| Previous changeset 1:51b4590a972d (2017-09-18) Next changeset 3:1c9810ba0638 (2017-09-22) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b |
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modified:
RepEnrich.py edgeR_repenrich.R edger-repenrich.xml repenrich.xml test-data/353_fraction_counts.tab test-data/354_fraction_counts.tab test-data/355_fraction_counts.tab test-data/356_fraction_counts.tab test-data/Normalized_counts_file.tab test-data/Samp-paired_class_fraction_counts.tab test-data/Samp-paired_family_fraction_counts.tab test-data/Samp_class_fraction_counts.tabular test-data/Samp_family_fraction_counts.tabular test-data/aligned_353.tab test-data/aligned_354.tab test-data/aligned_355.tab test-data/aligned_356.tab test-data/aligned_reads.tab test-data/edgeR_plots.pdf test-data/edgeR_result_file.tab test-data/paired-aligned_reads.tab |
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| diff -r 51b4590a972d -r 15e3e29f310e RepEnrich.py --- a/RepEnrich.py Mon Sep 18 17:22:07 2017 -0400 +++ b/RepEnrich.py Tue Sep 19 17:23:15 2017 -0400 |
| [ |
| @@ -431,34 +431,34 @@ if allcountmethod == "TRUE": fout1 = open(outputfolder + os.path.sep + outputfile_prefix + '_total_counts.txt', 'w') - for key in reptotalcounts.keys(): + for key in sorted(reptotalcounts.keys()): fout1.write(str(key) + '\t' + repeatclass[key] + '\t' + repeatfamily[key] + '\t' + str(reptotalcounts[key]) + '\n') fout2 = open(outputfolder + os.path.sep + outputfile_prefix + '_class_total_counts.txt', 'w') - for key in classtotalcounts.keys(): + for key in sorted(classtotalcounts.keys()): fout2.write(str(key) + '\t' + str(classtotalcounts[key]) + '\n') fout3 = open(outputfolder + os.path.sep + outputfile_prefix + '_family_total_counts.txt', 'w') - for key in familytotalcounts.keys(): + for key in sorted(familytotalcounts.keys()): fout3.write(str(key) + '\t' + str(familytotalcounts[key]) + '\n') fout4 = open(outputfolder + os.path.sep + outputfile_prefix + '_unique_counts.txt', 'w') - for key in repcounts2.keys(): + for key in sorted(repcounts2.keys()): fout4.write(str(key) + '\t' + repeatclass[key] + '\t' + repeatfamily[key] + '\t' + str(repcounts2[key]) + '\n') fout5 = open(outputfolder + os.path.sep + outputfile_prefix + '_class_fraction_counts.txt', 'w') - for key in classfractionalcounts.keys(): + for key in sorted(classfractionalcounts.keys()): fout5.write(str(key) + '\t' + str(classfractionalcounts[key]) + '\n') fout6 = open(outputfolder + os.path.sep + outputfile_prefix + '_family_fraction_counts.txt', 'w') - for key in familyfractionalcounts.keys(): + for key in sorted(familyfractionalcounts.keys()): fout6.write(str(key) + '\t' + str(familyfractionalcounts[key]) + '\n') fout7 = open(outputfolder + os.path.sep + outputfile_prefix + '_fraction_counts.txt', 'w') - for key in fractionalcounts.keys(): + for key in sorted(fractionalcounts.keys()): fout7.write(str(key) + '\t' + repeatclass[key] + '\t' + repeatfamily[key] + '\t' + str(int(fractionalcounts[key])) + '\n') @@ -472,15 +472,15 @@ else: fout1 = open(outputfolder + os.path.sep + outputfile_prefix + '_class_fraction_counts.txt', 'w') - for key in classfractionalcounts.keys(): + for key in sorted(classfractionalcounts.keys()): fout1.write(str(key) + '\t' + str(classfractionalcounts[key]) + '\n') fout2 = open(outputfolder + os.path.sep + outputfile_prefix + '_family_fraction_counts.txt', 'w') - for key in familyfractionalcounts.keys(): + for key in sorted(familyfractionalcounts.keys()): fout2.write(str(key) + '\t' + str(familyfractionalcounts[key]) + '\n') fout3 = open(outputfolder + os.path.sep + outputfile_prefix + '_fraction_counts.txt', 'w') - for key in fractionalcounts.keys(): + for key in sorted(fractionalcounts.keys()): fout3.write(str(key) + '\t' + repeatclass[key] + '\t' + repeatfamily[key] + '\t' + str(int(fractionalcounts[key])) + '\n') |
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| diff -r 51b4590a972d -r 15e3e29f310e edgeR_repenrich.R --- a/edgeR_repenrich.R Mon Sep 18 17:22:07 2017 -0400 +++ b/edgeR_repenrich.R Tue Sep 19 17:23:15 2017 -0400 |
| [ |
| @@ -101,10 +101,10 @@ filesj <- fromJSON(opt$alignmentB, method = "C", unexpected.escape = "error") sizes <- c() for (file in filesi) { - sizes <- c(sizes, read.delim(file, header=FALSE)[1,1]) + sizes <- c(sizes, read.delim(file, header=TRUE)[1,1]) } for (file in filesj) { - sizes <- c(sizes, read.delim(file, header=FALSE)[1,1]) + sizes <- c(sizes, read.delim(file, header=TRUE)[1,1]) } # build a meta data object |
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| diff -r 51b4590a972d -r 15e3e29f310e edger-repenrich.xml --- a/edger-repenrich.xml Mon Sep 18 17:22:07 2017 -0400 +++ b/edger-repenrich.xml Tue Sep 19 17:23:15 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="edger-repenrich" name="edgeR-repenrich" version="1.4.1"> +<tool id="edger-repenrich" name="edgeR-repenrich" version="1.4.2"> <description>Determines differentially expressed features from RepEnrich counts</description> <requirements> <requirement type="package" version="3.16.5">bioconductor-edger</requirement> |
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| diff -r 51b4590a972d -r 15e3e29f310e repenrich.xml --- a/repenrich.xml Mon Sep 18 17:22:07 2017 -0400 +++ b/repenrich.xml Tue Sep 19 17:23:15 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="repenrich" name="RepEnrich" version="1.4.1"> +<tool id="repenrich" name="RepEnrich" version="1.4.2"> <description>Repeat Element Profiling</description> <requirements> <requirement type="package" version="1.2.0">bowtie</requirement> @@ -24,12 +24,14 @@ bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt && TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) && NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && - echo \$((\$TOTAL-\$NONALIGNED)) > bowtie_aligned.numb && + echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb && + echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb && #else: bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq -1 ${input_base}.fastq -2 ${input_base}_2.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt && TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) && NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && - echo \$((\$TOTAL-\$NONALIGNED)) > bowtie_aligned.numb && + echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb && + echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb && #end if samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam && samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted && @@ -65,14 +67,10 @@ </inputs> <outputs> - <data format="tabular" name="bowtie_alignments" label="RepEnrich on ${on_string}: reads aligned" from_work_dir="bowtie_aligned.numb"> - </data> - <data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tabular"> - </data> - <data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tabular"> - </data> - <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tabular"> - </data> + <data format="tabular" name="bowtie_alignments" label="RepEnrich on ${on_string}: reads aligned" from_work_dir="bowtie_aligned.numb" /> + <data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tabular" /> + <data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tabular" /> + <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tabular" /> </outputs> <tests> |
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| diff -r 51b4590a972d -r 15e3e29f310e test-data/353_fraction_counts.tab --- a/test-data/353_fraction_counts.tab Mon Sep 18 17:22:07 2017 -0400 +++ b/test-data/353_fraction_counts.tab Tue Sep 19 17:23:15 2017 -0400 |
