f test-data/callpeak_part.bed --- a/test-data/callpeak_part.bed Mon Oct 12 11:24:39 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1000 +0,0 @@\n-chr1\t840081\t840400\t319\t840240\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_1\n-chr1\t919419\t919785\t366\t919550\t5.00\t12.44147\t5.85158\t8.70937\tMACS2_peak_2\n-chr1\t937220\t937483\t263\t937375\t4.00\t10.06728\t4.87632\t6.61760\tMACS2_peak_3\n-chr1\t954742\t954996\t254\t954814\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_4\n-chr1\t994762\t995016\t254\t994906\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_5\n-chr1\t1057394\t1057648\t254\t1057509\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_6\n-chr1\t1240579\t1241004\t425\t1240777\t3.00\t7.77216\t3.90105\t4.60941\tMACS2_peak_7\n-chr1\t1307392\t1307735\t343\t1307601\t5.00\t12.44147\t5.85158\t8.70937\tMACS2_peak_8\n-chr1\t1440350\t1440633\t283\t1440462\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_9\n-chr1\t1555432\t1555725\t293\t1555571\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_10\n-chr1\t1590667\t1590946\t279\t1590840\t4.00\t10.06728\t4.87632\t6.61760\tMACS2_peak_11\n-chr1\t1837668\t1838104\t436\t1837886\t6.00\t14.88255\t6.82684\t10.84923\tMACS2_peak_12\n-chr1\t1840365\t1840828\t463\t1840547\t5.00\t13.74439\t5.90922\t9.80599\tMACS2_peak_13\n-chr1\t1976399\t1976653\t254\t1976469\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_14\n-chr1\t2071301\t2071627\t326\t2071423\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_15\n-chr1\t2105716\t2106140\t424\t2105919\t4.00\t7.70001\t4.64644\t4.60941\tMACS2_peak_16\n-chr1\t2126521\t2126861\t340\t2126648\t4.00\t10.06728\t4.87632\t6.61760\tMACS2_peak_17\n-chr1\t2246520\t2246954\t434\t2246712\t5.00\t9.59761\t5.57573\t6.23290\tMACS2_peak_18\n-chr1\t2313157\t2313560\t403\t2313353\t5.00\t13.74439\t5.90922\t9.80599\tMACS2_peak_19\n-chr1\t2345827\t2346242\t415\t2346028\t7.00\t17.38158\t7.80211\t13.02599\tMACS2_peak_20\n-chr1\t2510054\t2510308\t254\t2510213\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_21\n-chr1\t3341407\t3341661\t254\t3341461\t3.00\t7.77216\t3.90105\t4.60941\tMACS2_peak_22\n-chr1\t3369638\t3369892\t254\t3369863\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_23\n-chr1\t3400440\t3400769\t329\t3400610\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_24\n-chr1\t3407840\t3408094\t254\t3407975\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_25\n-chr1\t3481747\t3482245\t498\t3481863\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_26\n-chr1\t3535561\t3535821\t260\t3535663\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_27\n-chr1\t3537756\t3538010\t254\t3537960\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_28\n-chr1\t3593609\t3593863\t254\t3593838\t3.00\t7.77216\t3.90105\t4.60941\tMACS2_peak_29\n-chr1\t3640883\t3641366\t483\t3641134\t12.00\t30.54970\t12.67843\t24.90332\tMACS2_peak_30\n-chr1\t3702143\t3702397\t254\t3702260\t3.00\t7.77216\t3.90105\t4.60941\tMACS2_peak_31\n-chr1\t3773698\t3774058\t360\t3773876\t7.00\t19.11990\t7.87896\t14.58582\tMACS2_peak_32\n-chr1\t3827305\t3827722\t417\t3827525\t5.00\t13.74439\t5.90922\t9.80599\tMACS2_peak_33\n-chr1\t4712783\t4713037\t254\t4712904\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_34\n-chr1\t4886186\t4886440\t254\t4886326\t3.00\t7.77216\t3.90105\t4.60941\tMACS2_peak_35\n-chr1\t5569918\t5570198\t280\t5570056\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_36\n-chr1\t5574776\t5575080\t304\t5574838\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_37\n-chr1\t5805837\t5806091\t254\t5805965\t2.00\t6.22382\t2.95461\t3.18933\tMACS2_peak_38\n-chr1\t5976145\t5976399\t254\t5976235\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_39\n-chr1\t6094645\t6094899\t254\t6094678\t2.00\t6.22382\t2.95461\t3.18933\tMACS2_peak_40\n-chr1\t6112956\t6113210\t254\t6113135\t3.00\t6.57684\t3.80689\t3.50365\tMACS2_peak_41\n-chr1\t6265252\t6265640\t388\t6265437\t6.00\t11.56197\t6.50502\t7.91704\tMACS2_peak_42\n-chr1\t6305228\t6305482\t254\t6305299\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_43\n-chr1\t6306873\t6307127\t254\t6307013\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_44\n-chr1\t6403480\t6403843\t363\t6403679\t6.00\t16.40316\t6.89409\t12.16639\tMACS2_peak_45\n-chr1\t6464656\t6465096\t440\t6464869\t6.00\t11.56197\t6.50502\t7.91704\tMACS2_peak_46\n-chr1\t6483603\t6483857\t254\t6483739\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_47\n-chr1\t6498109\t6498494\t385\t6498258\t6.00\t14.88255\t6.82684\t10.84923\tMACS2_peak_48\n-chr1\t6535512\t6535838\t326\t6535591\t5.00\t13.74439\t5.90922\t9.80599\tMACS2_peak_49\n-chr1\t6614467\t6614882\t415\t6614708\t4.00\t10.06728\t4.87632\t6.61760\tMACS2_peak_50\n-chr1\t6706585\t6706931\t346\t6706743\t5.00\t13.74439\t5.90922\t9.80599\tMACS2_peak_51\n-chr1\t6761832\t6762203\t371\t6762039\t7.00\t14.9'..b'ACS2_peak_953\n-chr1\t167411347\t167411617\t270\t167411