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| b'@@ -1,210 +1,210 @@\n-LSU-rRNA_Dme\trRNA\trRNA\t3078755\n-FW3_DM\tLINE\tJockey\t913\n-DMTOM1_LTR\tLTR\tGypsy\t1012\n-R1_DM\tLINE\tR1\t5407\n-TAHRE\tLINE\tJockey\t3914\n-G4_DM\tLINE\tJockey\t3407\n-BS\tLINE\tJockey\t5001\n-Stalker2_I-int\tLTR\tGypsy\t12474\n-Stalker3_LTR\tLTR\tGypsy\t439\n-TABOR_I-int\tLTR\tGypsy\t3081\n-G7_DM\tLINE\tJockey\t98\n-BEL_I-int\tLTR\tPao\t21860\n-Gypsy6_I-int\tLTR\tGypsy\t6746\n+5S_DM\tRNA\tRNA\t10392\n ACCORD_I-int\tLTR\tGypsy\t2165\n-DM412B_LTR\tLTR\tGypsy\t2910\n-G2_DM\tLINE\tJockey\t1132\n-SSU-rRNA_Hsa\trRNA\trRNA\t172100\n-TART_B1\tLINE\tJockey\t21513\n-S2_DM\tDNA\tTcMar-Tc1\t733\n-LOOPER1_DM\tDNA\tPiggyBac\t589\n-HOBO\tDNA\thAT-hobo\t4404\n+ACCORD_LTR\tLTR\tGypsy\t220\n+ACCORD2_I-int\tLTR\tGypsy\t2458\n+ACCORD2_LTR\tLTR\tGypsy\t192\n+ALA_DM\tUnknown\tUnknown\t6\n ARS406_DM\tUnknown\tUnknown\t719\n-G6_DM\tLINE\tJockey\t3473\n-DOC2_DM\tLINE\tJockey\t4538\n Baggins1\tLINE\tLOA\t3893\n-NINJA_LTR\tLTR\tPao\t406\n-TRANSIB2\tDNA\tCMC-Transib\t3076\n-Gypsy5_LTR\tLTR\tGypsy\t451\n-MDG3_LTR\tLTR\tGypsy\t848\n-Gypsy12A_LTR\tLTR\tGypsy\t2242\n-Gypsy_LTR\tLTR\tGypsy\t917\n-TIRANT_LTR\tLTR\tGypsy\t1279\n-I_DM\tLINE\tI\t7013\n-DIVER2_I-int\tLTR\tPao\t5627\n-P-1_DY\tDNA\tP\t2\n-Invader2_I-int\tLTR\tGypsy\t5510\n-DOC6_DM\tLINE\tJockey\t1240\n-BURDOCK_LTR\tLTR\tGypsy\t370\n-SSU-rRNA_Dme\trRNA\trRNA\t4153\n-MAX_LTR\tLTR\tPao\t753\n-STALKER4_LTR\tLTR\tGypsy\t1210\n-XDMR_DM\tUnknown\tUnknown\t4328\n BARI_DM\tDNA\tTcMar-Tc1\t902\n-Transib-N1_DM\tDNA\tCMC-Transib\t371\n-Gypsy5_I-int\tLTR\tGypsy\t2186\n-XDMR\tUnknown\tUnknown\t1440\n-ACCORD2_LTR\tLTR\tGypsy\t192\n-POGON1\tDNA\tTcMar-Pogo\t403\n+BARI1\tDNA\tTcMar-Tc1\t322\n+BATUMI_I-int\tLTR\tPao\t4789\n+BATUMI_LTR\tLTR\tPao\t403\n+BEL_I-int\tLTR\tPao\t21860\n+BEL_LTR\tLTR\tPao\t858\n+Bica_I-int\tLTR\tGypsy\t1390\n+Bica_LTR\tLTR\tGypsy\t125\n+BLASTOPIA_I-int\tLTR\tGypsy\t9540\n+BLASTOPIA_LTR\tLTR\tGypsy\t478\n+BLOOD_I-int\tLTR\tGypsy\t17222\n+BLOOD_LTR\tLTR\tGypsy\t746\n+BS\tLINE\tJockey\t5001\n+BS2\tLINE\tJockey\t4991\n+BS3_DM\tLINE\tJockey\t877\n BS4_DM\tLINE\tJockey\t21\n-ALA_DM\tUnknown\tUnknown\t6\n-Gypsy1-I_DM\tLTR\tGypsy\t6297\n-ACCORD_LTR\tLTR\tGypsy\t220\n BURDOCK_I-int\tLTR\tGypsy\t3332\n-ZAM_I-int\tLTR\tGypsy\t4426\n-Invader5_I-int\tLTR\tGypsy\t335\n-G3_DM\tLINE\tJockey\t556\n-ROOA_I-int\tLTR\tPao\t4589\n-Gypsy1-LTR_DM\tLTR\tGypsy\t795\n+BURDOCK_LTR\tLTR\tGypsy\t370\n+Chimpo_I-int\tLTR\tGypsy\t1060\n+Chimpo_LTR\tLTR\tGypsy\t120\n+Chouto_I-int\tLTR\tGypsy\t1304\n+Chouto_LTR\tLTR\tGypsy\t281\n+CIRCE\tLTR\tGypsy\t3323\n+Copia_I-int\tLTR\tCopia\t26733\n+Copia_LTR\tLTR\tCopia\t1129\n+Copia1-I_DM\tLTR\tCopia\t3518\n+Copia1-LTR_DM\tLTR\tCopia\t566\n+Copia2_I-int\tLTR\tCopia\t3455\n+Copia2_LTR_DM\tLTR\tCopia\t486\n+DIVER_I-int\tLTR\tPao\t15627\n+DIVER_LTR\tLTR\tPao\t429\n+DIVER2_I-int\tLTR\tPao\t5627\n+DIVER2_LTR\tLTR\tPao\t535\n DM1731_I-int\tLTR\tCopia\t4881\n-ROO_I-int\tLTR\tPao\t28034\n+DM1731_LTR\tLTR\tCopia\t440\n+DM176_I-int\tLTR\tGypsy\t2813\n+DM176_LTR\tLTR\tGypsy\t872\n+DM297_I-int\tLTR\tGypsy\t11530\n+DM297_LTR\tLTR\tGypsy\t1478\n DM412\tLTR\tGypsy\t23566\n-PROTOP\tDNA\tP\t4353\n-TART-A\tLINE\tJockey\t3408\n-ROO_LTR\tLTR\tPao\t1851\n-DIVER_LTR\tLTR\tPao\t429\n-Gypsy3_I-int\tLTR\tGypsy\t2753\n-BATUMI_LTR\tLTR\tPao\t403\n-IDEFIX_LTR\tLTR\tGypsy\t1844\n-G5_DM\tLINE\tJockey\t2551\n-HETA\tLINE\tJockey\t24397\n-Gypsy11_I-int\tLTR\tGypsy\t560\n-R1-2_DM\tLINE\tR1\t177\n-Gypsy11_LTR\tLTR\tGypsy\t149\n-HELENA_RT\tLINE\tJockey\t627\n-FTZ_DM\tUnknown\tUnknown\t0\n-MICROPIA_I-int\tLTR\tGypsy\t10355\n-Invader4_I-int\tLTR\tGypsy\t1219\n-PLACW_DM\tDNA\tP\t127\n-BLOOD_LTR\tLTR\tGypsy\t746\n-R2_DM\tLINE\tR2\t8407\n-Copia1-I_DM\tLTR\tCopia\t3518\n-Gypsy4_I-int\tLTR\tGypsy\t10056\n-Chouto_LTR\tLTR\tGypsy\t281\n-BATUMI_I-int\tLTR\tPao\t4789\n-DNAREP1_DM\tRC\tHelitron\t63954\n+DM412B_LTR\tLTR\tGypsy\t2910\n+DMCR1A\tLINE\tCR1\t17957\n+DMLTR5\tLTR\tGypsy\t160\n+DMRP1\tUnknown\tUnknown\t227\n+DMRPR\tUnknown\tUnknown\t187\n+DMRT1A\tLINE\tR1\t3540\n DMRT1B\tLINE\tR1\t7119\n DMRT1C\tLINE\tR1\t2087\n-TLD2\tLTR\tGypsy\t17\n-DMRT1A\tLINE\tR1\t3540\n-DM1731_LTR\tLTR\tCopia\t440\n-LSU-rRNA_Cel\trRNA\trRNA\t326925\n-Copia_LTR\tLTR\tCopia\t1129\n+DMTOM1_LTR\tLTR\tGypsy\t1012\n+DNAREP1_DM\tRC\tHelitron\t63954\n+DOC\tLINE\tJockey\t16414\n+DOC2_DM\tLINE\tJockey\t4538\n+DOC3_DM\tLINE\tJockey\t10659\n+DOC4_DM\tLINE\tJockey\t830\n+DOC5_DM\tLINE\tJockey\t2183\n+DOC6_DM\tLINE\tJockey\t1240\n+FB4_DM\tDNA\tTcMar-Tc1\t6939\n+FROGGER_I-int\tLTR\tCopia\t1361\n+FROGGER_LTR\tLTR\tCopia\t54\n+FTZ_DM\tUnknown\tUnknown\t0\n+FUSHI_DM\tUnknown\tUnknown\t0\n+FW2_DM\tLINE\tJockey\t13847\n+FW3_DM\tLINE\tJocke'..b'go\t403\n+PROTOP\tDNA\tP\t4353\n+PROTOP_A\tDNA\tP\t3384\n+PROTOP_B\tDNA\tP\t8285\n+QUASIMODO_I-int\tLTR\tGypsy\t13018\n QUASIMODO_LTR\tLTR\tGypsy\t1174\n-TABOR_LTR\tLTR\tGypsy\t273\n-Stalker2_LTR\tLTR\tGypsy\t672\n-MICROPIA_LTR\tLTR\tGypsy\t863\n-Gypsy9_I-int\tLTR\tGypsy\t474\n-STALKER4_I-int\tLTR\tGypsy\t5741\n-TRANSIB1\tDNA\tCMC-Transib\t2116\n-DOC\tLINE\tJockey\t16414\n-TRANSIB3\tDNA\tCMC-Transib\t1132\n-Copia_I-int\tLTR\tCopia\t26733\n-TRANSIB4\tDNA\tCMC-Transib\t571\n-Gypsy10_LTR\tLTR\tGypsy\t368\n-Invader3_I-int\tLTR\tGypsy\t3722\n-Invader1_I-int\tLTR\tGypsy\t1672\n-BS3_DM\tLINE\tJockey\t877\n-Gypsy2-LTR_DM\tLTR\tGypsy\t690\n-LSU-rRNA_Hsa\trRNA\trRNA\t0\n-NOMAD_LTR\tLTR\tGypsy\t822\n-Helitron1_DM\tRC\tHelitron\t6\n-LINEJ1_DM\tLINE\tJockey\t6329\n-Invader4_LTR\tLTR\tGypsy\t1228\n-MDG3_I-int\tLTR\tGypsy\t4971\n-LmeSINE1c\tSINE\ttRNA-Deu-L2\t1414\n+QUASIMODO2-I_DM\tLTR\tGypsy\t2225\n+QUASIMODO2-LTR_DM\tLTR\tGypsy\t200\n+R1_DM\tLINE\tR1\t5407\n+R1-2_DM\tLINE\tR1\t177\n+R2_DM\tLINE\tR2\t8407\n+ROO_I-int\tLTR\tPao\t28034\n+ROO_LTR\tLTR\tPao\t1851\n+ROOA_I-int\tLTR\tPao\t4589\n+ROOA_LTR\tLTR\tPao\t483\n+ROVER-I_DM\tLTR\tGypsy\t5589\n ROVER-LTR_DM\tLTR\tGypsy\t415\n S_DM\tDNA\tTcMar-Tc1\t3476\n-Invader6_I-int\tLTR\tGypsy\t6701\n-ROVER-I_DM\tLTR\tGypsy\t5589\n-QUASIMODO_I-int\tLTR\tGypsy\t13018\n-Chouto_I-int\tLTR\tGypsy\t1304\n-NTS_DM\tOther\tOther\t36205\n-Gypsy3_LTR\tLTR\tGypsy\t447\n+S2_DM\tDNA\tTcMar-Tc1\t733\n SSU-rRNA_Cel\trRNA\trRNA\t2183\n-MINOS\tDNA\tTcMar-Tc1\t226\n-DOC4_DM\tLINE\tJockey\t830\n-ZAM_LTR\tLTR\tGypsy\t225\n-QUASIMODO2-LTR_DM\tLTR\tGypsy\t200\n-Gypsy2-I_DM\tLTR\tGypsy\t3896\n-TRANSPAC_I-int\tLTR\tGypsy\t14982\n-Bica_I-int\tLTR\tGypsy\t1390\n-BS2\tLINE\tJockey\t4991\n-BLOOD_I-int\tLTR\tGypsy\t17222\n-DMCR1A\tLINE\tCR1\t17957\n-QUASIMODO2-I_DM\tLTR\tGypsy\t2225\n-HMSBEAGLE_I-int\tLTR\tGypsy\t5908\n-DMLTR5\tLTR\tGypsy\t160\n-Gypsy7_LTR\tLTR\tGypsy\t87\n-G5A_DM\tLINE\tJockey\t1595\n-MDG1_I-int\tLTR\tGypsy\t13740\n-Gypsy2_I-int\tLTR\tGypsy\t3453\n-BARI1\tDNA\tTcMar-Tc1\t322\n-Invader5_LTR\tLTR\tGypsy\t64\n-DM176_LTR\tLTR\tGypsy\t872\n-DOC3_DM\tLINE\tJockey\t10659\n-Copia1-LTR_DM\tLTR\tCopia\t566\n-TOM_I-int\tLTR\tGypsy\t2311\n-NOF_FB\tDNA\tMULE-NOF\t960\n-Chimpo_I-int\tLTR\tGypsy\t1060\n-DIVER_I-int\tLTR\tPao\t15627\n+SSU-rRNA_Dme\trRNA\trRNA\t4153\n+SSU-rRNA_Hsa\trRNA\trRNA\t172100\n+Stalker2_I-int\tLTR\tGypsy\t12474\n+Stalker2_LTR\tLTR\tGypsy\t672\n+Stalker3_LTR\tLTR\tGypsy\t439\n+STALKER4_I-int\tLTR\tGypsy\t5741\n+STALKER4_LTR\tLTR\tGypsy\t1210\n+TABOR_I-int\tLTR\tGypsy\t3081\n+TABOR_LTR\tLTR\tGypsy\t273\n+TAHRE\tLINE\tJockey\t3914\n+TART_B1\tLINE\tJockey\t21513\n+TART-A\tLINE\tJockey\t3408\n+TC1_DM\tDNA\tTcMar-Tc1\t1960\n+TC1-2_DM\tDNA\tTcMar-Tc1\t3948\n TIRANT_I-int\tLTR\tGypsy\t8559\n-Gypsy2_LTR\tLTR\tGypsy\t485\n-FB4_DM\tDNA\tTcMar-Tc1\t6939\n-GTWIN_LTR\tLTR\tGypsy\t467\n-Invader6_LTR\tLTR\tGypsy\t588\n-Gypsy8_I-int\tLTR\tGypsy\t4083\n-G_DM\tLINE\tJockey\t8035\n-TRANSPAC_LTR\tLTR\tGypsy\t555\n-FUSHI_DM\tUnknown\tUnknown\t0\n+TIRANT_LTR\tLTR\tGypsy\t1279\n+TLD2\tLTR\tGypsy\t17\n+TOM_I-int\tLTR\tGypsy\t2311\n+Transib-N1_DM\tDNA\tCMC-Transib\t371\n+TRANSIB1\tDNA\tCMC-Transib\t2116\n+TRANSIB2\tDNA\tCMC-Transib\t3076\n+TRANSIB3\tDNA\tCMC-Transib\t1132\n+TRANSIB4\tDNA\tCMC-Transib\t571\n Transib5\tDNA\tCMC-Transib\t965\n-MuDR-1_DEl\tDNA\tMULE-NOF\t9\n-Mariner2_DM\tDNA\tTcMar-Tc1\t1591\n-DOC5_DM\tLINE\tJockey\t2183\n-TC1_DM\tDNA\tTcMar-Tc1\t1960\n-Gypsy9_LTR\tLTR\tGypsy\t42\n-DMRP1\tUnknown\tUnknown\t227\n-Gypsy10_I-int\tLTR\tGypsy\t1930\n-Gypsy4_LTR\tLTR\tGypsy\t194\n-DM297_LTR\tLTR\tGypsy\t1478\n-ACCORD2_I-int\tLTR\tGypsy\t2458\n-Invader1_LTR\tLTR\tGypsy\t1931\n-BEL_LTR\tLTR\tPao\t858\n-IVK_DM\tLINE\tI\t2921\n-M4DM\tDNA\tCMC-Transib\t1650\n-FW2_DM\tLINE\tJockey\t13847\n-Copia2_I-int\tLTR\tCopia\t3455\n-MDG1_LTR\tLTR\tGypsy\t582\n-Gypsy12_LTR\tLTR\tGypsy\t5934\n-Gypsy7_I-int\tLTR\tGypsy\t1009\n-FROGGER_I-int\tLTR\tCopia\t1361\n-Gypsy_I-int\tLTR\tGypsy\t5634\n-5S_DM\tRNA\tRNA\t10392\n-GTWIN_I-int\tLTR\tGypsy\t5054\n-CIRCE\tLTR\tGypsy\t3323\n-DIVER2_LTR\tLTR\tPao\t535\n-POGO\tDNA\tTcMar-Pogo\t2492\n-Gypsy6A_LTR\tLTR\tGypsy\t573\n-MAX_I-int\tLTR\tPao\t9201\n-ROOA_LTR\tLTR\tPao\t483\n-DM176_I-int\tLTR\tGypsy\t2813\n-Copia2_LTR_DM\tLTR\tCopia\t486\n-DM297_I-int\tLTR\tGypsy\t11530\n-IDEFIX_I-int\tLTR\tGypsy\t5547\n-Jockey2\tLINE\tJockey\t1588\n-TC1-2_DM\tDNA\tTcMar-Tc1\t3948\n-DMRPR\tUnknown\tUnknown\t187\n+TRANSPAC_I-int\tLTR\tGypsy\t14982\n+TRANSPAC_LTR\tLTR\tGypsy\t555\n+XDMR\tUnknown\tUnknown\t1440\n+XDMR_DM\tUnknown\tUnknown\t4328\n+ZAM_I-int\tLTR\tGypsy\t4426\n+ZAM_LTR\tLTR\tGypsy\t225\n' |
| b |
| diff -r 51b4590a972d -r 15e3e29f310e test-data/354_fraction_counts.tab --- a/test-data/354_fraction_counts.tab Mon Sep 18 17:22:07 2017 -0400 +++ b/test-data/354_fraction_counts.tab Tue Sep 19 17:23:15 2017 -0400 |
| b |
| b'@@ -1,210 +1,210 @@\n-LSU-rRNA_Dme\trRNA\trRNA\t3659329\n-FW3_DM\tLINE\tJockey\t831\n-DMTOM1_LTR\tLTR\tGypsy\t1004\n-R1_DM\tLINE\tR1\t7343\n-TAHRE\tLINE\tJockey\t4560\n-G4_DM\tLINE\tJockey\t3668\n-BS\tLINE\tJockey\t7296\n-Stalker2_I-int\tLTR\tGypsy\t12252\n-Stalker3_LTR\tLTR\tGypsy\t593\n-TABOR_I-int\tLTR\tGypsy\t3947\n-G7_DM\tLINE\tJockey\t162\n-BEL_I-int\tLTR\tPao\t23757\n-Gypsy6_I-int\tLTR\tGypsy\t7489\n+5S_DM\tRNA\tRNA\t6317\n ACCORD_I-int\tLTR\tGypsy\t2723\n-DM412B_LTR\tLTR\tGypsy\t3078\n-G2_DM\tLINE\tJockey\t1328\n-SSU-rRNA_Hsa\trRNA\trRNA\t318045\n-TART_B1\tLINE\tJockey\t25248\n-S2_DM\tDNA\tTcMar-Tc1\t765\n-LOOPER1_DM\tDNA\tPiggyBac\t821\n-HOBO\tDNA\thAT-hobo\t5031\n+ACCORD_LTR\tLTR\tGypsy\t295\n+ACCORD2_I-int\tLTR\tGypsy\t2934\n+ACCORD2_LTR\tLTR\tGypsy\t235\n+ALA_DM\tUnknown\tUnknown\t5\n ARS406_DM\tUnknown\tUnknown\t563\n-G6_DM\tLINE\tJockey\t4827\n-DOC2_DM\tLINE\tJockey\t4438\n Baggins1\tLINE\tLOA\t5136\n-NINJA_LTR\tLTR\tPao\t491\n-TRANSIB2\tDNA\tCMC-Transib\t3197\n-Gypsy5_LTR\tLTR\tGypsy\t651\n-MDG3_LTR\tLTR\tGypsy\t1037\n-Gypsy12A_LTR\tLTR\tGypsy\t3059\n-Gypsy_LTR\tLTR\tGypsy\t1306\n-TIRANT_LTR\tLTR\tGypsy\t1371\n-I_DM\tLINE\tI\t7987\n-DIVER2_I-int\tLTR\tPao\t6679\n-P-1_DY\tDNA\tP\t8\n-Invader2_I-int\tLTR\tGypsy\t6823\n-DOC6_DM\tLINE\tJockey\t1259\n-BURDOCK_LTR\tLTR\tGypsy\t287\n-SSU-rRNA_Dme\trRNA\trRNA\t7113\n-MAX_LTR\tLTR\tPao\t1017\n-STALKER4_LTR\tLTR\tGypsy\t1292\n-XDMR_DM\tUnknown\tUnknown\t3317\n BARI_DM\tDNA\tTcMar-Tc1\t990\n-Transib-N1_DM\tDNA\tCMC-Transib\t308\n-Gypsy5_I-int\tLTR\tGypsy\t2448\n-XDMR\tUnknown\tUnknown\t1249\n-ACCORD2_LTR\tLTR\tGypsy\t235\n-POGON1\tDNA\tTcMar-Pogo\t331\n+BARI1\tDNA\tTcMar-Tc1\t395\n+BATUMI_I-int\tLTR\tPao\t6395\n+BATUMI_LTR\tLTR\tPao\t554\n+BEL_I-int\tLTR\tPao\t23757\n+BEL_LTR\tLTR\tPao\t875\n+Bica_I-int\tLTR\tGypsy\t1852\n+Bica_LTR\tLTR\tGypsy\t140\n+BLASTOPIA_I-int\tLTR\tGypsy\t10309\n+BLASTOPIA_LTR\tLTR\tGypsy\t550\n+BLOOD_I-int\tLTR\tGypsy\t22330\n+BLOOD_LTR\tLTR\tGypsy\t748\n+BS\tLINE\tJockey\t7296\n+BS2\tLINE\tJockey\t5595\n+BS3_DM\tLINE\tJockey\t1252\n BS4_DM\tLINE\tJockey\t34\n-ALA_DM\tUnknown\tUnknown\t5\n-Gypsy1-I_DM\tLTR\tGypsy\t8160\n-ACCORD_LTR\tLTR\tGypsy\t295\n BURDOCK_I-int\tLTR\tGypsy\t3119\n-ZAM_I-int\tLTR\tGypsy\t5129\n-Invader5_I-int\tLTR\tGypsy\t416\n-G3_DM\tLINE\tJockey\t797\n-ROOA_I-int\tLTR\tPao\t4985\n-Gypsy1-LTR_DM\tLTR\tGypsy\t1042\n+BURDOCK_LTR\tLTR\tGypsy\t287\n+Chimpo_I-int\tLTR\tGypsy\t1288\n+Chimpo_LTR\tLTR\tGypsy\t94\n+Chouto_I-int\tLTR\tGypsy\t1690\n+Chouto_LTR\tLTR\tGypsy\t299\n+CIRCE\tLTR\tGypsy\t3767\n+Copia_I-int\tLTR\tCopia\t27612\n+Copia_LTR\tLTR\tCopia\t1408\n+Copia1-I_DM\tLTR\tCopia\t3588\n+Copia1-LTR_DM\tLTR\tCopia\t771\n+Copia2_I-int\tLTR\tCopia\t4218\n+Copia2_LTR_DM\tLTR\tCopia\t891\n+DIVER_I-int\tLTR\tPao\t13178\n+DIVER_LTR\tLTR\tPao\t469\n+DIVER2_I-int\tLTR\tPao\t6679\n+DIVER2_LTR\tLTR\tPao\t793\n DM1731_I-int\tLTR\tCopia\t5180\n-ROO_I-int\tLTR\tPao\t31793\n+DM1731_LTR\tLTR\tCopia\t577\n+DM176_I-int\tLTR\tGypsy\t3627\n+DM176_LTR\tLTR\tGypsy\t899\n+DM297_I-int\tLTR\tGypsy\t11837\n+DM297_LTR\tLTR\tGypsy\t1489\n DM412\tLTR\tGypsy\t24086\n-PROTOP\tDNA\tP\t4942\n-TART-A\tLINE\tJockey\t3697\n-ROO_LTR\tLTR\tPao\t1639\n-DIVER_LTR\tLTR\tPao\t469\n-Gypsy3_I-int\tLTR\tGypsy\t3399\n-BATUMI_LTR\tLTR\tPao\t554\n-IDEFIX_LTR\tLTR\tGypsy\t2191\n-G5_DM\tLINE\tJockey\t2601\n-HETA\tLINE\tJockey\t23025\n-Gypsy11_I-int\tLTR\tGypsy\t671\n-R1-2_DM\tLINE\tR1\t267\n-Gypsy11_LTR\tLTR\tGypsy\t134\n-HELENA_RT\tLINE\tJockey\t653\n-FTZ_DM\tUnknown\tUnknown\t0\n-MICROPIA_I-int\tLTR\tGypsy\t10149\n-Invader4_I-int\tLTR\tGypsy\t1439\n-PLACW_DM\tDNA\tP\t149\n-BLOOD_LTR\tLTR\tGypsy\t748\n-R2_DM\tLINE\tR2\t15327\n-Copia1-I_DM\tLTR\tCopia\t3588\n-Gypsy4_I-int\tLTR\tGypsy\t12113\n-Chouto_LTR\tLTR\tGypsy\t299\n-BATUMI_I-int\tLTR\tPao\t6395\n-DNAREP1_DM\tRC\tHelitron\t67821\n+DM412B_LTR\tLTR\tGypsy\t3078\n+DMCR1A\tLINE\tCR1\t20380\n+DMLTR5\tLTR\tGypsy\t161\n+DMRP1\tUnknown\tUnknown\t262\n+DMRPR\tUnknown\tUnknown\t128\n+DMRT1A\tLINE\tR1\t4456\n DMRT1B\tLINE\tR1\t9706\n DMRT1C\tLINE\tR1\t2530\n-TLD2\tLTR\tGypsy\t65\n-DMRT1A\tLINE\tR1\t4456\n-DM1731_LTR\tLTR\tCopia\t577\n-LSU-rRNA_Cel\trRNA\trRNA\t520168\n-Copia_LTR\tLTR\tCopia\t1408\n+DMTOM1_LTR\tLTR\tGypsy\t1004\n+DNAREP1_DM\tRC\tHelitron\t67821\n+DOC\tLINE\tJockey\t17883\n+DOC2_DM\tLINE\tJockey\t4438\n+DOC3_DM\tLINE\tJockey\t11941\n+DOC4_DM\tLINE\tJockey\t813\n+DOC5_DM\tLINE\tJockey\t3037\n+DOC6_DM\tLINE\tJockey\t1259\n+FB4_DM\tDNA\tTcMar-Tc1\t7149\n+FROGGER_I-int\tLTR\tCopia\t1611\n+FROGGER_LTR\tLTR\tCopia\t41\n+FTZ_DM\tUnknown\tUnknown\t0\n+FUSHI_DM\tUnknown\tUnknown\t0\n+FW2_DM\tLINE\tJockey\t14234\n+FW3_DM\tLINE'..b'331\n+PROTOP\tDNA\tP\t4942\n+PROTOP_A\tDNA\tP\t3533\n+PROTOP_B\tDNA\tP\t8690\n+QUASIMODO_I-int\tLTR\tGypsy\t14906\n QUASIMODO_LTR\tLTR\tGypsy\t1332\n-TABOR_LTR\tLTR\tGypsy\t384\n-Stalker2_LTR\tLTR\tGypsy\t726\n-MICROPIA_LTR\tLTR\tGypsy\t797\n-Gypsy9_I-int\tLTR\tGypsy\t504\n-STALKER4_I-int\tLTR\tGypsy\t6207\n-TRANSIB1\tDNA\tCMC-Transib\t2082\n-DOC\tLINE\tJockey\t17883\n-TRANSIB3\tDNA\tCMC-Transib\t1184\n-Copia_I-int\tLTR\tCopia\t27612\n-TRANSIB4\tDNA\tCMC-Transib\t635\n-Gypsy10_LTR\tLTR\tGypsy\t314\n-Invader3_I-int\tLTR\tGypsy\t4667\n-Invader1_I-int\tLTR\tGypsy\t1832\n-BS3_DM\tLINE\tJockey\t1252\n-Gypsy2-LTR_DM\tLTR\tGypsy\t966\n-LSU-rRNA_Hsa\trRNA\trRNA\t5\n-NOMAD_LTR\tLTR\tGypsy\t619\n-Helitron1_DM\tRC\tHelitron\t3\n-LINEJ1_DM\tLINE\tJockey\t7025\n-Invader4_LTR\tLTR\tGypsy\t1420\n-MDG3_I-int\tLTR\tGypsy\t5392\n-LmeSINE1c\tSINE\ttRNA-Deu-L2\t599\n+QUASIMODO2-I_DM\tLTR\tGypsy\t2717\n+QUASIMODO2-LTR_DM\tLTR\tGypsy\t313\n+R1_DM\tLINE\tR1\t7343\n+R1-2_DM\tLINE\tR1\t267\n+R2_DM\tLINE\tR2\t15327\n+ROO_I-int\tLTR\tPao\t31793\n+ROO_LTR\tLTR\tPao\t1639\n+ROOA_I-int\tLTR\tPao\t4985\n+ROOA_LTR\tLTR\tPao\t400\n+ROVER-I_DM\tLTR\tGypsy\t6513\n ROVER-LTR_DM\tLTR\tGypsy\t564\n S_DM\tDNA\tTcMar-Tc1\t3612\n-Invader6_I-int\tLTR\tGypsy\t6931\n-ROVER-I_DM\tLTR\tGypsy\t6513\n-QUASIMODO_I-int\tLTR\tGypsy\t14906\n-Chouto_I-int\tLTR\tGypsy\t1690\n-NTS_DM\tOther\tOther\t65954\n-Gypsy3_LTR\tLTR\tGypsy\t566\n+S2_DM\tDNA\tTcMar-Tc1\t765\n SSU-rRNA_Cel\trRNA\trRNA\t3463\n-MINOS\tDNA\tTcMar-Tc1\t173\n-DOC4_DM\tLINE\tJockey\t813\n-ZAM_LTR\tLTR\tGypsy\t259\n-QUASIMODO2-LTR_DM\tLTR\tGypsy\t313\n-Gypsy2-I_DM\tLTR\tGypsy\t4606\n-TRANSPAC_I-int\tLTR\tGypsy\t9674\n-Bica_I-int\tLTR\tGypsy\t1852\n-BS2\tLINE\tJockey\t5595\n-BLOOD_I-int\tLTR\tGypsy\t22330\n-DMCR1A\tLINE\tCR1\t20380\n-QUASIMODO2-I_DM\tLTR\tGypsy\t2717\n-HMSBEAGLE_I-int\tLTR\tGypsy\t7239\n-DMLTR5\tLTR\tGypsy\t161\n-Gypsy7_LTR\tLTR\tGypsy\t112\n-G5A_DM\tLINE\tJockey\t1804\n-MDG1_I-int\tLTR\tGypsy\t16315\n-Gypsy2_I-int\tLTR\tGypsy\t3190\n-BARI1\tDNA\tTcMar-Tc1\t395\n-Invader5_LTR\tLTR\tGypsy\t69\n-DM176_LTR\tLTR\tGypsy\t899\n-DOC3_DM\tLINE\tJockey\t11941\n-Copia1-LTR_DM\tLTR\tCopia\t771\n-TOM_I-int\tLTR\tGypsy\t2563\n-NOF_FB\tDNA\tMULE-NOF\t1272\n-Chimpo_I-int\tLTR\tGypsy\t1288\n-DIVER_I-int\tLTR\tPao\t13178\n+SSU-rRNA_Dme\trRNA\trRNA\t7113\n+SSU-rRNA_Hsa\trRNA\trRNA\t318045\n+Stalker2_I-int\tLTR\tGypsy\t12252\n+Stalker2_LTR\tLTR\tGypsy\t726\n+Stalker3_LTR\tLTR\tGypsy\t593\n+STALKER4_I-int\tLTR\tGypsy\t6207\n+STALKER4_LTR\tLTR\tGypsy\t1292\n+TABOR_I-int\tLTR\tGypsy\t3947\n+TABOR_LTR\tLTR\tGypsy\t384\n+TAHRE\tLINE\tJockey\t4560\n+TART_B1\tLINE\tJockey\t25248\n+TART-A\tLINE\tJockey\t3697\n+TC1_DM\tDNA\tTcMar-Tc1\t1840\n+TC1-2_DM\tDNA\tTcMar-Tc1\t3807\n TIRANT_I-int\tLTR\tGypsy\t10917\n-Gypsy2_LTR\tLTR\tGypsy\t479\n-FB4_DM\tDNA\tTcMar-Tc1\t7149\n-GTWIN_LTR\tLTR\tGypsy\t598\n-Invader6_LTR\tLTR\tGypsy\t649\n-Gypsy8_I-int\tLTR\tGypsy\t4809\n-G_DM\tLINE\tJockey\t8905\n-TRANSPAC_LTR\tLTR\tGypsy\t538\n-FUSHI_DM\tUnknown\tUnknown\t0\n+TIRANT_LTR\tLTR\tGypsy\t1371\n+TLD2\tLTR\tGypsy\t65\n+TOM_I-int\tLTR\tGypsy\t2563\n+Transib-N1_DM\tDNA\tCMC-Transib\t308\n+TRANSIB1\tDNA\tCMC-Transib\t2082\n+TRANSIB2\tDNA\tCMC-Transib\t3197\n+TRANSIB3\tDNA\tCMC-Transib\t1184\n+TRANSIB4\tDNA\tCMC-Transib\t635\n