508\t9.00\t9.70719\t6.63448\t6.34225\tMACS2_peak_954\n-chr1\t167509676\t167509994\t318\t167509766\t5.00\t13.74439\t5.90922\t9.80599\tMACS2_peak_955\n-chr1\t167606642\t167606904\t262\t167606794\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_956\n-chr1\t167657153\t167657498\t345\t167657336\t7.00\t17.38158\t7.80211\t13.02599\tMACS2_peak_957\n-chr1\t167684255\t167684787\t532\t167684669\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_958\n-chr1\t168051429\t168051903\t474\t168051540\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_959\n-chr1\t168054014\t168054268\t254\t168054128\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_960\n-chr1\t168115054\t168115312\t258\t168115182\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_961\n-chr1\t168312029\t168312283\t254\t168312087\t2.00\t6.22382\t2.95461\t3.18933\tMACS2_peak_962\n-chr1\t168409107\t168409398\t291\t168409236\t5.00\t12.44147\t5.85158\t8.70937\tMACS2_peak_963\n-chr1\t169317675\t169317929\t254\t169317779\t7.00\t9.46957\t6.38142\t6.11150\tMACS2_peak_964\n-chr1\t169435646\t169435900\t254\t169435730\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_965\n-chr1\t169515618\t169516039\t421\t169515830\t6.00\t14.88255\t6.82684\t10.84923\tMACS2_peak_966\n-chr1\t169570238\t169570598\t360\t169570357\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_967\n-chr1\t169681091\t169681643\t552\t169681360\t6.00\t14.88255\t6.82684\t10.84923\tMACS2_peak_968\n-chr1\t169778761\t169779123\t362\t169778927\t6.00\t16.40316\t6.89409\t12.16639\tMACS2_peak_969\n-chr1\t169898084\t169898451\t367\t169898207\t7.00\t17.38158\t7.80211\t13.02599\tMACS2_peak_970\n-chr1\t169979564\t169979919\t355\t169979736\t5.00\t13.74439\t5.90922\t9.80599\tMACS2_peak_971\n-chr1\t170658710\t170659105\t395\t170658858\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_972\n-chr1\t170936227\t170936611\t384\t170936406\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_973\n-chr1\t171157806\t171158175\t369\t171157946\t6.00\t12.78498\t6.66205\t9.02328\tMACS2_peak_974\n-chr1\t171454166\t171454693\t527\t171454409\t5.00\t12.44147\t5.85158\t8.70937\tMACS2_peak_975\n-chr1\t171624733\t171624987\t254\t171624826\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_976\n-chr1\t171770672\t171770926\t254\t171770811\t3.00\t6.57684\t3.80689\t3.50365\tMACS2_peak_977\n-chr1\t171952729\t171952983\t254\t171952866\t3.00\t7.77216\t3.90105\t4.60941\tMACS2_peak_978\n-chr1\t171953940\t171954438\t498\t171954190\t4.00\t10.06728\t4.87632\t6.61760\tMACS2_peak_979\n-chr1\t171971859\t171972280\t421\t171972046\t6.00\t16.40316\t6.89409\t12.16639\tMACS2_peak_980\n-chr1\t172104225\t172104597\t372\t172104448\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_981\n-chr1\t172398514\t172398852\t338\t172398693\t4.00\t10.06728\t4.87632\t6.61760\tMACS2_peak_982\n-chr1\t172688764\t172689204\t440\t172688964\t7.00\t9.46957\t6.38142\t6.11150\tMACS2_peak_983\n-chr1\t172711842\t172712109\t267\t172712013\t4.00\t10.06728\t4.87632\t6.61760\tMACS2_peak_984\n-chr1\t172714120\t172714382\t262\t172714306\t5.00\t12.44147\t5.85158\t8.70937\tMACS2_peak_985\n-chr1\t173171628\t173171882\t254\t173171751\t3.00\t5.88126\t3.71716\t3.00791\tMACS2_peak_986\n-chr1\t173389467\t173389819\t352\t173389640\t8.00\t17.23237\t8.56549\t12.97385\tMACS2_peak_987\n-chr1\t173400334\t173400718\t384\t173400558\t5.00\t12.44147\t5.85158\t8.70937\tMACS2_peak_988\n-chr1\t173684280\t173684534\t254\t173684329\t2.00\t5.57376\t2.92579\t2.70691\tMACS2_peak_989\n-chr1\t173794183\t173794465\t282\t173794324\t4.00\t7.70001\t4.64644\t4.60941\tMACS2_peak_990\n-chr1\t173883385\t173883681\t296\t173883565\t5.00\t13.74439\t5.90922\t9.80599\tMACS2_peak_991\n-chr1\t174084042\t174084320\t278\t174084167\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_992\n-chr1\t174186861\t174187115\t254\t174187033\t9.00\t6.95863\t5.00355\t3.88437\tMACS2_peak_993\n-chr1\t174227188\t174227538\t350\t174227378\t5.00\t12.44147\t5.85158\t8.70937\tMACS2_peak_994\n-chr1\t174695684\t174695942\t258\t174695865\t4.00\t10.06728\t4.87632\t6.61760\tMACS2_peak_995\n-chr1\t174713257\t174713511\t254\t174713320\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_996\n-chr1\t174739198\t174739503\t305\t174739348\t4.00\t8.57130\t4.75861\t5.28945\tMACS2_peak_997\n-chr1\t174967683\t174968030\t347\t174967847\t10.00\t8.00416\t5.50391\t4.83430\tMACS2_peak_998\n-chr1\t174998798\t174999052\t254\t174998982\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_999\n-chr1\t175094595\t175094849\t254\t175094659\t3.00\t7.77216\t3.90105\t4.60941\tMACS2_peak_1000\n' |
| b |
| diff -r bfe57d6e0c4c -r 6d4babad010f test-data/callpeak_part.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/callpeak_part.tabular Wed Jan 27 15:23:25 2016 -0500 |
| [ |