Transib5\tDNA\tCMC-Transib\t1123\n-MuDR-1_DEl\tDNA\tMULE-NOF\t6\n-Mariner2_DM\tDNA\tTcMar-Tc1\t2011\n-DOC5_DM\tLINE\tJockey\t3037\n-TC1_DM\tDNA\tTcMar-Tc1\t1840\n-Gypsy9_LTR\tLTR\tGypsy\t51\n-DMRP1\tUnknown\tUnknown\t262\n-Gypsy10_I-int\tLTR\tGypsy\t2258\n-Gypsy4_LTR\tLTR\tGypsy\t274\n-DM297_LTR\tLTR\tGypsy\t1489\n-ACCORD2_I-int\tLTR\tGypsy\t2934\n-Invader1_LTR\tLTR\tGypsy\t3346\n-BEL_LTR\tLTR\tPao\t875\n-IVK_DM\tLINE\tI\t3349\n-M4DM\tDNA\tCMC-Transib\t1727\n-FW2_DM\tLINE\tJockey\t14234\n-Copia2_I-int\tLTR\tCopia\t4218\n-MDG1_LTR\tLTR\tGypsy\t690\n-Gypsy12_LTR\tLTR\tGypsy\t6292\n-Gypsy7_I-int\tLTR\tGypsy\t1256\n-FROGGER_I-int\tLTR\tCopia\t1611\n-Gypsy_I-int\tLTR\tGypsy\t6822\n-5S_DM\tRNA\tRNA\t6317\n-GTWIN_I-int\tLTR\tGypsy\t5448\n-CIRCE\tLTR\tGypsy\t3767\n-DIVER2_LTR\tLTR\tPao\t793\n-POGO\tDNA\tTcMar-Pogo\t2427\n-Gypsy6A_LTR\tLTR\tGypsy\t617\n-MAX_I-int\tLTR\tPao\t12395\n-ROOA_LTR\tLTR\tPao\t400\n-DM176_I-int\tLTR\tGypsy\t3627\n-Copia2_LTR_DM\tLTR\tCopia\t891\n-DM297_I-int\tLTR\tGypsy\t11837\n-IDEFIX_I-int\tLTR\tGypsy\t6193\n-Jockey2\tLINE\tJockey\t1770\n-TC1-2_DM\tDNA\tTcMar-Tc1\t3807\n-DMRPR\tUnknown\tUnknown\t128\n+TRANSPAC_I-int\tLTR\tGypsy\t9674\n+TRANSPAC_LTR\tLTR\tGypsy\t538\n+XDMR\tUnknown\tUnknown\t1249\n+XDMR_DM\tUnknown\tUnknown\t3317\n+ZAM_I-int\tLTR\tGypsy\t5129\n+ZAM_LTR\tLTR\tGypsy\t259\n' |
| b |
| diff -r 51b4590a972d -r 15e3e29f310e test-data/355_fraction_counts.tab --- a/test-data/355_fraction_counts.tab Mon Sep 18 17:22:07 2017 -0400 +++ b/test-data/355_fraction_counts.tab Tue Sep 19 17:23:15 2017 -0400 |
| b |
| b'@@ -1,210 +1,210 @@\n-LSU-rRNA_Dme\trRNA\trRNA\t4126525\n-FW3_DM\tLINE\tJockey\t376\n-DMTOM1_LTR\tLTR\tGypsy\t458\n-R1_DM\tLINE\tR1\t6019\n-TAHRE\tLINE\tJockey\t1417\n-G4_DM\tLINE\tJockey\t1225\n-BS\tLINE\tJockey\t4135\n-Stalker2_I-int\tLTR\tGypsy\t4814\n-Stalker3_LTR\tLTR\tGypsy\t235\n-TABOR_I-int\tLTR\tGypsy\t3691\n-G7_DM\tLINE\tJockey\t418\n-BEL_I-int\tLTR\tPao\t15192\n-Gypsy6_I-int\tLTR\tGypsy\t3763\n+5S_DM\tRNA\tRNA\t4146\n ACCORD_I-int\tLTR\tGypsy\t2031\n-DM412B_LTR\tLTR\tGypsy\t3001\n-G2_DM\tLINE\tJockey\t764\n-SSU-rRNA_Hsa\trRNA\trRNA\t301813\n-TART_B1\tLINE\tJockey\t5089\n-S2_DM\tDNA\tTcMar-Tc1\t205\n-LOOPER1_DM\tDNA\tPiggyBac\t31\n-HOBO\tDNA\thAT-hobo\t2119\n+ACCORD_LTR\tLTR\tGypsy\t344\n+ACCORD2_I-int\tLTR\tGypsy\t1200\n+ACCORD2_LTR\tLTR\tGypsy\t76\n+ALA_DM\tUnknown\tUnknown\t0\n ARS406_DM\tUnknown\tUnknown\t230\n-G6_DM\tLINE\tJockey\t786\n-DOC2_DM\tLINE\tJockey\t2052\n Baggins1\tLINE\tLOA\t1832\n-NINJA_LTR\tLTR\tPao\t114\n-TRANSIB2\tDNA\tCMC-Transib\t1484\n-Gypsy5_LTR\tLTR\tGypsy\t326\n-MDG3_LTR\tLTR\tGypsy\t454\n-Gypsy12A_LTR\tLTR\tGypsy\t1077\n-Gypsy_LTR\tLTR\tGypsy\t1737\n-TIRANT_LTR\tLTR\tGypsy\t1596\n-I_DM\tLINE\tI\t11149\n-DIVER2_I-int\tLTR\tPao\t2668\n-P-1_DY\tDNA\tP\t4\n-Invader2_I-int\tLTR\tGypsy\t3157\n-DOC6_DM\tLINE\tJockey\t768\n-BURDOCK_LTR\tLTR\tGypsy\t193\n-SSU-rRNA_Dme\trRNA\trRNA\t3822\n-MAX_LTR\tLTR\tPao\t343\n-STALKER4_LTR\tLTR\tGypsy\t803\n-XDMR_DM\tUnknown\tUnknown\t1587\n BARI_DM\tDNA\tTcMar-Tc1\t522\n-Transib-N1_DM\tDNA\tCMC-Transib\t130\n-Gypsy5_I-int\tLTR\tGypsy\t1036\n-XDMR\tUnknown\tUnknown\t903\n-ACCORD2_LTR\tLTR\tGypsy\t76\n-POGON1\tDNA\tTcMar-Pogo\t256\n+BARI1\tDNA\tTcMar-Tc1\t125\n+BATUMI_I-int\tLTR\tPao\t1842\n+BATUMI_LTR\tLTR\tPao\t169\n+BEL_I-int\tLTR\tPao\t15192\n+BEL_LTR\tLTR\tPao\t605\n+Bica_I-int\tLTR\tGypsy\t618\n+Bica_LTR\tLTR\tGypsy\t67\n+BLASTOPIA_I-int\tLTR\tGypsy\t12045\n+BLASTOPIA_LTR\tLTR\tGypsy\t919\n+BLOOD_I-int\tLTR\tGypsy\t13280\n+BLOOD_LTR\tLTR\tGypsy\t542\n+BS\tLINE\tJockey\t4135\n+BS2\tLINE\tJockey\t2086\n+BS3_DM\tLINE\tJockey\t453\n BS4_DM\tLINE\tJockey\t23\n-ALA_DM\tUnknown\tUnknown\t0\n-Gypsy1-I_DM\tLTR\tGypsy\t22753\n-ACCORD_LTR\tLTR\tGypsy\t344\n BURDOCK_I-int\tLTR\tGypsy\t2232\n-ZAM_I-int\tLTR\tGypsy\t2892\n-Invader5_I-int\tLTR\tGypsy\t117\n-G3_DM\tLINE\tJockey\t250\n-ROOA_I-int\tLTR\tPao\t2579\n-Gypsy1-LTR_DM\tLTR\tGypsy\t576\n+BURDOCK_LTR\tLTR\tGypsy\t193\n+Chimpo_I-int\tLTR\tGypsy\t370\n+Chimpo_LTR\tLTR\tGypsy\t33\n+Chouto_I-int\tLTR\tGypsy\t518\n+Chouto_LTR\tLTR\tGypsy\t159\n+CIRCE\tLTR\tGypsy\t1570\n+Copia_I-int\tLTR\tCopia\t87220\n+Copia_LTR\tLTR\tCopia\t3075\n+Copia1-I_DM\tLTR\tCopia\t1946\n+Copia1-LTR_DM\tLTR\tCopia\t389\n+Copia2_I-int\tLTR\tCopia\t1892\n+Copia2_LTR_DM\tLTR\tCopia\t460\n+DIVER_I-int\tLTR\tPao\t11751\n+DIVER_LTR\tLTR\tPao\t328\n+DIVER2_I-int\tLTR\tPao\t2668\n+DIVER2_LTR\tLTR\tPao\t240\n DM1731_I-int\tLTR\tCopia\t6873\n-ROO_I-int\tLTR\tPao\t22941\n+DM1731_LTR\tLTR\tCopia\t321\n+DM176_I-int\tLTR\tGypsy\t2298\n+DM176_LTR\tLTR\tGypsy\t330\n+DM297_I-int\tLTR\tGypsy\t42705\n+DM297_LTR\tLTR\tGypsy\t2516\n DM412\tLTR\tGypsy\t23508\n-PROTOP\tDNA\tP\t2059\n-TART-A\tLINE\tJockey\t1825\n-ROO_LTR\tLTR\tPao\t1453\n-DIVER_LTR\tLTR\tPao\t328\n-Gypsy3_I-int\tLTR\tGypsy\t2258\n-BATUMI_LTR\tLTR\tPao\t169\n-IDEFIX_LTR\tLTR\tGypsy\t1012\n-G5_DM\tLINE\tJockey\t1300\n-HETA\tLINE\tJockey\t10327\n-Gypsy11_I-int\tLTR\tGypsy\t168\n-R1-2_DM\tLINE\tR1\t68\n-Gypsy11_LTR\tLTR\tGypsy\t48\n-HELENA_RT\tLINE\tJockey\t416\n-FTZ_DM\tUnknown\tUnknown\t0\n-MICROPIA_I-int\tLTR\tGypsy\t3327\n-Invader4_I-int\tLTR\tGypsy\t1180\n-PLACW_DM\tDNA\tP\t204\n-BLOOD_LTR\tLTR\tGypsy\t542\n-R2_DM\tLINE\tR2\t15128\n-Copia1-I_DM\tLTR\tCopia\t1946\n-Gypsy4_I-int\tLTR\tGypsy\t5348\n-Chouto_LTR\tLTR\tGypsy\t159\n-BATUMI_I-int\tLTR\tPao\t1842\n-DNAREP1_DM\tRC\tHelitron\t36953\n+DM412B_LTR\tLTR\tGypsy\t3001\n+DMCR1A\tLINE\tCR1\t8072\n+DMLTR5\tLTR\tGypsy\t94\n+DMRP1\tUnknown\tUnknown\t144\n+DMRPR\tUnknown\tUnknown\t136\n+DMRT1A\tLINE\tR1\t1235\n DMRT1B\tLINE\tR1\t4115\n DMRT1C\tLINE\tR1\t670\n-TLD2\tLTR\tGypsy\t1\n-DMRT1A\tLINE\tR1\t1235\n-DM1731_LTR\tLTR\tCopia\t321\n-LSU-rRNA_Cel\trRNA\trRNA\t251671\n-Copia_LTR\tLTR\tCopia\t3075\n+DMTOM1_LTR\tLTR\tGypsy\t458\n+DNAREP1_DM\tRC\tHelitron\t36953\n+DOC\tLINE\tJockey\t21700\n+DOC2_DM\tLINE\tJockey\t2052\n+DOC3_DM\tLINE\tJockey\t5205\n+DOC4_DM\tLINE\tJockey\t658\n+DOC5_DM\tLINE\tJockey\t752\n+DOC6_DM\tLINE\tJockey\t768\n+FB4_DM\tDNA\tTcMar-Tc1\t3348\n+FROGGER_I-int\tLTR\tCopia\t546\n+FROGGER_LTR\tLTR\tCopia\t57\n+FTZ_DM\tUnknown\tUnknown\t0\n+FUSHI_DM\tUnknown\tUnknown\t0\n+FW2_DM\tLINE\tJockey\t8864\n+FW3_DM\tLINE\tJockey\t376\n+G_DM\tLINE\tJockey\t4'..b'r-Pogo\t1032\n+POGON1\tDNA\tTcMar-Pogo\t256\n+PROTOP\tDNA\tP\t2059\n+PROTOP_A\tDNA\tP\t1988\n+PROTOP_B\tDNA\tP\t4300\n+QUASIMODO_I-int\tLTR\tGypsy\t8000\n QUASIMODO_LTR\tLTR\tGypsy\t528\n-TABOR_LTR\tLTR\tGypsy\t88\n-Stalker2_LTR\tLTR\tGypsy\t356\n-MICROPIA_LTR\tLTR\tGypsy\t149\n-Gypsy9_I-int\tLTR\tGypsy\t188\n-STALKER4_I-int\tLTR\tGypsy\t3132\n-TRANSIB1\tDNA\tCMC-Transib\t289\n-DOC\tLINE\tJockey\t21700\n-TRANSIB3\tDNA\tCMC-Transib\t741\n-Copia_I-int\tLTR\tCopia\t87220\n-TRANSIB4\tDNA\tCMC-Transib\t153\n-Gypsy10_LTR\tLTR\tGypsy\t162\n-Invader3_I-int\tLTR\tGypsy\t2022\n-Invader1_I-int\tLTR\tGypsy\t1768\n-BS3_DM\tLINE\tJockey\t453\n-Gypsy2-LTR_DM\tLTR\tGypsy\t385\n-LSU-rRNA_Hsa\trRNA\trRNA\t11\n-NOMAD_LTR\tLTR\tGypsy\t277\n-Helitron1_DM\tRC\tHelitron\t0\n-LINEJ1_DM\tLINE\tJockey\t15939\n-Invader4_LTR\tLTR\tGypsy\t679\n-MDG3_I-int\tLTR\tGypsy\t3770\n-LmeSINE1c\tSINE\ttRNA-Deu-L2\t653\n+QUASIMODO2-I_DM\tLTR\tGypsy\t1811\n+QUASIMODO2-LTR_DM\tLTR\tGypsy\t105\n+R1_DM\tLINE\tR1\t6019\n+R1-2_DM\tLINE\tR1\t68\n+R2_DM\tLINE\tR2\t15128\n+ROO_I-int\tLTR\tPao\t22941\n+ROO_LTR\tLTR\tPao\t1453\n+ROOA_I-int\tLTR\tPao\t2579\n+ROOA_LTR\tLTR\tPao\t276\n+ROVER-I_DM\tLTR\tGypsy\t3069\n ROVER-LTR_DM\tLTR\tGypsy\t168\n S_DM\tDNA\tTcMar-Tc1\t2041\n-Invader6_I-int\tLTR\tGypsy\t3298\n-ROVER-I_DM\tLTR\tGypsy\t3069\n-QUASIMODO_I-int\tLTR\tGypsy\t8000\n-Chouto_I-int\tLTR\tGypsy\t518\n-NTS_DM\tOther\tOther\t21753\n-Gypsy3_LTR\tLTR\tGypsy\t212\n+S2_DM\tDNA\tTcMar-Tc1\t205\n