| b'@@ -0,0 +1,1020 @@\n+# effective genome size = 3.30e+09\n+# band width = 300\n+# model fold = [5, 50]\n+# qvalue cutoff = 5.00e-02\n+# Larger dataset will be scaled towards smaller dataset.\n+# Range for calculating regional lambda is: 1000 bps and 10000 bps\n+# Broad region calling is off\n+\n+# tag size is determined as 100 bps\n+# total tags in treatment: 199977\n+# tags after filtering in treatment: 199583\n+# maximum duplicate tags at the same position in treatment = 1\n+# Redundant rate in treatment: 0.00\n+# total tags in control: 199978\n+# tags after filtering in control: 199867\n+# maximum duplicate tags at the same position in control = 1\n+# Redundant rate in control: 0.00\n+# d = 254\n+# alternative fragment length(s) may be 254 bps\n+chr\tstart\tend\tlength\tabs_summit\tpileup\t-log10(pvalue)\tfold_enrichment\t-log10(qvalue)\tname\n+chr1\t840082\t840400\t319\t840240\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_1\n+chr1\t919420\t919785\t366\t919550\t5.00\t12.44148\t5.85158\t8.70936\tMACS2_peak_2\n+chr1\t937221\t937483\t263\t937375\t4.00\t10.06728\t4.87632\t6.61759\tMACS2_peak_3\n+chr1\t954743\t954996\t254\t954814\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_4\n+chr1\t994763\t995016\t254\t994906\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_5\n+chr1\t1057395\t1057648\t254\t1057509\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_6\n+chr1\t1240580\t1241004\t425\t1240777\t3.00\t7.77216\t3.90105\t4.60940\tMACS2_peak_7\n+chr1\t1307393\t1307735\t343\t1307601\t5.00\t12.44148\t5.85158\t8.70936\tMACS2_peak_8\n+chr1\t1440351\t1440633\t283\t1440462\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_9\n+chr1\t1555433\t1555725\t293\t1555571\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_10\n+chr1\t1590668\t1590946\t279\t1590840\t4.00\t10.06728\t4.87632\t6.61759\tMACS2_peak_11\n+chr1\t1837669\t1838104\t436\t1837886\t6.00\t14.88256\t6.82684\t10.84922\tMACS2_peak_12\n+chr1\t1840366\t1840828\t463\t1840547\t5.00\t13.74439\t5.90922\t9.80598\tMACS2_peak_13\n+chr1\t1976400\t1976653\t254\t1976469\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_14\n+chr1\t2071302\t2071627\t326\t2071423\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_15\n+chr1\t2105717\t2106140\t424\t2105919\t4.00\t7.70001\t4.64644\t4.60940\tMACS2_peak_16\n+chr1\t2126522\t2126861\t340\t2126648\t4.00\t10.06728\t4.87632\t6.61759\tMACS2_peak_17\n+chr1\t2246521\t2246954\t434\t2246712\t5.00\t9.59761\t5.57573\t6.23289\tMACS2_peak_18\n+chr1\t2313158\t2313560\t403\t2313353\t5.00\t13.74439\t5.90922\t9.80598\tMACS2_peak_19\n+chr1\t2345828\t2346242\t415\t2346028\t7.00\t17.38158\t7.80211\t13.02598\tMACS2_peak_20\n+chr1\t2510055\t2510308\t254\t2510213\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_21\n+chr1\t3341408\t3341661\t254\t3341461\t3.00\t7.77216\t3.90105\t4.60940\tMACS2_peak_22\n+chr1\t3369639\t3369892\t254\t3369863\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_23\n+chr1\t3400441\t3400769\t329\t3400610\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_24\n+chr1\t3407841\t3408094\t254\t3407975\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_25\n+chr1\t3481748\t3482245\t498\t3481863\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_26\n+chr1\t3535562\t3535821\t260\t3535663\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_27\n+chr1\t3537757\t3538010\t254\t3537960\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_28\n+chr1\t3593610\t3593863\t254\t3593838\t3.00\t7.77216\t3.90105\t4.60940\tMACS2_peak_29\n+chr1\t3640884\t3641366\t483\t3641134\t12.00\t30.54970\t12.67843\t24.90331\tMACS2_peak_30\n+chr1\t3702144\t3702397\t254\t3702260\t3.00\t7.77216\t3.90105\t4.60940\tMACS2_peak_31\n+chr1\t3773699\t3774058\t360\t3773876\t7.00\t19.11990\t7.87896\t14.58582\tMACS2_peak_32\n+chr1\t3827306\t3827722\t417\t3827525\t5.00\t13.74439\t5.90922\t9.80598\tMACS2_peak_33\n+chr1\t4712784\t4713037\t254\t4712904\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_34\n+chr1\t4886187\t4886440\t254\t4886326\t3.00\t7.77216\t3.90105\t4.60940\tMACS2_peak_35\n+chr1\t5569919\t5570198\t280\t5570056\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_36\n+chr1\t5574777\t5575080\t304\t5574838\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_37\n+chr1\t5805838\t5806091\t254\t5805965\t2.00\t6.22382\t2.95461\t3.18932\tMACS2_peak_38\n+chr1\t5976146\t5976399\t254\t5976235\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_39\n+chr1\t6094646\t6094899\t254\t6094678\t2.00\t6.22382\t2.95461\t3.18932\tMACS2_peak_40\n+chr1\t6112957\t6113210\t254\t6113135\t3.00\t6.57684\t3.80689\t3.50364\tMACS2_peak_41\n+chr1\t6265253'..b'ACS2_peak_953\n+chr1\t167411348\t167411617\t270\t167411508\t9.00\t9.70719\t6.63448\t6.34225\tMACS2_peak_954\n+chr1\t167509677\t167509994\t318\t167509766\t5.00\t13.74439\t5.90922\t9.80598\tMACS2_peak_955\n+chr1\t167606643\t167606904\t262\t167606794\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_956\n+chr1\t167657154\t167657498\t345\t167657336\t7.00\t17.38158\t7.80211\t13.02598\tMACS2_peak_957\n+chr1\t167684256\t167684787\t532\t167684669\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_958\n+chr1\t168051430\t168051903\t474\t168051540\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_959\n+chr1\t168054015\t168054268\t254\t168054128\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_960\n+chr1\t168115055\t168115312\t258\t168115182\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_961\n+chr1\t168312030\t168312283\t254\t168312087\t2.00\t6.22382\t2.95461\t3.18932\tMACS2_peak_962\n+chr1\t168409108\t168409398\t291\t168409236\t5.00\t12.44148\t5.85158\t8.70936\tMACS2_peak_963\n+chr1\t169317676\t169317929\t254\t169317779\t7.00\t9.46957\t6.38142\t6.11149\tMACS2_peak_964\n+chr1\t169435647\t169435900\t254\t169435730\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_965\n+chr1\t169515619\t169516039\t421\t169515830\t6.00\t14.88256\t6.82684\t10.84922\tMACS2_peak_966\n+chr1\t169570239\t169570598\t360\t169570357\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_967\n+chr1\t169681092\t169681643\t552\t169681360\t6.00\t14.88256\t6.82684\t10.84922\tMACS2_peak_968\n+chr1\t169778762\t169779123\t362\t169778927\t6.00\t16.40316\t6.89409\t12.16639\tMACS2_peak_969\n+chr1\t169898085\t169898451\t367\t169898207\t7.00\t17.38158\t7.80211\t13.02598\tMACS2_peak_970\n+chr1\t169979565\t169979919\t355\t169979736\t5.00\t13.74439\t5.90922\t9.80598\tMACS2_peak_971\n+chr1\t170658711\t170659105\t395\t170658858\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_972\n+chr1\t170936228\t170936611\t384\t170936406\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_973\n+chr1\t171157807\t171158175\t369\t171157946\t6.00\t12.78498\t6.66205\t9.02328\tMACS2_peak_974\n+chr1\t171454167\t171454693\t527\t171454409\t5.00\t12.44148\t5.85158\t8.70936\tMACS2_peak_975\n+chr1\t171624734\t171624987\t254\t171624826\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_976\n+chr1\t171770673\t171770926\t254\t171770811\t3.00\t6.57684\t3.80689\t3.50364\tMACS2_peak_977\n+chr1\t171952730\t171952983\t254\t171952866\t3.00\t7.77216\t3.90105\t4.60940\tMACS2_peak_978\n+chr1\t171953941\t171954438\t498\t171954190\t4.00\t10.06728\t4.87632\t6.61759\tMACS2_peak_979\n+chr1\t171971860\t171972280\t421\t171972046\t6.00\t16.40316\t6.89409\t12.16639\tMACS2_peak_980\n+chr1\t172104226\t172104597\t372\t172104448\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_981\n+chr1\t172398515\t172398852\t338\t172398693\t4.00\t10.06728\t4.87632\t6.61759\tMACS2_peak_982\n+chr1\t172688765\t172689204\t440\t172688964\t7.00\t9.46957\t6.38142\t6.11149\tMACS2_peak_983\n+chr1\t172711843\t172712109\t267\t172712013\t4.00\t10.06728\t4.87632\t6.61759\tMACS2_peak_984\n+chr1\t172714121\t172714382\t262\t172714306\t5.00\t12.44148\t5.85158\t8.70936\tMACS2_peak_985\n+chr1\t173171629\t173171882\t254\t173171751\t3.00\t5.88127\t3.71716\t3.00790\tMACS2_peak_986\n+chr1\t173389468\t173389819\t352\t173389640\t8.00\t17.23237\t8.56549\t12.97384\tMACS2_peak_987\n+chr1\t173400335\t173400718\t384\t173400558\t5.00\t12.44148\t5.85158\t8.70936\tMACS2_peak_988\n+chr1\t173684281\t173684534\t254\t173684329\t2.00\t5.57376\t2.92579\t2.70690\tMACS2_peak_989\n+chr1\t173794184\t173794465\t282\t173794324\t4.00\t7.70001\t4.64644\t4.60940\tMACS2_peak_990\n+chr1\t173883386\t173883681\t296\t173883565\t5.00\t13.74439\t5.90922\t9.80598\tMACS2_peak_991\n+chr1\t174084043\t174084320\t278\t174084167\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_992\n+chr1\t174186862\t174187115\t254\t174187033\t9.00\t6.95863\t5.00355\t3.88436\tMACS2_peak_993\n+chr1\t174227189\t174227538\t350\t174227378\t5.00\t12.44148\t5.85158\t8.70936\tMACS2_peak_994\n+chr1\t174695685\t174695942\t258\t174695865\t4.00\t10.06728\t4.87632\t6.61759\tMACS2_peak_995\n+chr1\t174713258\t174713511\t254\t174713320\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_996\n+chr1\t174739199\t174739503\t305\t174739348\t4.00\t8.57130\t4.75861\t5.28944\tMACS2_peak_997\n+chr1\t174967684\t174968030\t347\t174967847\t10.00\t8.00416\t5.50391\t4.83429\tMACS2_peak_998\n+chr1\t174998799\t174999052\t254\t174998982\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_999\n+chr1\t175094596\t175094849\t254\t175094659\t3.00\t7.77216\t3.90105\t4.60940\tMACS2_peak_1000\n' |
| b |
| diff -r bfe57d6e0c4c -r 6d4babad010f test-data/callpeak_summits_part.bed --- a/test-data/callpeak_summits_part.bed Mon Oct 12 11:24:39 2015 -0400 +++ b/test-data/callpeak_summits_part.bed Wed Jan 27 15:23:25 2016 -0500 |
| b |