SSU-rRNA_Cel\trRNA\trRNA\t1817\n-MINOS\tDNA\tTcMar-Tc1\t93\n-DOC4_DM\tLINE\tJockey\t658\n-ZAM_LTR\tLTR\tGypsy\t118\n-QUASIMODO2-LTR_DM\tLTR\tGypsy\t105\n-Gypsy2-I_DM\tLTR\tGypsy\t2658\n-TRANSPAC_I-int\tLTR\tGypsy\t16760\n-Bica_I-int\tLTR\tGypsy\t618\n-BS2\tLINE\tJockey\t2086\n-BLOOD_I-int\tLTR\tGypsy\t13280\n-DMCR1A\tLINE\tCR1\t8072\n-QUASIMODO2-I_DM\tLTR\tGypsy\t1811\n-HMSBEAGLE_I-int\tLTR\tGypsy\t4079\n-DMLTR5\tLTR\tGypsy\t94\n-Gypsy7_LTR\tLTR\tGypsy\t39\n-G5A_DM\tLINE\tJockey\t582\n-MDG1_I-int\tLTR\tGypsy\t8043\n-Gypsy2_I-int\tLTR\tGypsy\t1552\n-BARI1\tDNA\tTcMar-Tc1\t125\n-Invader5_LTR\tLTR\tGypsy\t23\n-DM176_LTR\tLTR\tGypsy\t330\n-DOC3_DM\tLINE\tJockey\t5205\n-Copia1-LTR_DM\tLTR\tCopia\t389\n-TOM_I-int\tLTR\tGypsy\t3390\n-NOF_FB\tDNA\tMULE-NOF\t63\n-Chimpo_I-int\tLTR\tGypsy\t370\n-DIVER_I-int\tLTR\tPao\t11751\n+SSU-rRNA_Dme\trRNA\trRNA\t3822\n+SSU-rRNA_Hsa\trRNA\trRNA\t301813\n+Stalker2_I-int\tLTR\tGypsy\t4814\n+Stalker2_LTR\tLTR\tGypsy\t356\n+Stalker3_LTR\tLTR\tGypsy\t235\n+STALKER4_I-int\tLTR\tGypsy\t3132\n+STALKER4_LTR\tLTR\tGypsy\t803\n+TABOR_I-int\tLTR\tGypsy\t3691\n+TABOR_LTR\tLTR\tGypsy\t88\n+TAHRE\tLINE\tJockey\t1417\n+TART_B1\tLINE\tJockey\t5089\n+TART-A\tLINE\tJockey\t1825\n+TC1_DM\tDNA\tTcMar-Tc1\t1485\n+TC1-2_DM\tDNA\tTcMar-Tc1\t2287\n TIRANT_I-int\tLTR\tGypsy\t12728\n-Gypsy2_LTR\tLTR\tGypsy\t250\n-FB4_DM\tDNA\tTcMar-Tc1\t3348\n-GTWIN_LTR\tLTR\tGypsy\t938\n-Invader6_LTR\tLTR\tGypsy\t146\n-Gypsy8_I-int\tLTR\tGypsy\t1247\n-G_DM\tLINE\tJockey\t4582\n-TRANSPAC_LTR\tLTR\tGypsy\t979\n-FUSHI_DM\tUnknown\tUnknown\t0\n+TIRANT_LTR\tLTR\tGypsy\t1596\n+TLD2\tLTR\tGypsy\t1\n+TOM_I-int\tLTR\tGypsy\t3390\n+Transib-N1_DM\tDNA\tCMC-Transib\t130\n+TRANSIB1\tDNA\tCMC-Transib\t289\n+TRANSIB2\tDNA\tCMC-Transib\t1484\n+TRANSIB3\tDNA\tCMC-Transib\t741\n+TRANSIB4\tDNA\tCMC-Transib\t153\n Transib5\tDNA\tCMC-Transib\t328\n-MuDR-1_DEl\tDNA\tMULE-NOF\t4\n-Mariner2_DM\tDNA\tTcMar-Tc1\t926\n-DOC5_DM\tLINE\tJockey\t752\n-TC1_DM\tDNA\tTcMar-Tc1\t1485\n-Gypsy9_LTR\tLTR\tGypsy\t8\n-DMRP1\tUnknown\tUnknown\t144\n-Gypsy10_I-int\tLTR\tGypsy\t927\n-Gypsy4_LTR\tLTR\tGypsy\t218\n-DM297_LTR\tLTR\tGypsy\t2516\n-ACCORD2_I-int\tLTR\tGypsy\t1200\n-Invader1_LTR\tLTR\tGypsy\t1903\n-BEL_LTR\tLTR\tPao\t605\n-IVK_DM\tLINE\tI\t1769\n-M4DM\tDNA\tCMC-Transib\t918\n-FW2_DM\tLINE\tJockey\t8864\n-Copia2_I-int\tLTR\tCopia\t1892\n-MDG1_LTR\tLTR\tGypsy\t281\n-Gypsy12_LTR\tLTR\tGypsy\t2680\n-Gypsy7_I-int\tLTR\tGypsy\t742\n-FROGGER_I-int\tLTR\tCopia\t546\n-Gypsy_I-int\tLTR\tGypsy\t11161\n-5S_DM\tRNA\tRNA\t4146\n-GTWIN_I-int\tLTR\tGypsy\t2930\n-CIRCE\tLTR\tGypsy\t1570\n-DIVER2_LTR\tLTR\tPao\t240\n-POGO\tDNA\tTcMar-Pogo\t1032\n-Gypsy6A_LTR\tLTR\tGypsy\t219\n-MAX_I-int\tLTR\tPao\t3905\n-ROOA_LTR\tLTR\tPao\t276\n-DM176_I-int\tLTR\tGypsy\t2298\n-Copia2_LTR_DM\tLTR\tCopia\t460\n-DM297_I-int\tLTR\tGypsy\t42705\n-IDEFIX_I-int\tLTR\tGypsy\t3286\n-Jockey2\tLINE\tJockey\t760\n-TC1-2_DM\tDNA\tTcMar-Tc1\t2287\n-DMRPR\tUnknown\tUnknown\t136\n+TRANSPAC_I-int\tLTR\tGypsy\t16760\n+TRANSPAC_LTR\tLTR\tGypsy\t979\n+XDMR\tUnknown\tUnknown\t903\n+XDMR_DM\tUnknown\tUnknown\t1587\n+ZAM_I-int\tLTR\tGypsy\t2892\n+ZAM_LTR\tLTR\tGypsy\t118\n' |
| b |
| diff -r 51b4590a972d -r 15e3e29f310e test-data/356_fraction_counts.tab --- a/test-data/356_fraction_counts.tab Mon Sep 18 17:22:07 2017 -0400 +++ b/test-data/356_fraction_counts.tab Tue Sep 19 17:23:15 2017 -0400 |
| b |
| b'@@ -1,210 +1,210 @@\n-LSU-rRNA_Dme\trRNA\trRNA\t5583038\n-FW3_DM\tLINE\tJockey\t647\n-DMTOM1_LTR\tLTR\tGypsy\t1403\n-R1_DM\tLINE\tR1\t15424\n-TAHRE\tLINE\tJockey\t3806\n-G4_DM\tLINE\tJockey\t2223\n-BS\tLINE\tJockey\t5200\n-Stalker2_I-int\tLTR\tGypsy\t10966\n-Stalker3_LTR\tLTR\tGypsy\t543\n-TABOR_I-int\tLTR\tGypsy\t5504\n-G7_DM\tLINE\tJockey\t1949\n-BEL_I-int\tLTR\tPao\t29338\n-Gypsy6_I-int\tLTR\tGypsy\t11381\n+5S_DM\tRNA\tRNA\t6331\n ACCORD_I-int\tLTR\tGypsy\t4103\n-DM412B_LTR\tLTR\tGypsy\t5607\n-G2_DM\tLINE\tJockey\t1235\n-SSU-rRNA_Hsa\trRNA\trRNA\t563673\n-TART_B1\tLINE\tJockey\t13382\n-S2_DM\tDNA\tTcMar-Tc1\t716\n-LOOPER1_DM\tDNA\tPiggyBac\t220\n-HOBO\tDNA\thAT-hobo\t4375\n+ACCORD_LTR\tLTR\tGypsy\t790\n+ACCORD2_I-int\tLTR\tGypsy\t2286\n+ACCORD2_LTR\tLTR\tGypsy\t213\n+ALA_DM\tUnknown\tUnknown\t9\n ARS406_DM\tUnknown\tUnknown\t755\n-G6_DM\tLINE\tJockey\t2874\n-DOC2_DM\tLINE\tJockey\t4511\n Baggins1\tLINE\tLOA\t5500\n-NINJA_LTR\tLTR\tPao\t297\n-TRANSIB2\tDNA\tCMC-Transib\t3357\n-Gypsy5_LTR\tLTR\tGypsy\t502\n-MDG3_LTR\tLTR\tGypsy\t926\n-Gypsy12A_LTR\tLTR\tGypsy\t2436\n-Gypsy_LTR\tLTR\tGypsy\t3771\n-TIRANT_LTR\tLTR\tGypsy\t3225\n-I_DM\tLINE\tI\t11479\n-DIVER2_I-int\tLTR\tPao\t6446\n-P-1_DY\tDNA\tP\t13\n-Invader2_I-int\tLTR\tGypsy\t5970\n-DOC6_DM\tLINE\tJockey\t1718\n-BURDOCK_LTR\tLTR\tGypsy\t543\n-SSU-rRNA_Dme\trRNA\trRNA\t9958\n-MAX_LTR\tLTR\tPao\t958\n-STALKER4_LTR\tLTR\tGypsy\t2040\n-XDMR_DM\tUnknown\tUnknown\t4049\n BARI_DM\tDNA\tTcMar-Tc1\t1117\n-Transib-N1_DM\tDNA\tCMC-Transib\t366\n-Gypsy5_I-int\tLTR\tGypsy\t2834\n-XDMR\tUnknown\tUnknown\t1771\n-ACCORD2_LTR\tLTR\tGypsy\t213\n-POGON1\tDNA\tTcMar-Pogo\t641\n+BARI1\tDNA\tTcMar-Tc1\t370\n+BATUMI_I-int\tLTR\tPao\t4723\n+BATUMI_LTR\tLTR\tPao\t348\n+BEL_I-int\tLTR\tPao\t29338\n+BEL_LTR\tLTR\tPao\t927\n+Bica_I-int\tLTR\tGypsy\t1561\n+Bica_LTR\tLTR\tGypsy\t123\n+BLASTOPIA_I-int\tLTR\tGypsy\t13780\n+BLASTOPIA_LTR\tLTR\tGypsy\t1038\n+BLOOD_I-int\tLTR\tGypsy\t27362\n+BLOOD_LTR\tLTR\tGypsy\t1269\n+BS\tLINE\tJockey\t5200\n+BS2\tLINE\tJockey\t5214\n+BS3_DM\tLINE\tJockey\t851\n BS4_DM\tLINE\tJockey\t8\n-ALA_DM\tUnknown\tUnknown\t9\n-Gypsy1-I_DM\tLTR\tGypsy\t36962\n-ACCORD_LTR\tLTR\tGypsy\t790\n BURDOCK_I-int\tLTR\tGypsy\t5190\n-ZAM_I-int\tLTR\tGypsy\t6896\n-Invader5_I-int\tLTR\tGypsy\t191\n-G3_DM\tLINE\tJockey\t480\n-ROOA_I-int\tLTR\tPao\t4103\n-Gypsy1-LTR_DM\tLTR\tGypsy\t1432\n+BURDOCK_LTR\tLTR\tGypsy\t543\n+Chimpo_I-int\tLTR\tGypsy\t1366\n+Chimpo_LTR\tLTR\tGypsy\t107\n+Chouto_I-int\tLTR\tGypsy\t1231\n+Chouto_LTR\tLTR\tGypsy\t162\n+CIRCE\tLTR\tGypsy\t3676\n+Copia_I-int\tLTR\tCopia\t50888\n+Copia_LTR\tLTR\tCopia\t2612\n+Copia1-I_DM\tLTR\tCopia\t4100\n+Copia1-LTR_DM\tLTR\tCopia\t600\n+Copia2_I-int\tLTR\tCopia\t3614\n+Copia2_LTR_DM\tLTR\tCopia\t747\n+DIVER_I-int\tLTR\tPao\t24742\n+DIVER_LTR\tLTR\tPao\t547\n+DIVER2_I-int\tLTR\tPao\t6446\n+DIVER2_LTR\tLTR\tPao\t648\n DM1731_I-int\tLTR\tCopia\t18829\n-ROO_I-int\tLTR\tPao\t34023\n+DM1731_LTR\tLTR\tCopia\t1274\n+DM176_I-int\tLTR\tGypsy\t4726\n+DM176_LTR\tLTR\tGypsy\t560\n+DM297_I-int\tLTR\tGypsy\t82387\n+DM297_LTR\tLTR\tGypsy\t6128\n DM412\tLTR\tGypsy\t43689\n-PROTOP\tDNA\tP\t4775\n-TART-A\tLINE\tJockey\t5092\n-ROO_LTR\tLTR\tPao\t2219\n-DIVER_LTR\tLTR\tPao\t547\n-Gypsy3_I-int\tLTR\tGypsy\t5766\n-BATUMI_LTR\tLTR\tPao\t348\n-IDEFIX_LTR\tLTR\tGypsy\t2538\n-G5_DM\tLINE\tJockey\t2714\n-HETA\tLINE\tJockey\t22459\n-Gypsy11_I-int\tLTR\tGypsy\t487\n-R1-2_DM\tLINE\tR1\t184\n-Gypsy11_LTR\tLTR\tGypsy\t159\n-HELENA_RT\tLINE\tJockey\t934\n-FTZ_DM\tUnknown\tUnknown\t0\n-MICROPIA_I-int\tLTR\tGypsy\t6941\n-Invader4_I-int\tLTR\tGypsy\t1888\n-PLACW_DM\tDNA\tP\t277\n-BLOOD_LTR\tLTR\tGypsy\t1269\n-R2_DM\tLINE\tR2\t54042\n-Copia1-I_DM\tLTR\tCopia\t4100\n-Gypsy4_I-int\tLTR\tGypsy\t13114\n-Chouto_LTR\tLTR\tGypsy\t162\n-BATUMI_I-int\tLTR\tPao\t4723\n-DNAREP1_DM\tRC\tHelitron\t76851\n+DM412B_LTR\tLTR\tGypsy\t5607\n+DMCR1A\tLINE\tCR1\t17489\n+DMLTR5\tLTR\tGypsy\t189\n+DMRP1\tUnknown\tUnknown\t295\n+DMRPR\tUnknown\tUnknown\t221\n+DMRT1A\tLINE\tR1\t3797\n DMRT1B\tLINE\tR1\t9003\n DMRT1C\tLINE\tR1\t1907\n-TLD2\tLTR\tGypsy\t33\n-DMRT1A\tLINE\tR1\t3797\n-DM1731_LTR\tLTR\tCopia\t1274\n-LSU-rRNA_Cel\trRNA\trRNA\t363697\n-Copia_LTR\tLTR\tCopia\t2612\n+DMTOM1_LTR\tLTR\tGypsy\t1403\n+DNAREP1_DM\tRC\tHelitron\t76851\n+DOC\tLINE\tJockey\t29082\n+DOC2_DM\tLINE\tJockey\t4511\n+DOC3_DM\tLINE\tJockey\t11067\n+DOC4_DM\tLINE\tJockey\t1030\n+DOC5_DM\tLINE\tJockey\t1793\n+DOC6_DM\tLINE\tJockey\t1718\n+FB4_DM\tDNA\tTcMar-Tc1\t7840\n+FROGGER_I-int\tLTR\tCopia\t1075\n+FROGGER_LTR\tLTR\tCopia\t85\n+FTZ_DM\tUnknown\tUnknown\t0\n+FUSHI_DM\tUnknown\tUnknown\t0\n+FW2_DM\tLINE\tJockey\t17723\n+F'..b'TOP\tDNA\tP\t4775\n+PROTOP_A\tDNA\tP\t4465\n+PROTOP_B\tDNA\tP\t9371\n+QUASIMODO_I-int\tLTR\tGypsy\t17910\n QUASIMODO_LTR\tLTR\tGypsy\t1625\n-TABOR_LTR\tLTR\tGypsy\t443\n-Stalker2_LTR\tLTR\tGypsy\t790\n-MICROPIA_LTR\tLTR\tGypsy\t460\n-Gypsy9_I-int\tLTR\tGypsy\t429\n-STALKER4_I-int\tLTR\tGypsy\t7287\n-TRANSIB1\tDNA\tCMC-Transib\t1229\n-DOC\tLINE\tJockey\t29082\n-TRANSIB3\tDNA\tCMC-Transib\t1802\n-Copia_I-int\tLTR\tCopia\t50888\n-TRANSIB4\tDNA\tCMC-Transib\t364\n-Gypsy10_LTR\tLTR\tGypsy\t363\n-Invader3_I-int\tLTR\tGypsy\t4411\n-Invader1_I-int\tLTR\tGypsy\t2993\n-BS3_DM\tLINE\tJockey\t851\n-Gypsy2-LTR_DM\tLTR\tGypsy\t1155\n-LSU-rRNA_Hsa\trRNA\trRNA\t15\n-NOMAD_LTR\tLTR\tGypsy\t757\n-Helitron1_DM\tRC\tHelitron\t0\n-LINEJ1_DM\tLINE\tJockey\t24891\n-Invader4_LTR\tLTR\tGypsy\t1624\n-MDG3_I-int\tLTR\tGypsy\t7857\n-LmeSINE1c\tSINE\ttRNA-Deu-L2\t627\n+QUASIMODO2-I_DM\tLTR\tGypsy\t3977\n+QUASIMODO2-LTR_DM\tLTR\tGypsy\t298\n+R1_DM\tLINE\tR1\t15424\n+R1-2_DM\tLINE\tR1\t184\n+R2_DM\tLINE\tR2\t54042\n+ROO_I-int\tLTR\tPao\t34023\n+ROO_LTR\tLTR\tPao\t2219\n+ROOA_I-int\tLTR\tPao\t4103\n+ROOA_LTR\tLTR\tPao\t435\n+ROVER-I_DM\tLTR\tGypsy\t6947\n