| b'@@ -1,1000 +1,1000 @@\n-chr1\t840239\t840240\tMACS2_peak_1\t7.51487\n-chr1\t919549\t919550\tMACS2_peak_2\t8.70937\n-chr1\t937374\t937375\tMACS2_peak_3\t6.61760\n-chr1\t954813\t954814\tMACS2_peak_4\t5.28945\n-chr1\t994905\t994906\tMACS2_peak_5\t5.28945\n-chr1\t1057508\t1057509\tMACS2_peak_6\t5.28945\n-chr1\t1240776\t1240777\tMACS2_peak_7\t4.60941\n-chr1\t1307600\t1307601\tMACS2_peak_8\t8.70937\n-chr1\t1440461\t1440462\tMACS2_peak_9\t7.51487\n-chr1\t1555570\t1555571\tMACS2_peak_10\t7.51487\n-chr1\t1590839\t1590840\tMACS2_peak_11\t6.61760\n-chr1\t1837885\t1837886\tMACS2_peak_12\t10.84923\n-chr1\t1840546\t1840547\tMACS2_peak_13\t9.80599\n-chr1\t1976468\t1976469\tMACS2_peak_14\t5.28945\n-chr1\t2071422\t2071423\tMACS2_peak_15\t7.51487\n-chr1\t2105918\t2105919\tMACS2_peak_16\t4.60941\n-chr1\t2126647\t2126648\tMACS2_peak_17\t6.61760\n-chr1\t2246711\t2246712\tMACS2_peak_18\t6.23290\n-chr1\t2313352\t2313353\tMACS2_peak_19\t9.80599\n-chr1\t2346027\t2346028\tMACS2_peak_20\t13.02599\n-chr1\t2510212\t2510213\tMACS2_peak_21\t5.28945\n-chr1\t3341460\t3341461\tMACS2_peak_22\t4.60941\n-chr1\t3369862\t3369863\tMACS2_peak_23\t5.28945\n-chr1\t3400609\t3400610\tMACS2_peak_24\t7.51487\n-chr1\t3407974\t3407975\tMACS2_peak_25\t5.28945\n-chr1\t3481862\t3481863\tMACS2_peak_26\t7.51487\n-chr1\t3535662\t3535663\tMACS2_peak_27\t5.28945\n-chr1\t3537959\t3537960\tMACS2_peak_28\t5.28945\n-chr1\t3593837\t3593838\tMACS2_peak_29\t4.60941\n-chr1\t3641133\t3641134\tMACS2_peak_30\t24.90332\n-chr1\t3702259\t3702260\tMACS2_peak_31\t4.60941\n-chr1\t3773875\t3773876\tMACS2_peak_32\t14.58582\n-chr1\t3827524\t3827525\tMACS2_peak_33\t9.80599\n-chr1\t4712903\t4712904\tMACS2_peak_34\t5.28945\n-chr1\t4886325\t4886326\tMACS2_peak_35\t4.60941\n-chr1\t5570055\t5570056\tMACS2_peak_36\t7.51487\n-chr1\t5574837\t5574838\tMACS2_peak_37\t5.28945\n-chr1\t5805964\t5805965\tMACS2_peak_38\t3.18933\n-chr1\t5976234\t5976235\tMACS2_peak_39\t5.28945\n-chr1\t6094677\t6094678\tMACS2_peak_40\t3.18933\n-chr1\t6113134\t6113135\tMACS2_peak_41\t3.50365\n-chr1\t6265436\t6265437\tMACS2_peak_42\t7.91704\n-chr1\t6305298\t6305299\tMACS2_peak_43\t5.28945\n-chr1\t6307012\t6307013\tMACS2_peak_44\t5.28945\n-chr1\t6403678\t6403679\tMACS2_peak_45\t12.16639\n-chr1\t6464868\t6464869\tMACS2_peak_46\t7.91704\n-chr1\t6483738\t6483739\tMACS2_peak_47\t5.28945\n-chr1\t6498257\t6498258\tMACS2_peak_48\t10.84923\n-chr1\t6535590\t6535591\tMACS2_peak_49\t9.80599\n-chr1\t6614707\t6614708\tMACS2_peak_50\t6.61760\n-chr1\t6706742\t6706743\tMACS2_peak_51\t9.80599\n-chr1\t6762038\t6762039\tMACS2_peak_52\t10.92185\n-chr1\t6780328\t6780329\tMACS2_peak_53\t12.16639\n-chr1\t6787703\t6787704\tMACS2_peak_54\t14.58582\n-chr1\t6950152\t6950153\tMACS2_peak_55\t7.17294\n-chr1\t7102914\t7102915\tMACS2_peak_56\t7.51487\n-chr1\t7278482\t7278483\tMACS2_peak_57\t12.16639\n-chr1\t7868576\t7868577\tMACS2_peak_58\t7.51487\n-chr1\t7962861\t7962862\tMACS2_peak_59\t4.60941\n-chr1\t8042490\t8042491\tMACS2_peak_60\t10.84923\n-chr1\t8075251\t8075252\tMACS2_peak_61\t9.02328\n-chr1\t8076738\t8076739\tMACS2_peak_62\t5.28945\n-chr1\t8091351\t8091352\tMACS2_peak_63\t7.51487\n-chr1\t8374569\t8374570\tMACS2_peak_64\t12.16639\n-chr1\t8409217\t8409218\tMACS2_peak_65\t7.51487\n-chr1\t8731569\t8731570\tMACS2_peak_66\t6.61760\n-chr1\t8786755\t8786756\tMACS2_peak_67\t8.86076\n-chr1\t8909001\t8909002\tMACS2_peak_68\t2.70691\n-chr1\t8978355\t8978356\tMACS2_peak_69\t9.80599\n-chr1\t9048259\t9048260\tMACS2_peak_70\t5.28945\n-chr1\t9065348\t9065349\tMACS2_peak_71\t9.80599\n-chr1\t9070210\t9070211\tMACS2_peak_72\t7.51487\n-chr1\t9161796\t9161797\tMACS2_peak_73\t7.51487\n-chr1\t9202501\t9202502\tMACS2_peak_74\t17.04807\n-chr1\t9349216\t9349217\tMACS2_peak_75\t9.80599\n-chr1\t9515966\t9515967\tMACS2_peak_76\t8.70937\n-chr1\t9551282\t9551283\tMACS2_peak_77\t15.26510\n-chr1\t9555464\t9555465\tMACS2_peak_78\t5.28945\n-chr1\t9633927\t9633928\tMACS2_peak_79\t7.51487\n-chr1\t9687168\t9687169\tMACS2_peak_80\t17.04807\n-chr1\t9785326\t9785327\tMACS2_peak_81\t7.51487\n-chr1\t9844799\t9844800\tMACS2_peak_82\t13.02599\n-chr1\t9927731\t9927732\tMACS2_peak_83\t12.16639\n-chr1\t9935117\t9935118\tMACS2_peak_84\t22.22259\n-chr1\t10002611\t10002612\tMACS2_peak_85\t10.84923\n-chr1\t10094708\t10094709\tMACS2_peak_86\t4.60941\n-chr1\t10213169\t10213170\tMACS2_peak_87\t5.28945\n-chr1\t10270453\t10270454\tMACS2_peak_88\t4.60941\n-chr1\t10398241\t10398242\tMACS2_peak_89\t5.28945\n-chr1\t10437671\t10437672\tMACS2_peak_90\t6.61760\n-chr1'..b'947\t46\t.\t3.90105\t7.77216\t4.60940\t55\n+chr1\t166134133\t166134388\tMACS2_peak_948\t66\t.\t4.87632\t10.06728\t6.61759\t208\n+chr1\t166448255\t166448688\tMACS2_peak_949\t108\t.\t6.82684\t14.88256\t10.84922\t215\n+chr1\t167028343\t167028616\tMACS2_peak_950\t47\t.\t5.58374\t7.96913\t4.79957\t215\n+chr1\t167035942\t167036261\tMACS2_peak_951\t66\t.\t4.87632\t10.06728\t6.61759\t95\n+chr1\t167237143\t167237397\tMACS2_peak_952\t35\t.\t3.80689\t6.57684\t3.50364\t152\n+chr1\t167370456\t167370840\tMACS2_peak_953\t66\t.\t4.87632\t10.06728\t6.61759\t230\n+chr1\t167411347\t167411617\tMACS2_peak_954\t63\t.\t6.63448\t9.70719\t6.34225\t160\n+chr1\t167509676\t167509994\tMACS2_peak_955\t98\t.\t5.90922\t13.74439\t9.80598\t89\n+chr1\t167606642\t167606904\tMACS2_peak_956\t75\t.\t4.92435\t11.15252\t7.51486\t151\n+chr1\t167657153\t167657498\tMACS2_peak_957\t130\t.\t7.80211\t17.38158\t13.02598\t182\n+chr1\t167684255\t167684787\tMACS2_peak_958\t52\t.\t3.93948\t8.63977\t5.28944\t413\n+chr1\t168051429\t168051903\tMACS2_peak_959\t75\t.\t4.92435\t11.15252\t7.51486\t110\n+chr1\t168054014\t168054268\tMACS2_peak_960\t52\t.\t3.93948\t8.63977\t5.28944\t113\n+chr1\t168115054\t168115312\tMACS2_peak_961\t75\t.\t4.92435\t11.15252\t7.51486\t127\n+chr1\t168312029\t168312283\tMACS2_peak_962\t31\t.\t2.95461\t6.22382\t3.18932\t57\n+chr1\t168409107\t168409398\tMACS2_peak_963\t87\t.\t5.85158\t12.44148\t8.70936\t128\n+chr1\t169317675\t169317929\tMACS2_peak_964\t61\t.\t6.38142\t9.46957\t6.11149\t103\n+chr1\t169435646\t169435900\tMACS2_peak_965\t52\t.\t3.93948\t8.63977\t5.28944\t83\n+chr1\t169515618\t169516039\tMACS2_peak_966\t108\t.\t6.82684\t14.88256\t10.84922\t211\n+chr1\t169570238\t169570598\tMACS2_peak_967\t75\t.\t4.92435\t11.15252\t7.51486\t118\n+chr1\t169681091\t169681643\tMACS2_peak_968\t108\t.\t6.82684\t14.88256\t10.84922\t268\n+chr1\t169778761\t169779123\tMACS2_peak_969\t121\t.\t6.89409\t16.40316\t12.16639\t165\n+chr1\t169898084\t169898451\tMACS2_peak_970\t130\t.\t7.80211\t17.38158\t13.02598\t122\n+chr1\t169979564\t169979919\tMACS2_peak_971\t98\t.\t5.90922\t13.74439\t9.80598\t171\n+chr1\t170658710\t170659105\tMACS2_peak_972\t75\t.\t4.92435\t11.15252\t7.51486\t147\n+chr1\t170936227\t170936611\tMACS2_peak_973\t75\t.\t4.92435\t11.15252\t7.51486\t178\n+chr1\t171157806\t171158175\tMACS2_peak_974\t90\t.\t6.66205\t12.78498\t9.02328\t139\n+chr1\t171454166\t171454693\tMACS2_peak_975\t87\t.\t5.85158\t12.44148\t8.70936\t242\n+chr1\t171624733\t171624987\tMACS2_peak_976\t52\t.\t3.93948\t8.63977\t5.28944\t92\n+chr1\t171770672\t171770926\tMACS2_peak_977\t35\t.\t3.80689\t6.57684\t3.50364\t138\n+chr1\t171952729\t171952983\tMACS2_peak_978\t46\t.\t3.90105\t7.77216\t4.60940\t136\n+chr1\t171953940\t171954438\tMACS2_peak_979\t66\t.\t4.87632\t10.06728\t6.61759\t249\n+chr1\t171971859\t171972280\tMACS2_peak_980\t121\t.\t6.89409\t16.40316\t12.16639\t186\n+chr1\t172104225\t172104597\tMACS2_peak_981\t75\t.\t4.92435\t11.15252\t7.51486\t222\n+chr1\t172398514\t172398852\tMACS2_peak_982\t66\t.\t4.87632\t10.06728\t6.61759\t178\n+chr1\t172688764\t172689204\tMACS2_peak_983\t61\t.\t6.38142\t9.46957\t6.11149\t199\n+chr1\t172711842\t172712109\tMACS2_peak_984\t66\t.\t4.87632\t10.06728\t6.61759\t170\n+chr1\t172714120\t172714382\tMACS2_peak_985\t87\t.\t5.85158\t12.44148\t8.70936\t185\n+chr1\t173171628\t173171882\tMACS2_peak_986\t30\t.\t3.71716\t5.88127\t3.00790\t122\n+chr1\t173389467\t173389819\tMACS2_peak_987\t129\t.\t8.56549\t17.23237\t12.97384\t172\n+chr1\t173400334\t173400718\tMACS2_peak_988\t87\t.\t5.85158\t12.44148\t8.70936\t223\n+chr1\t173684280\t173684534\tMACS2_peak_989\t27\t.\t2.92579\t5.57376\t2.70690\t48\n+chr1\t173794183\t173794465\tMACS2_peak_990\t46\t.\t4.64644\t7.70001\t4.60940\t140\n+chr1\t173883385\t173883681\tMACS2_peak_991\t98\t.\t5.90922\t13.74439\t9.80598\t179\n+chr1\t174084042\t174084320\tMACS2_peak_992\t75\t.\t4.92435\t11.15252\t7.51486\t124\n+chr1\t174186861\t174187115\tMACS2_peak_993\t38\t.\t5.00355\t6.95863\t3.88436\t171\n+chr1\t174227188\t174227538\tMACS2_peak_994\t87\t.\t5.85158\t12.44148\t8.70936\t189\n+chr1\t174695684\t174695942\tMACS2_peak_995\t66\t.\t4.87632\t10.06728\t6.61759\t180\n+chr1\t174713257\t174713511\tMACS2_peak_996\t52\t.\t3.93948\t8.63977\t5.28944\t62\n+chr1\t174739198\t174739503\tMACS2_peak_997\t52\t.\t4.75861\t8.57130\t5.28944\t149\n+chr1\t174967683\t174968030\tMACS2_peak_998\t48\t.\t5.50391\t8.00416\t4.83429\t163\n+chr1\t174998798\t174999052\tMACS2_peak_999\t52\t.\t3.93948\t8.63977\t5.28944\t183\n+chr1\t175094595\t175094849\tMACS2_peak_1000\t46\t.\t3.90105\t7.77216\t4.60940\t63\n' |
| b |
| diff -r bfe57d6e0c4c -r 6d4babad010f test-data/predictd_on_ChIP_200K_and_Control_200K.pdf |
| b |
| Binary file test-data/predictd_on_ChIP_200K_and_Control_200K.pdf has changed |
| b |
| diff -r bfe57d6e0c4c -r 6d4babad010f test-data/predictd_on_ChIP_200K_and_Control_200K.txt --- a/test-data/predictd_on_ChIP_200K_and_Control_200K.txt Mon Oct 12 11:24:39 2015 -0400 +++ b/test-data/predictd_on_ChIP_200K_and_Control_200K.txt Wed Jan 27 15:23:25 2016 -0500 |
| b |
| @@ -6,6 +6,7 @@ # tag size = 86 # total tags in alignment file # Build Peak Model... +#2 looking for paired plus/minus strand peaks... #2 number of paired peaks start model_add_line... start X-correlation... |
| b |
| diff -r bfe57d6e0c4c -r 6d4babad010f test-data/refinepeak_ChIP_and_summits.bed --- a/test-data/refinepeak_ChIP_and_summits.bed Mon Oct 12 11:24:39 2015 -0400 +++ b/test-data/refinepeak_ChIP_and_summits.bed Wed Jan 27 15:23:25 2016 -0500 |
| b |