ROVER-LTR_DM\tLTR\tGypsy\t415\n S_DM\tDNA\tTcMar-Tc1\t4974\n-Invader6_I-int\tLTR\tGypsy\t6566\n-ROVER-I_DM\tLTR\tGypsy\t6947\n-QUASIMODO_I-int\tLTR\tGypsy\t17910\n-Chouto_I-int\tLTR\tGypsy\t1231\n-NTS_DM\tOther\tOther\t56043\n-Gypsy3_LTR\tLTR\tGypsy\t681\n+S2_DM\tDNA\tTcMar-Tc1\t716\n SSU-rRNA_Cel\trRNA\trRNA\t3855\n-MINOS\tDNA\tTcMar-Tc1\t273\n-DOC4_DM\tLINE\tJockey\t1030\n-ZAM_LTR\tLTR\tGypsy\t377\n-QUASIMODO2-LTR_DM\tLTR\tGypsy\t298\n-Gypsy2-I_DM\tLTR\tGypsy\t7374\n-TRANSPAC_I-int\tLTR\tGypsy\t28474\n-Bica_I-int\tLTR\tGypsy\t1561\n-BS2\tLINE\tJockey\t5214\n-BLOOD_I-int\tLTR\tGypsy\t27362\n-DMCR1A\tLINE\tCR1\t17489\n-QUASIMODO2-I_DM\tLTR\tGypsy\t3977\n-HMSBEAGLE_I-int\tLTR\tGypsy\t7863\n-DMLTR5\tLTR\tGypsy\t189\n-Gypsy7_LTR\tLTR\tGypsy\t80\n-G5A_DM\tLINE\tJockey\t1578\n-MDG1_I-int\tLTR\tGypsy\t16306\n-Gypsy2_I-int\tLTR\tGypsy\t4226\n-BARI1\tDNA\tTcMar-Tc1\t370\n-Invader5_LTR\tLTR\tGypsy\t47\n-DM176_LTR\tLTR\tGypsy\t560\n-DOC3_DM\tLINE\tJockey\t11067\n-Copia1-LTR_DM\tLTR\tCopia\t600\n-TOM_I-int\tLTR\tGypsy\t6929\n-NOF_FB\tDNA\tMULE-NOF\t228\n-Chimpo_I-int\tLTR\tGypsy\t1366\n-DIVER_I-int\tLTR\tPao\t24742\n+SSU-rRNA_Dme\trRNA\trRNA\t9958\n+SSU-rRNA_Hsa\trRNA\trRNA\t563673\n+Stalker2_I-int\tLTR\tGypsy\t10966\n+Stalker2_LTR\tLTR\tGypsy\t790\n+Stalker3_LTR\tLTR\tGypsy\t543\n+STALKER4_I-int\tLTR\tGypsy\t7287\n+STALKER4_LTR\tLTR\tGypsy\t2040\n+TABOR_I-int\tLTR\tGypsy\t5504\n+TABOR_LTR\tLTR\tGypsy\t443\n+TAHRE\tLINE\tJockey\t3806\n+TART_B1\tLINE\tJockey\t13382\n+TART-A\tLINE\tJockey\t5092\n+TC1_DM\tDNA\tTcMar-Tc1\t2618\n+TC1-2_DM\tDNA\tTcMar-Tc1\t4438\n TIRANT_I-int\tLTR\tGypsy\t23165\n-Gypsy2_LTR\tLTR\tGypsy\t869\n-FB4_DM\tDNA\tTcMar-Tc1\t7840\n-GTWIN_LTR\tLTR\tGypsy\t2533\n-Invader6_LTR\tLTR\tGypsy\t312\n-Gypsy8_I-int\tLTR\tGypsy\t4176\n-G_DM\tLINE\tJockey\t10948\n-TRANSPAC_LTR\tLTR\tGypsy\t1457\n-FUSHI_DM\tUnknown\tUnknown\t0\n+TIRANT_LTR\tLTR\tGypsy\t3225\n+TLD2\tLTR\tGypsy\t33\n+TOM_I-int\tLTR\tGypsy\t6929\n+Transib-N1_DM\tDNA\tCMC-Transib\t366\n+TRANSIB1\tDNA\tCMC-Transib\t1229\n+TRANSIB2\tDNA\tCMC-Transib\t3357\n+TRANSIB3\tDNA\tCMC-Transib\t1802\n+TRANSIB4\tDNA\tCMC-Transib\t364\n Transib5\tDNA\tCMC-Transib\t973\n-MuDR-1_DEl\tDNA\tMULE-NOF\t32\n-Mariner2_DM\tDNA\tTcMar-Tc1\t1096\n-DOC5_DM\tLINE\tJockey\t1793\n-TC1_DM\tDNA\tTcMar-Tc1\t2618\n-Gypsy9_LTR\tLTR\tGypsy\t62\n-DMRP1\tUnknown\tUnknown\t295\n-Gypsy10_I-int\tLTR\tGypsy\t2236\n-Gypsy4_LTR\tLTR\tGypsy\t390\n-DM297_LTR\tLTR\tGypsy\t6128\n-ACCORD2_I-int\tLTR\tGypsy\t2286\n-Invader1_LTR\tLTR\tGypsy\t2525\n-BEL_LTR\tLTR\tPao\t927\n-IVK_DM\tLINE\tI\t3025\n-M4DM\tDNA\tCMC-Transib\t1880\n-FW2_DM\tLINE\tJockey\t17723\n-Copia2_I-int\tLTR\tCopia\t3614\n-MDG1_LTR\tLTR\tGypsy\t650\n-Gypsy12_LTR\tLTR\tGypsy\t7572\n-Gypsy7_I-int\tLTR\tGypsy\t1162\n-FROGGER_I-int\tLTR\tCopia\t1075\n-Gypsy_I-int\tLTR\tGypsy\t24082\n-5S_DM\tRNA\tRNA\t6331\n-GTWIN_I-int\tLTR\tGypsy\t7568\n-CIRCE\tLTR\tGypsy\t3676\n-DIVER2_LTR\tLTR\tPao\t648\n-POGO\tDNA\tTcMar-Pogo\t2909\n-Gypsy6A_LTR\tLTR\tGypsy\t793\n-MAX_I-int\tLTR\tPao\t8914\n-ROOA_LTR\tLTR\tPao\t435\n-DM176_I-int\tLTR\tGypsy\t4726\n-Copia2_LTR_DM\tLTR\tCopia\t747\n-DM297_I-int\tLTR\tGypsy\t82387\n-IDEFIX_I-int\tLTR\tGypsy\t7222\n-Jockey2\tLINE\tJockey\t1823\n-TC1-2_DM\tDNA\tTcMar-Tc1\t4438\n-DMRPR\tUnknown\tUnknown\t221\n+TRANSPAC_I-int\tLTR\tGypsy\t28474\n+TRANSPAC_LTR\tLTR\tGypsy\t1457\n+XDMR\tUnknown\tUnknown\t1771\n+XDMR_DM\tUnknown\tUnknown\t4049\n+ZAM_I-int\tLTR\tGypsy\t6896\n+ZAM_LTR\tLTR\tGypsy\t377\n' |
| b |
| diff -r 51b4590a972d -r 15e3e29f310e test-data/Normalized_counts_file.tab --- a/test-data/Normalized_counts_file.tab Mon Sep 18 17:22:07 2017 -0400 +++ b/test-data/Normalized_counts_file.tab Tue Sep 19 17:23:15 2017 -0400 |
| b |
| b'@@ -1,211 +1,211 @@\n Tag\tMutant_1\tMutant_2\tWildtype_1\tWildtype_2\n-LSU-rRNA_Dme\t218650.181450173\t354466.098949349\t157455.221275418\t149201.031867455\n-FW3_DM\t25.3386538652006\t32.2981814492716\t35.756634311884\t44.2453336153694\n-DMTOM1_LTR\t54.9461072223747\t39.3419337866127\t43.2005545717588\t49.0430203929395\n-R1_DM\t604.054709763298\t517.028601444589\t315.957840856997\t262.031236427494\n-TAHRE\t149.055512536249\t121.719476366005\t196.209690086873\t189.678242903128\n-G4_DM\t87.0600116574048\t105.226787966377\t157.828320885669\t165.108271224056\n-BS\t203.649150075801\t355.194096523239\t313.935504138996\t242.355874491196\n-Stalker2_I-int\t429.46472687139\t413.519801853174\t527.184456786045\t604.508533973842\n-Stalker3_LTR\t21.2656708636846\t20.1863634057947\t25.5158653994552\t21.2745908621546\n-TABOR_I-int\t215.554792695617\t317.054754599099\t169.833255871247\t149.309827895896\n-G7_DM\t76.3292679803337\t35.9059570366902\t6.97060741098101\t4.74922529496845\n-BEL_I-int\t1148.97283940843\t1304.98396962057\t1022.22666828812\t1059.36800967358\n-Gypsy6_I-int\t445.717495579363\t323.23951274896\t322.239993215042\t326.921161631196\n+5S_DM\t247.942840217287\t356.138990129468\t271.810660587451\t503.611727197063\n ACCORD_I-int\t160.687012069425\t174.461719477315\t117.166444321613\t104.919109832721\n-DM412B_LTR\t219.588612399041\t257.784155662936\t132.441540808639\t141.022914371002\n-G2_DM\t48.3666731430026\t65.6271559235199\t57.1417693937208\t54.8583983051458\n-SSU-rRNA_Hsa\t22075.2937251301\t25925.561270609\t13684.9804569472\t8340.22115575582\n-TART_B1\t524.083255060455\t437.142142008891\t1086.38207353363\t1042.55187521078\n-S2_DM\t28.0409214335141\t17.6093808433528\t32.9167572185214\t35.52226674706\n-LOOPER1_DM\t8.61592558013002\t2.66288198118994\t35.3263499037988\t28.5438132524124\n-HOBO\t171.339429150313\t182.020868327145\t216.476085707688\t213.42436937797\n+ACCORD_LTR\t30.9390054922851\t29.5494000493336\t12.6933900385148\t10.6615261723782\n+ACCORD2_I-int\t89.5272994371693\t103.079302497675\t126.245445332212\t119.118324235025\n+ACCORD2_LTR\t8.34178249348953\t6.52835582485276\t10.1116835900033\t9.30460465953003\n+ALA_DM\t0.352469682823501\t0\t0.215142204042624\t0.290768895610313\n ARS406_DM\t29.5682900590826\t19.7568663120544\t24.2250121751994\t34.8438059906359\n-G6_DM\t112.555318714971\t67.5169431359773\t207.698283782749\t168.30672907577\n-DOC2_DM\t176.665637690757\t176.265607271025\t190.960220308233\t219.9182080466\n Baggins1\t215.398139503251\t157.367735146451\t220.994071992583\t188.660551768492\n-NINJA_LTR\t11.6314995331755\t9.79253373727915\t21.1269644369856\t19.6753619362979\n-TRANSIB2\t131.471191693166\t127.474737422125\t137.561925264854\t149.067520482887\n-Gypsy5_LTR\t19.6599756419331\t28.0032105118684\t28.0115149663496\t21.8561286533752\n-MDG3_LTR\t36.2652140327291\t38.9983361116205\t44.6204931184401\t41.0953372462576\n-Gypsy12A_LTR\t95.4017941508943\t92.5136739916635\t131.624000433277\t108.650643993054\n-Gypsy_LTR\t147.684797103047\t149.207290365385\t56.1951436959333\t44.4391795457762\n-TIRANT_LTR\t126.301636345088\t137.095472321908\t58.9919923484874\t61.9822362475985\n-I_DM\t449.55549879233\t957.692619622151\t343.668156737687\t339.860377485855\n-DIVER2_I-int\t252.44661949781\t229.179649219831\t287.386956160137\t272.692762599872\n-P-1_DY\t0.509122875189502\t0.343597674992251\t0.344227526468198\t0.0969229652034378\n-Invader2_I-int\t233.804889606256\t271.184464987634\t293.583051636564\t267.022769135471\n-DOC6_DM\t67.2825461211972\t65.9707535985121\t54.1728069779326\t60.0922384261314\n+BARI_DM\t43.7454039682056\t44.8394965864887\t42.5981564004395\t43.7122573067505\n+BARI1\t14.490420293855\t10.7374273435078\t16.9962341193673\t15.6045973977535\n+BATUMI_I-int\t184.968256886155\t158.226729333931\t275.166878970516\t232.082040179632\n+BATUMI_LTR\t13.628827735842\t14.5170017684226\t23.8377562079227\t19.5299774884927\n+BEL_I-int\t1148.97283940843\t1304.98396962057\t1022.22666828812\t1059.36800967358\n+BEL_LTR\t36.3043773308206\t51.9691483425779\t37.6498857074591\t41.5799520722748\n+Bica_I-int\t61.1339083208317\t53.0858407863027\t79.6886723773878\t67.3614608163893\n+Bica_LTR\t4.81708566525451\t5.7552610561202\t6.02398171319346\t6.05768532521486\n+BLASTOPIA_I-int\t539.67024770087'..b'01636345088\t137.095472321908\t58.9919923484874\t61.9822362475985\n+TLD2\t1.2923888370195\t0.0858994187480627\t2.79684865255411\t0.823845204229221\n+TOM_I-int\t271.362492476004\t291.199029555932\t110.281893792249\t111.994486292572\n+Transib-N1_DM\t14.333767101489\t11.1669244372481\t13.2527597690256\t17.9792100452377\n+TRANSIB1\t48.1316933544536\t24.8249320181901\t89.5852137633485\t102.544497185237\n+TRANSIB2\t131.471191693166\t127.474737422125\t137.561925264854\t149.067520482887\n+TRANSIB3\t70.5722631608832\t63.6514692923144\t50.9456739172933\t54.8583983051458\n+TRANSIB4\t14.255440505306\t13.1426110684536\t27.3230599134132\t27.6715065655815\n