| b'@@ -2,999 +2,999 @@\n chr1\t919487\t919488\tMACS2_peak_2_F\t2.46\n chr1\t937350\t937351\tMACS2_peak_3_F\t2.83\n chr1\t954797\t954798\tMACS2_peak_4_F\t2.83\n-chr1\t994890\t994891\tMACS2_peak_5_F\t2.83\n-chr1\t1057493\t1057494\tMACS2_peak_6_F\t2.83\n+chr1\t994890\t994891\tMACS2_peak_5_F\t1.83\n+chr1\t1057493\t1057494\tMACS2_peak_6_F\t1.83\n chr1\t1240751\t1240752\tMACS2_peak_7_F\t1.83\n chr1\t1307482\t1307483\tMACS2_peak_8_F\t4.00\n-chr1\t1440462\t1440463\tMACS2_peak_9_F\t1.83\n+chr1\t1440462\t1440463\tMACS2_peak_9_F\t2.83\n chr1\t1555487\t1555488\tMACS2_peak_10_F\t4.00\n-chr1\t1590693\t1590694\tMACS2_peak_11_F\t0.00\n+chr1\t1590885\t1590886\tMACS2_peak_11_F\t1.00\n chr1\t1837880\t1837881\tMACS2_peak_12_F\t4.90\n-chr1\t1840575\t1840576\tMACS2_peak_13_F\t4.00\n-chr1\t1976454\t1976455\tMACS2_peak_14_F\t2.00\n-chr1\t2071222\t2071223\tMACS2_peak_15_F\t0.00\n-chr1\t2105890\t2105891\tMACS2_peak_16_F\t0.00\n-chr1\t2126608\t2126609\tMACS2_peak_17_F\t3.46\n-chr1\t2246764\t2246765\tMACS2_peak_18_F\t2.83\n+chr1\t1840542\t1840543\tMACS2_peak_13_F\t2.00\n+chr1\t1976454\t1976455\tMACS2_peak_14_F\t2.83\n+chr1\t2071356\t2071357\tMACS2_peak_15_F\t2.00\n+chr1\t2105941\t2105942\tMACS2_peak_16_F\t1.00\n+chr1\t2126608\t2126609\tMACS2_peak_17_F\t2.46\n+chr1\t2246764\t2246765\tMACS2_peak_18_F\t3.00\n chr1\t2313333\t2313334\tMACS2_peak_19_F\t3.46\n-chr1\t2346010\t2346011\tMACS2_peak_20_R\t5.66\n-chr1\t2510125\t2510126\tMACS2_peak_21_F\t2.83\n-chr1\t3341443\t3341444\tMACS2_peak_22_F\t0.00\n+chr1\t2346043\t2346044\tMACS2_peak_20_F\t4.66\n+chr1\t2510125\t2510126\tMACS2_peak_21_F\t1.83\n+chr1\t3341443\t3341444\tMACS2_peak_22_F\t-1.00\n chr1\t3369851\t3369852\tMACS2_peak_23_F\t2.83\n-chr1\t3400563\t3400564\tMACS2_peak_24_F\t3.46\n-chr1\t3407907\t3407908\tMACS2_peak_25_F\t0.00\n+chr1\t3400563\t3400564\tMACS2_peak_24_F\t2.46\n+chr1\t3407907\t3407908\tMACS2_peak_25_F\t-1.00\n chr1\t3481992\t3481993\tMACS2_peak_26_F\t4.00\n chr1\t3535802\t3535803\tMACS2_peak_27_F\t2.00\n-chr1\t3537759\t3537760\tMACS2_peak_28_F\t0.00\n+chr1\t3537556\t3537557\tMACS2_peak_28_F\t0.00\n chr1\t3593823\t3593824\tMACS2_peak_29_F\t2.83\n chr1\t3641130\t3641131\tMACS2_peak_30_R\t10.00\n chr1\t3702198\t3702199\tMACS2_peak_31_F\t2.83\n-chr1\t3773867\t3773868\tMACS2_peak_32_R\t6.32\n-chr1\t3827469\t3827470\tMACS2_peak_33_F\t4.00\n+chr1\t3773867\t3773868\tMACS2_peak_32_R\t5.32\n+chr1\t3827546\t3827547\tMACS2_peak_33_F\t4.90\n chr1\t4712838\t4712839\tMACS2_peak_34_F\t2.83\n chr1\t4886247\t4886248\tMACS2_peak_35_F\t2.83\n chr1\t5570049\t5570050\tMACS2_peak_36_F\t4.00\n-chr1\t5574872\t5574873\tMACS2_peak_37_F\t0.00\n-chr1\t5805892\t5805893\tMACS2_peak_38_F\t2.00\n-chr1\t5976034\t5976035\tMACS2_peak_39_F\t0.00\n-chr1\t6094646\t6094647\tMACS2_peak_40_F\t0.00\n-chr1\t6113105\t6113106\tMACS2_peak_41_F\t2.00\n-chr1\t6265402\t6265403\tMACS2_peak_42_F\t4.00\n-chr1\t6305237\t6305238\tMACS2_peak_43_F\t2.83\n+chr1\t5574881\t5574882\tMACS2_peak_37_F\t1.83\n+chr1\t5805892\t5805893\tMACS2_peak_38_F\t1.00\n+chr1\t5975945\t5975946\tMACS2_peak_39_F\t0.00\n+chr1\t6094766\t6094767\tMACS2_peak_40_F\t1.00\n+chr1\t6113105\t6113106\tMACS2_peak_41_F\t2.83\n+chr1\t6265402\t6265403\tMACS2_peak_42_F\t3.90\n+chr1\t6305237\t6305238\tMACS2_peak_43_F\t1.83\n chr1\t6307000\t6307001\tMACS2_peak_44_F\t2.83\n-chr1\t6403590\t6403591\tMACS2_peak_45_F\t3.46\n-chr1\t6464859\t6464860\tMACS2_peak_46_F\t3.46\n-chr1\t6483666\t6483667\tMACS2_peak_47_F\t2.83\n-chr1\t6498287\t6498288\tMACS2_peak_48_F\t4.90\n-chr1\t6535636\t6535637\tMACS2_peak_49_F\t3.46\n+chr1\t6403695\t6403696\tMACS2_peak_45_F\t4.90\n+chr1\t6464897\t6464898\tMACS2_peak_46_F\t4.90\n+chr1\t6483666\t6483667\tMACS2_peak_47_F\t1.83\n+chr1\t6498295\t6498296\tMACS2_peak_48_R\t5.66\n+chr1\t6535639\t6535640\tMACS2_peak_49_F\t4.90\n chr1\t6614629\t6614630\tMACS2_peak_50_F\t2.83\n chr1\t6706734\t6706735\tMACS2_peak_51_F\t4.90\n-chr1\t6762004\t6762005\tMACS2_peak_52_R\t5.66\n-chr1\t6780313\t6780314\tMACS2_peak_53_F\t4.00\n+chr1\t6762051\t6762052\tMACS2_peak_52_R\t6.32\n+chr1\t6780313\t6780314\tMACS2_peak_53_F\t3.00\n chr1\t6787701\t6787702\tMACS2_peak_54_R\t5.93\n-chr1\t6950124\t6950125\tMACS2_peak_55_F\t3.46\n+chr1\t6950124\t6950125\tMACS2_peak_55_F\t4.00\n chr1\t7102878\t7102879\tMACS2_peak_56_F\t3.46\n-chr1\t7278465\t7278466\tMACS2_peak_57_F\t0.00\n-chr1\t7868491\t7868492\tMACS2_peak_58_F\t3.46\n+chr1\t7278530\t7278531\tMACS2_peak_57_F\t2.46\n+chr1\t7868491\t7868492\tMACS2_peak_58_F\t2.46\n chr1\t7962955\t7962956\tMACS2_peak_59_F\t2.8'..b'+chr1\t167411459\t167411460\tMACS2_peak_954_R\t6.48\n chr1\t167509745\t167509746\tMACS2_peak_955_F\t4.00\n-chr1\t167606712\t167606713\tMACS2_peak_956_F\t0.00\n+chr1\t167606712\t167606713\tMACS2_peak_956_F\t-1.00\n chr1\t167657299\t167657300\tMACS2_peak_957_F\t4.90\n-chr1\t167684581\t167684582\tMACS2_peak_958_F\t0.00\n-chr1\t168051650\t168051651\tMACS2_peak_959_F\t1.83\n-chr1\t168054094\t168054095\tMACS2_peak_960_F\t2.83\n-chr1\t168114981\t168114982\tMACS2_peak_961_F\t0.00\n-chr1\t168312030\t168312031\tMACS2_peak_962_F\t2.00\n-chr1\t168409222\t168409223\tMACS2_peak_963_F\t4.00\n+chr1\t167684256\t167684257\tMACS2_peak_958_F\t-1.00\n+chr1\t168051650\t168051651\tMACS2_peak_959_F\t2.46\n+chr1\t168054094\t168054095\tMACS2_peak_960_F\t1.83\n+chr1\t168114854\t168114855\tMACS2_peak_961_F\t0.00\n+chr1\t168312030\t168312031\tMACS2_peak_962_F\t1.00\n+chr1\t168409222\t168409223\tMACS2_peak_963_F\t3.00\n chr1\t169317755\t169317756\tMACS2_peak_964_R\t5.66\n chr1\t169435717\t169435718\tMACS2_peak_965_F\t2.83\n-chr1\t169515822\t169515823\tMACS2_peak_966_F\t2.83\n-chr1\t169570156\t169570157\tMACS2_peak_967_F\t0.00\n-chr1\t169681329\t169681330\tMACS2_peak_968_F\t3.90\n-chr1\t169778870\t169778871\tMACS2_peak_969_F\t4.00\n+chr1\t169515840\t169515841\tMACS2_peak_966_F\t2.46\n+chr1\t169570038\t169570039\tMACS2_peak_967_F\t0.00\n+chr1\t169681401\t169681402\tMACS2_peak_968_F\t4.00\n+chr1\t169778870\t169778871\tMACS2_peak_969_F\t3.90\n chr1\t169898139\t169898140\tMACS2_peak_970_F\t4.00\n-chr1\t169979682\t169979683\tMACS2_peak_971_F\t4.47\n-chr1\t170658657\t170658658\tMACS2_peak_972_F\t0.00\n-chr1\t170936375\t170936376\tMACS2_peak_973_F\t3.46\n-chr1\t171157922\t171157923\tMACS2_peak_974_F\t0.00\n-chr1\t171454456\t171454457\tMACS2_peak_975_F\t4.90\n+chr1\t169979682\t169979683\tMACS2_peak_971_F\t4.00\n+chr1\t170658510\t170658511\tMACS2_peak_972_F\t0.00\n+chr1\t170936375\t170936376\tMACS2_peak_973_F\t2.46\n+chr1\t171157970\t171157971\tMACS2_peak_974_F\t3.00\n+chr1\t171454456\t171454457\tMACS2_peak_975_F\t2.90\n chr1\t171624794\t171624795\tMACS2_peak_976_F\t2.83\n-chr1\t171770610\t171770611\tMACS2_peak_977_F\t0.00\n+chr1\t171770472\t171770473\tMACS2_peak_977_F\t0.00\n chr1\t171952803\t171952804\tMACS2_peak_978_F\t2.83\n-chr1\t171954349\t171954350\tMACS2_peak_979_F\t0.00\n+chr1\t171954349\t171954350\tMACS2_peak_979_F\t3.00\n chr1\t171972029\t171972030\tMACS2_peak_980_R\t6.00\n-chr1\t172104344\t172104345\tMACS2_peak_981_F\t2.00\n-chr1\t172398492\t172398493\tMACS2_peak_982_F\t0.00\n-chr1\t172688955\t172688956\tMACS2_peak_983_F\t4.90\n-chr1\t172711856\t172711857\tMACS2_peak_984_F\t0.00\n-chr1\t172714264\t172714265\tMACS2_peak_985_F\t4.00\n-chr1\t173171741\t173171742\tMACS2_peak_986_F\t2.83\n-chr1\t173389620\t173389621\tMACS2_peak_987_R\t8.00\n+chr1\t172104344\t172104345\tMACS2_peak_981_F\t2.83\n+chr1\t172398314\t172398315\tMACS2_peak_982_F\t0.00\n+chr1\t172688955\t172688956\tMACS2_peak_983_F\t3.90\n+chr1\t172712016\t172712017\tMACS2_peak_984_F\t1.83\n+chr1\t172714264\t172714265\tMACS2_peak_985_F\t4.90\n+chr1\t173171741\t173171742\tMACS2_peak_986_F\t1.83\n+chr1\t173389620\t173389621\tMACS2_peak_987_R\t7.00\n chr1\t173400465\t173400466\tMACS2_peak_988_F\t4.90\n-chr1\t173684281\t173684282\tMACS2_peak_989_F\t0.00\n-chr1\t173794123\t173794124\tMACS2_peak_990_F\t0.00\n+chr1\t173684478\t173684479\tMACS2_peak_989_F\t1.00\n+chr1\t173794266\t173794267\tMACS2_peak_990_F\t2.83\n chr1\t173883547\t173883548\tMACS2_peak_991_F\t4.00\n-chr1\t174084082\t174084083\tMACS2_peak_992_F\t0.00\n-chr1\t174186991\t174186992\tMACS2_peak_993_R\t8.00\n-chr1\t174227339\t174227340\tMACS2_peak_994_F\t4.00\n+chr1\t174084082\t174084083\tMACS2_peak_992_F\t-1.00\n+chr1\t174186991\t174186992\tMACS2_peak_993_R\t8.94\n+chr1\t174227339\t174227340\tMACS2_peak_994_F\t3.90\n chr1\t174695830\t174695831\tMACS2_peak_995_F\t4.00\n-chr1\t174713262\t174713263\tMACS2_peak_996_F\t0.00\n-chr1\t174739304\t174739305\tMACS2_peak_997_F\t2.00\n-chr1\t174967837\t174967838\tMACS2_peak_998_R\t7.80\n-chr1\t174998966\t174998967\tMACS2_peak_999_F\t0.00\n-chr1\t175094596\t175094597\tMACS2_peak_1000_F\t2.00\n\\ No newline at end of file\n+chr1\t174713262\t174713263\tMACS2_peak_996_F\t-1.00\n+chr1\t174739304\t174739305\tMACS2_peak_997_F\t1.83\n+chr1\t174967837\t174967838\tMACS2_peak_998_R\t6.80\n+chr1\t174998966\t174998967\tMACS2_peak_999_F\t-1.00\n+chr1\t175094672\t175094673\tMACS2_peak_1000_F\t1.83\n\\ No newline at end of file\n' |
| b |
| diff -r bfe57d6e0c4c -r 6d4babad010f tool_dependencies.xml --- a/tool_dependencies.xml Mon Oct 12 11:24:39 2015 -0400 +++ b/tool_dependencies.xml Wed Jan 27 15:23:25 2016 -0500 |
| b |
| @@ -6,14 +6,14 @@ <package name="scipy" version="0.12.0"> <repository changeset_revision="cfbbe183f8a7" name="package_scipy_0_12" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="R_3_0_1" version="3.0.1"> - <repository changeset_revision="59b82e6e0801" name="package_r_3_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="R" version="3.1.2"> + <repository changeset_revision="c987143177d4" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="gnu_awk" version="4.1.0"> - <repository changeset_revision="52a8268bb49f" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="f145f856ec57" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="macs2" version="2.1.0"> - <repository changeset_revision="4d7ef54c3fa4" name="package_macs2_2_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="macs2" version="2.1.0.20151222"> + <repository changeset_revision="ae3cfa214a33" name="package_macs2_2_1_0_20151222" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <set_environment version="1.0"> <environment_variable action="set_to" name="MACS2_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> |