Transib5\t38.1058890430296\t28.1750093493646\t48.3209390279733\t46.7653307106587\n-MuDR-1_DEl\t1.253225538928\t0.343597674992251\t0.258170644851148\t0.43615334341547\n-Mariner2_DM\t42.9229747082841\t79.542861760706\t86.5301944659432\t77.1022188193348\n-DOC5_DM\t70.2197934780597\t64.5963628985431\t130.67737473549\t105.791416519552\n-TC1_DM\t102.529514403547\t127.560636840873\t79.1723310876855\t94.9845058993691\n-Gypsy9_LTR\t2.42812448167301\t0.687195349984501\t2.19445048123476\t2.03538226927219\n-DMRP1\t11.5531729369925\t12.369516299721\t11.2734514918335\t11.0007565505902\n-Gypsy10_I-int\t87.5691345325943\t79.6287611794541\t97.1582193456488\t93.5306614213175\n-Gypsy4_LTR\t15.273686255685\t18.7260732870777\t11.7897927815358\t9.40152762473347\n-DM297_LTR\t239.992690704713\t216.122937570126\t64.0693483638933\t71.6260712853405\n-ACCORD2_I-int\t89.5272994371693\t103.079302497675\t126.245445332212\t119.118324235025\n-Invader1_LTR\t98.8873276810378\t163.466593877563\t143.973162945324\t93.5791229039192\n-BEL_LTR\t36.3043773308206\t51.9691483425779\t37.6498857074591\t41.5799520722748\n-IVK_DM\t118.468976726788\t151.956071765323\t144.102248267749\t141.555990679621\n-M4DM\t73.6270004120202\t78.8556664107215\t74.3101172763222\t79.9614462928362\n-FW2_DM\t694.091132075657\t761.412447782827\t612.466826468541\t671.046149586002\n-Copia2_I-int\t141.536159302681\t162.521700271335\t181.493963330357\t167.434422388939\n-MDG1_LTR\t25.4561437594751\t24.1377366682056\t29.6896241578821\t28.2045828742004\n-Gypsy12_LTR\t296.544493148839\t230.210442244808\t270.734949567238\t287.5704377586\n-Gypsy7_I-int\t45.5077523823231\t63.7373687110625\t54.0437216555071\t48.8976359451344\n-FROGGER_I-int\t42.1005454483626\t46.9010826364422\t69.3188181425333\t65.9560778209394\n-Gypsy_I-int\t943.130544639506\t958.723412647127\t293.540023195756\t273.031992978084\n-5S_DM\t247.942840217287\t356.138990129468\t271.810660587451\t503.611727197063\n-GTWIN_I-int\t296.387839956473\t251.685296931824\t234.418945524843\t244.924333069087\n-CIRCE\t143.964283784354\t134.862087434458\t162.088136525713\t161.037506685512\n-DIVER2_LTR\t25.3778171632921\t20.615860499535\t34.1215535611601\t25.9268931919196\n-POGO\t113.926034148174\t88.6482001480007\t104.43002584229\t120.766014643484\n-Gypsy6A_LTR\t31.0564953865596\t18.8119727058257\t26.5485479788598\t27.7684295307849\n-MAX_I-int\t349.101639187632\t335.437230211185\t533.337523821664\t445.894101418416\n-ROOA_LTR\t17.0360346698026\t23.7082395744653\t17.2113763234099\t23.4068960966302\n-DM176_I-int\t185.08574678043\t197.396864283048\t156.064154812519\t136.322150558635\n-Copia2_LTR_DM\t29.2549836743506\t39.5137326241088\t38.3383407603955\t23.5522805444354\n-DM297_I-int\t3226.54663986442\t3668.33467763602\t509.327653850507\t558.760894397819\n-IDEFIX_I-int\t282.837338816814\t282.265490006134\t266.475133927194\t268.815843991735\n-Jockey2\t71.3946924208047\t65.2835582485276\t76.1603402310888\t76.9568343715296\n-TC1-2_DM\t173.806716930078\t196.451970676819\t163.809274158054\t191.325933311586\n-DMRPR\t8.65508887822152\t11.6823209497365\t5.50764042349117\t9.06229724652144\n+TRANSPAC_I-int\t1115.13574985737\t1439.67425821753\t416.257136381668\t726.049932338953\n+TRANSPAC_LTR\t57.0609253193157\t84.0955309543534\t23.1493011549863\t26.896122843954\n+XDMR\t69.3582009200467\t77.5671751295006\t53.7425225698474\t69.7845349464752\n+XDMR_DM\t158.572193972484\t136.322377553175\t142.725338161877\t209.741296700239\n+ZAM_I-int\t270.070103638985\t248.421119019397\t220.692872906923\t214.490521995208\n+ZAM_LTR\t14.7645633804955\t10.1361314122714\t11.1443661694079\t10.9038335853868\n' |
| b |
| diff -r 51b4590a972d -r 15e3e29f310e test-data/Samp-paired_class_fraction_counts.tab --- a/test-data/Samp-paired_class_fraction_counts.tab Mon Sep 18 17:22:07 2017 -0400 +++ b/test-data/Samp-paired_class_fraction_counts.tab Tue Sep 19 17:23:15 2017 -0400 |
| b |
| @@ -1,3 +1,3 @@ Low_complexity 2.0 +Simple_repeat 121.0 rRNA 111.0 -Simple_repeat 121.0 |
| b |
| diff -r 51b4590a972d -r 15e3e29f310e test-data/Samp-paired_family_fraction_counts.tab --- a/test-data/Samp-paired_family_fraction_counts.tab Mon Sep 18 17:22:07 2017 -0400 +++ b/test-data/Samp-paired_family_fraction_counts.tab Tue Sep 19 17:23:15 2017 -0400 |
| b |
| @@ -1,3 +1,3 @@ Low_complexity 2.0 +Simple_repeat 121.0 rRNA 111.0 -Simple_repeat 121.0 |
| b |
| diff -r 51b4590a972d -r 15e3e29f310e test-data/Samp_class_fraction_counts.tabular --- a/test-data/Samp_class_fraction_counts.tabular Mon Sep 18 17:22:07 2017 -0400 +++ b/test-data/Samp_class_fraction_counts.tabular Tue Sep 19 17:23:15 2017 -0400 |
| b |
| @@ -1,3 +1,3 @@ Low_complexity 0.0 +Simple_repeat 98.0 rRNA 772.0 -Simple_repeat 98.0 |
| b |
| diff -r 51b4590a972d -r 15e3e29f310e test-data/Samp_family_fraction_counts.tabular --- a/test-data/Samp_family_fraction_counts.tabular Mon Sep 18 17:22:07 2017 -0400 +++ b/test-data/Samp_family_fraction_counts.tabular Tue Sep 19 17:23:15 2017 -0400 |
| b |
| @@ -1,3 +1,3 @@ Low_complexity 0.0 +Simple_repeat 98.0 rRNA 772.0 -Simple_repeat 98.0 |
| b |
| diff -r 51b4590a972d -r 15e3e29f310e test-data/aligned_353.tab --- a/test-data/aligned_353.tab Mon Sep 18 17:22:07 2017 -0400 +++ b/test-data/aligned_353.tab Tue Sep 19 17:23:15 2017 -0400 |
| b |
| @@ -1,1 +1,2 @@ +# Total reads aligned to repeated sequences 15862067 |
| b |
| diff -r 51b4590a972d -r 15e3e29f310e test-data/aligned_354.tab --- a/test-data/aligned_354.tab Mon Sep 18 17:22:07 2017 -0400 +++ b/test-data/aligned_354.tab Tue Sep 19 17:23:15 2017 -0400 |
| b |
| @@ -1,1 +1,2 @@ +# Total reads aligned to repeated sequences 28421096 |
| b |
| diff -r 51b4590a972d -r 15e3e29f310e test-data/aligned_355.tab --- a/test-data/aligned_355.tab Mon Sep 18 17:22:07 2017 -0400 +++ b/test-data/aligned_355.tab Tue Sep 19 17:23:15 2017 -0400 |
| b |
| @@ -1,1 +1,2 @@ +# Total reads aligned to repeated sequences 10808170 |
| b |
| diff -r 51b4590a972d -r 15e3e29f310e test-data/aligned_356.tab --- a/test-data/aligned_356.tab Mon Sep 18 17:22:07 2017 -0400 +++ b/test-data/aligned_356.tab Tue Sep 19 17:23:15 2017 -0400 |
| b |
| @@ -1,1 +1,2 @@ +# Total reads aligned to repeated sequences 29256707 |
| b |
| diff -r 51b4590a972d -r 15e3e29f310e test-data/aligned_reads.tab --- a/test-data/aligned_reads.tab Mon Sep 18 17:22:07 2017 -0400 +++ b/test-data/aligned_reads.tab Tue Sep 19 17:23:15 2017 -0400 |
| b |
| @@ -1,1 +1,3 @@ +# Total reads aligned to repeated sequences + 2510 |
| b |
| diff -r 51b4590a972d -r 15e3e29f310e test-data/edgeR_plots.pdf |
| b |
| Binary file test-data/edgeR_plots.pdf has changed |
| b |
| diff -r 51b4590a972d -r 15e3e29f310e test-data/edgeR_result_file.tab --- a/test-data/edgeR_result_file.tab Mon Sep 18 17:22:07 2017 -0400 +++ b/test-data/edgeR_result_file.tab Tue Sep 19 17:23:15 2017 -0400 |
| b |
| b'@@ -52,9 +52,9 @@\n TAHRE\t-0.509503033739914\t0.0198535740576507\tLINE\tJockey\n Gypsy8_I-int\t-0.578276897527121\t0.0248976847994314\tLTR\tGypsy\n BLASTOPIA_I-int\t0.796987753936179\t0.0301824235833205\tLTR\tGypsy\n-Gypsy11_I-int\t-0.734634622561586\t0.0432538714324547\tLTR\tGypsy\n+DM176_LTR\t-0.691384671506076\t0.0432538714324547\tLTR\tGypsy\n DMRT1A\t-0.509608409844153\t0.0432538714324547\tLINE\tR1\n-DM176_LTR\t-0.691384671506076\t0.0432538714324547\tLTR\tGypsy\n+Gypsy11_I-int\t-0.734634622561586\t0.0432538714324547\tLTR\tGypsy\n QUASIMODO2-I_DM\t0.470057940126177\t0.044414105251971\tLTR\tGypsy\n MuDR-1_DEl\t1.35524442785064\t0.0532319546519159\tDNA\tMULE-NOF\n DM1731_LTR\t0.752238181600754\t0.0540130070646644\tLTR\tCopia\n@@ -71,14 +71,14 @@\n BATUMI_LTR\t-0.625598883331715\t0.112325719453317\tLTR\tPao\n Gypsy2-I_DM\t0.418860685191156\t0.127538985839499\tLTR\tGypsy\n Invader3_LTR\t-0.553726127316243\t0.130228544874336\tLTR\tGypsy\n+MDG3_I-int\t0.417195433411295\t0.130837858091619\tLTR\tGypsy\n SSU-rRNA_Dme\t0.50182621141568\t0.130837858091619\trRNA\trRNA\n-MDG3_I-int\t0.417195433411295\t0.130837858091619\tLTR\tGypsy\n G5A_DM\t-0.468375220785066\t0.142388172856184\tLINE\tJockey\n S2_DM\t-0.576444154651051\t0.154380925206633\tDNA\tTcMar-Tc1\n Stalker2_I-int\t-0.424817076156048\t0.157921464286182\tLTR\tGypsy\n-R1-2_DM\t-0.611853226580459\t0.158635278613665\tLINE\tR1\n BLOOD_LTR\t0.494999752604753\t0.158635278613665\tLTR\tGypsy\n Invader5_LTR\t-0.675984091871337\t0.158635278613665\tLTR\tGypsy\n+R1-2_DM\t-0.611853226580459\t0.158635278613665\tLINE\tR1\n Transib5\t-0.51646991193603\t0.158635278613665\tDNA\tCMC-Transib\n TLD2\t-1.24823548505769\t0.158665416598185\tLTR\tGypsy\n TC1_DM\t0.400572910860442\t0.167626897114732\tDNA\tTcMar-Tc1\n@@ -92,53 +92,53 @@\n POGON1\t0.482507112501569\t0.255779427421414\tDNA\tTcMar-Pogo\n HOBO\t-0.283220815078204\t0.273166685685814\tDNA\thAT-hobo\n BS3_DM\t-0.418041606433149\t0.277910060681416\tLINE\tJockey\n+Gypsy9_I-int\t-0.437336296478435\t0.280951304168472\tLTR\tGypsy\n P-1_DY\t0.969417874734635\t0.280951304168472\tDNA\tP\n-Gypsy9_I-int\t-0.437336296478435\t0.280951304168472\tLTR\tGypsy\n Bica_I-int\t-0.363151852276854\t0.287621291763315\tLTR\tGypsy\n DMCR1A\t-0.342108879038489\t0.320538100201906\tLINE\tCR1\n Mariner2_DM\t-0.422114252836712\t0.320538100201906\tDNA\tTcMar-Tc1\n+Gypsy7_LTR\t-0.484940393339899\t0.322658401361327\tLTR\tGypsy\n TRANSIB3\t0.344232145502121\t0.322658401361327\tDNA\tCMC-Transib\n-Gypsy7_LTR\t-0.484940393339899\t0.322658401361327\tLTR\tGypsy\n DMRPR\t0.474671090698546\t0.369600785239272\tUnknown\tUnknown\n DIVER2_LTR\t-0.381362071713278\t0.384462351162869\tLTR\tPao\n Gypsy1-LTR_DM\t0.341547880045558\t0.384860099197221\tLTR\tGypsy\n+DOC4_DM\t0.362114244909638\t0.389414554540185\tLINE\tJockey\n SSU-rRNA_Cel\t0.268693361351043\t0.389414554540185\trRNA\trRNA\n-DOC4_DM\t0.362114244909638\t0.389414554540185\tLINE\tJockey\n ZAM_I-int\t0.25296287202699\t0.397202788288282\tLTR\tGypsy\n XDMR_DM\t-0.256211211677393\t0.408914532732159\tUnknown\tUnknown\n Chimpo_LTR\t-0.460515218470088\t0.409319591327129\tLTR\tGypsy\n+5S_DM\t-0.36064468671157\t0.412039231991319\tRNA\tRNA\n+BLOOD_I-int\t0.301193505006723\t0.412039231991319\tLTR\tGypsy\n+CIRCE\t-0.21220098912431\t0.412039231991319\tLTR\tGypsy\n DOC2_DM\t-0.219218822289782\t0.412039231991319\tLINE\tJockey\n-PROTOP\t-0.21894181311432\t0.412039231991319\tDNA\tP\n-HETA\t-0.298692871636692\t0.412039231991319\tLINE\tJockey\n HELENA_RT\t0.306716860759321\t0.412039231991319\tLINE\tJockey\n+HETA\t-0.298692871636692\t0.412039231991319\tLINE\tJockey\n Invader2_LTR\t-0.349451178427879\t0.412039231991319\tLTR\tGypsy\n-BLOOD_I-int\t0.301193505006723\t0.412039231991319\tLTR\tGypsy\n-5S_DM\t-0.36064468671157\t0.412039231991319\tRNA\tRNA\n-CIRCE\t-0.21220098912431\t0.412039231991319\tLTR\tGypsy\n+PROTOP\t-0.21894181311432\t0.412039231991319\tDNA\tP\n ACCORD2_LTR\t-0.373877436518785\t0.415323684742582\tLTR\tGypsy\n BARI1\t-0.361825471165769\t0.439062969216072\tDNA\tTcMar-Tc1\n Copia2_I-int\t-0.199651272204726\t0.454016393978291\tLTR\tCopia\n Chouto_LTR\t-0.42256718750228\t0.457631460799645\tLTR\tGypsy\n S_DM\t0.193275098711318\t0.466588891242574\tDNA\tTcMar-Tc1\n+Chimpo_I-int\t-0.3198026895528\t0.469668398060595\tLTR\tGypsy\n+Gypsy2_LTR\t0.337405927915915\t0.469668398060595\tLTR\tGy'..b'79\tDNA\tP\n+Invader2_I-int\t-0.151224307192946\t0.653366733778121\tLTR\tGypsy\n MDG3_LTR\t-0.188668582948884\t0.653366733778121\tLTR\tGypsy\n-Invader2_I-int\t-0.151224307192946\t0.653366733778121\tLTR\tGypsy\n Jockey2\t-0.162959614427421\t0.6545684300628\tLINE\tJockey\n POGO\t-0.150727724968995\t0.655487951511946\tDNA\tTcMar-Pogo\n Baggins1\t-0.134826103211095\t0.693165877070164\tLINE\tLOA\n-Stalker3_LTR\t-0.174018068430168\t0.707635948527852\tLTR\tGypsy\n Bica_LTR\t-0.203027970314789\t0.707635948527852\tLTR\tGypsy\n HMSBEAGLE_I-int\t0.13884460350775\t0.707635948527852\tLTR\tGypsy\n+Stalker3_LTR\t-0.174018068430168\t0.707635948527852\tLTR\tGypsy\n+NTS_DM\t-0.176552072990723\t0.7126900116144\tOther\tOther\n TABOR_LTR\t-0.243243320673685\t0.7126900116144\tLTR\tGypsy\n-NTS_DM\t-0.176552072990723\t0.7126900116144\tOther\tOther\n ZAM_LTR\t0.185889162361338\t0.717882303973929\tLTR\tGypsy\n G5_DM\t-0.112256553949312\t0.728328879400999\tLINE\tJockey\n-QUASIMODO_I-int\t0.126271255526405\t0.756425760962704\tLTR\tGypsy\n+BEL_LTR\t0.152542861711851\t0.756425760962704\tLTR\tPao\n FB4_DM\t-0.114616335459739\t0.756425760962704\tDNA\tTcMar-Tc1\n Invader1_LTR\t0.141219962488351\t0.756425760962704\tLTR\tGypsy\n-BEL_LTR\t0.152542861711851\t0.756425760962704\tLTR\tPao\n+QUASIMODO_I-int\t0.126271255526405\t0.756425760962704\tLTR\tGypsy\n DMRT1B\t-0.111235216287692\t0.760051744799183\tLINE\tR1\n NOMAD_I-int\t-0.137546703453753\t0.760051744799183\tLTR\tGypsy\n LmeSINE1c\t-0.228543531933743\t0.760296029745035\tSINE\ttRNA-Deu-L2\n+Copia2_LTR_DM\t0.147979193864449\t0.76240178289376\tLTR\tCopia\n Gypsy10_LTR\t-0.154651074858764\t0.76240178289376\tLTR\tGypsy\n QUASIMODO2-LTR_DM\t-0.155430480903998\t0.76240178289376\tLTR\tGypsy\n-Copia2_LTR_DM\t0.147979193864449\t0.76240178289376\tLTR\tCopia\n BS4_DM\t-0.253251631796478\t0.81092436860891\tLINE\tJockey\n G_DM\t0.0902785903431559\t0.81092436860891\tLINE\tJockey\n IVK_DM\t-0.0807211765160779\t0.818709085450591\tLINE\tI\n+Gypsy12_LTR\t-0.0832045482918072\t0.835273508731359\tLTR\tGypsy\n Gypsy5_I-int\t-0.0774807293903186\t0.835273508731359\tLTR\tGypsy\n-Gypsy12_LTR\t-0.0832045482918072\t0.835273508731359\tLTR\tGypsy\n Gypsy6A_LTR\t-0.116239966704279\t0.835273508731359\tLTR\tGypsy\n IDEFIX_I-int\t0.0781972363147815\t0.835273508731359\tLTR\tGypsy\n+DMRP1\t0.100504519100353\t0.846311908195535\tUnknown\tUnknown\n PROTOP_B\t-0.0745501769371703\t0.846311908195535\tDNA\tP\n-DMRP1\t0.100504519100353\t0.846311908195535\tUnknown\tUnknown\n Copia1-LTR_DM\t-0.0961752276665428\t0.850550157756311\tLTR\tCopia\n TC1-2_DM\t0.0595720035046981\t0.853067020850826\tDNA\tTcMar-Tc1\n+Gypsy7_I-int\t0.0826410967604942\t0.861339242519926\tLTR\tGypsy\n LSU-rRNA_Cel\t-0.0920825033469626\t0.861339242519926\trRNA\trRNA\n-Gypsy7_I-int\t0.0826410967604942\t0.861339242519926\tLTR\tGypsy\n-Gypsy5_LTR\t-0.0710979993807782\t0.905487490633946\tLTR\tGypsy\n+DMLTR5\t0.0726894766496021\t0.905487490633946\tLTR\tGypsy\n+Gypsy2-LTR_DM\t0.0652192786223383\t0.905487490633946\tLTR\tGypsy\n Gypsy4_I-int\t-0.0516274039610208\t0.905487490633946\tLTR\tGypsy\n+Gypsy5_LTR\t-0.0710979993807782\t0.905487490633946\tLTR\tGypsy\n QUASIMODO_LTR\t-0.0643467685962964\t0.905487490633946\tLTR\tGypsy\n-Gypsy2-LTR_DM\t0.0652192786223383\t0.905487490633946\tLTR\tGypsy\n-DMLTR5\t0.0726894766496021\t0.905487490633946\tLTR\tGypsy\n Stalker2_LTR\t-0.0523210063310555\t0.917308330496379\tLTR\tGypsy\n ROVER-I_DM\t-0.0408110836395496\t0.922716163337686\tLTR\tGypsy\n MDG1_I-int\t-0.0411424164719924\t0.937452811422426\tLTR\tGypsy\n@@ -196,10 +196,10 @@\n BARI_DM\t0.0372716083617889\t0.949850971355763\tDNA\tTcMar-Tc1\n Gypsy2_I-int\t-0.0261599267227275\t0.951965771983562\tLTR\tGypsy\n DMTOM1_LTR\t0.0349640382618226\t0.953829042793374\tLTR\tGypsy\n+Gypsy3_LTR\t-0.0298883238815861\t0.957715681080923\tLTR\tGypsy\n IDEFIX_LTR\t0.0219961145617681\t0.957715681080923\tLTR\tGypsy\n+MINOS\t0.0330479824589295\t0.957715681080923\tDNA\tTcMar-Tc1\n STALKER4_I-int\t0.0241275307638275\t0.957715681080923\tLTR\tGypsy\n-Gypsy3_LTR\t-0.0298883238815861\t0.957715681080923\tLTR\tGypsy\n-MINOS\t0.0330479824589295\t0.957715681080923\tDNA\tTcMar-Tc1\n G2_DM\t0.0226097987515835\t0.962242582647045\tLINE\tJockey\n Copia1-I_DM\t0.0124236833262227\t0.963045943681341\tLTR\tCopia\n Invader4_LTR\t0.016495431966038\t0.963045943681341\tLTR\tGypsy\n' |
| b |
| diff -r 51b4590a972d -r 15e3e29f310e test-data/paired-aligned_reads.tab --- a/test-data/paired-aligned_reads.tab Mon Sep 18 17:22:07 2017 -0400 +++ b/test-data/paired-aligned_reads.tab Tue Sep 19 17:23:15 2017 -0400 |
| b |
| @@ -1,1 +1,3 @@ +# Total reads aligned to repeated sequences + 2082 |