Mercurial > repos > artbio > repenrich
changeset 2:15e3e29f310e draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
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--- 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')
--- 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
--- a/edger-repenrich.xml Mon Sep 18 17:22:07 2017 -0400 +++ b/edger-repenrich.xml Tue Sep 19 17:23:15 2017 -0400 @@ -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>
--- a/repenrich.xml Mon Sep 18 17:22:07 2017 -0400 +++ b/repenrich.xml Tue Sep 19 17:23:15 2017 -0400 @@ -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>
--- 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 @@ -1,210 +1,210 @@ -LSU-rRNA_Dme rRNA rRNA 3078755 -FW3_DM LINE Jockey 913 -DMTOM1_LTR LTR Gypsy 1012 -R1_DM LINE R1 5407 -TAHRE LINE Jockey 3914 -G4_DM LINE Jockey 3407 -BS LINE Jockey 5001 -Stalker2_I-int LTR Gypsy 12474 -Stalker3_LTR LTR Gypsy 439 -TABOR_I-int LTR Gypsy 3081 -G7_DM LINE Jockey 98 -BEL_I-int LTR Pao 21860 -Gypsy6_I-int LTR Gypsy 6746 +5S_DM RNA RNA 10392 ACCORD_I-int LTR Gypsy 2165 -DM412B_LTR LTR Gypsy 2910 -G2_DM LINE Jockey 1132 -SSU-rRNA_Hsa rRNA rRNA 172100 -TART_B1 LINE Jockey 21513 -S2_DM DNA TcMar-Tc1 733 -LOOPER1_DM DNA PiggyBac 589 -HOBO DNA hAT-hobo 4404 +ACCORD_LTR LTR Gypsy 220 +ACCORD2_I-int LTR Gypsy 2458 +ACCORD2_LTR LTR Gypsy 192 +ALA_DM Unknown Unknown 6 ARS406_DM Unknown Unknown 719 -G6_DM LINE Jockey 3473 -DOC2_DM LINE Jockey 4538 Baggins1 LINE LOA 3893 -NINJA_LTR LTR Pao 406 -TRANSIB2 DNA CMC-Transib 3076 -Gypsy5_LTR LTR Gypsy 451 -MDG3_LTR LTR Gypsy 848 -Gypsy12A_LTR LTR Gypsy 2242 -Gypsy_LTR LTR Gypsy 917 -TIRANT_LTR LTR Gypsy 1279 -I_DM LINE I 7013 -DIVER2_I-int LTR Pao 5627 -P-1_DY DNA P 2 -Invader2_I-int LTR Gypsy 5510 -DOC6_DM LINE Jockey 1240 -BURDOCK_LTR LTR Gypsy 370 -SSU-rRNA_Dme rRNA rRNA 4153 -MAX_LTR LTR Pao 753 -STALKER4_LTR LTR Gypsy 1210 -XDMR_DM Unknown Unknown 4328 BARI_DM DNA TcMar-Tc1 902 -Transib-N1_DM DNA CMC-Transib 371 -Gypsy5_I-int LTR Gypsy 2186 -XDMR Unknown Unknown 1440 -ACCORD2_LTR LTR Gypsy 192 -POGON1 DNA TcMar-Pogo 403 +BARI1 DNA TcMar-Tc1 322 +BATUMI_I-int LTR Pao 4789 +BATUMI_LTR LTR Pao 403 +BEL_I-int LTR Pao 21860 +BEL_LTR LTR Pao 858 +Bica_I-int LTR Gypsy 1390 +Bica_LTR LTR Gypsy 125 +BLASTOPIA_I-int LTR Gypsy 9540 +BLASTOPIA_LTR LTR Gypsy 478 +BLOOD_I-int LTR Gypsy 17222 +BLOOD_LTR LTR Gypsy 746 +BS LINE Jockey 5001 +BS2 LINE Jockey 4991 +BS3_DM LINE Jockey 877 BS4_DM LINE Jockey 21 -ALA_DM Unknown Unknown 6 -Gypsy1-I_DM LTR Gypsy 6297 -ACCORD_LTR LTR Gypsy 220 BURDOCK_I-int LTR Gypsy 3332 -ZAM_I-int LTR Gypsy 4426 -Invader5_I-int LTR Gypsy 335 -G3_DM LINE Jockey 556 -ROOA_I-int LTR Pao 4589 -Gypsy1-LTR_DM LTR Gypsy 795 +BURDOCK_LTR LTR Gypsy 370 +Chimpo_I-int LTR Gypsy 1060 +Chimpo_LTR LTR Gypsy 120 +Chouto_I-int LTR Gypsy 1304 +Chouto_LTR LTR Gypsy 281 +CIRCE LTR Gypsy 3323 +Copia_I-int LTR Copia 26733 +Copia_LTR LTR Copia 1129 +Copia1-I_DM LTR Copia 3518 +Copia1-LTR_DM LTR Copia 566 +Copia2_I-int LTR Copia 3455 +Copia2_LTR_DM LTR Copia 486 +DIVER_I-int LTR Pao 15627 +DIVER_LTR LTR Pao 429 +DIVER2_I-int LTR Pao 5627 +DIVER2_LTR LTR Pao 535 DM1731_I-int LTR Copia 4881 -ROO_I-int LTR Pao 28034 +DM1731_LTR LTR Copia 440 +DM176_I-int LTR Gypsy 2813 +DM176_LTR LTR Gypsy 872 +DM297_I-int LTR Gypsy 11530 +DM297_LTR LTR Gypsy 1478 DM412 LTR Gypsy 23566 -PROTOP DNA P 4353 -TART-A LINE Jockey 3408 -ROO_LTR LTR Pao 1851 -DIVER_LTR LTR Pao 429 -Gypsy3_I-int LTR Gypsy 2753 -BATUMI_LTR LTR Pao 403 -IDEFIX_LTR LTR Gypsy 1844 -G5_DM LINE Jockey 2551 -HETA LINE Jockey 24397 -Gypsy11_I-int LTR Gypsy 560 -R1-2_DM LINE R1 177 -Gypsy11_LTR LTR Gypsy 149 -HELENA_RT LINE Jockey 627 -FTZ_DM Unknown Unknown 0 -MICROPIA_I-int LTR Gypsy 10355 -Invader4_I-int LTR Gypsy 1219 -PLACW_DM DNA P 127 -BLOOD_LTR LTR Gypsy 746 -R2_DM LINE R2 8407 -Copia1-I_DM LTR Copia 3518 -Gypsy4_I-int LTR Gypsy 10056 -Chouto_LTR LTR Gypsy 281 -BATUMI_I-int LTR Pao 4789 -DNAREP1_DM RC Helitron 63954 +DM412B_LTR LTR Gypsy 2910 +DMCR1A LINE CR1 17957 +DMLTR5 LTR Gypsy 160 +DMRP1 Unknown Unknown 227 +DMRPR Unknown Unknown 187 +DMRT1A LINE R1 3540 DMRT1B LINE R1 7119 DMRT1C LINE R1 2087 -TLD2 LTR Gypsy 17 -DMRT1A LINE R1 3540 -DM1731_LTR LTR Copia 440 -LSU-rRNA_Cel rRNA rRNA 326925 -Copia_LTR LTR Copia 1129 +DMTOM1_LTR LTR Gypsy 1012 +DNAREP1_DM RC Helitron 63954 +DOC LINE Jockey 16414 +DOC2_DM LINE Jockey 4538 +DOC3_DM LINE Jockey 10659 +DOC4_DM LINE Jockey 830 +DOC5_DM LINE Jockey 2183 +DOC6_DM LINE Jockey 1240 +FB4_DM DNA TcMar-Tc1 6939 +FROGGER_I-int LTR Copia 1361 +FROGGER_LTR LTR Copia 54 +FTZ_DM Unknown Unknown 0 +FUSHI_DM Unknown Unknown 0 +FW2_DM LINE Jockey 13847 +FW3_DM LINE Jockey 913 +G_DM LINE Jockey 8035 +G2_DM LINE Jockey 1132 +G3_DM LINE Jockey 556 +G4_DM LINE Jockey 3407 +G5_DM LINE Jockey 2551 +G5A_DM LINE Jockey 1595 +G6_DM LINE Jockey 3473 +G7_DM LINE Jockey 98 +GTWIN_I-int LTR Gypsy 5054 +GTWIN_LTR LTR Gypsy 467 +Gypsy_I-int LTR Gypsy 5634 +Gypsy_LTR LTR Gypsy 917 +Gypsy1-I_DM LTR Gypsy 6297 +Gypsy1-LTR_DM LTR Gypsy 795 +Gypsy10_I-int LTR Gypsy 1930 +Gypsy10_LTR LTR Gypsy 368 +Gypsy11_I-int LTR Gypsy 560 +Gypsy11_LTR LTR Gypsy 149 +Gypsy12_I-int LTR Gypsy 9627 +Gypsy12_LTR LTR Gypsy 5934 +Gypsy12A_LTR LTR Gypsy 2242 +Gypsy2_I-int LTR Gypsy 3453 +Gypsy2_LTR LTR Gypsy 485 +Gypsy2-I_DM LTR Gypsy 3896 +Gypsy2-LTR_DM LTR Gypsy 690 +Gypsy3_I-int LTR Gypsy 2753 +Gypsy3_LTR LTR Gypsy 447 +Gypsy4_I-int LTR Gypsy 10056 +Gypsy4_LTR LTR Gypsy 194 +Gypsy5_I-int LTR Gypsy 2186 +Gypsy5_LTR LTR Gypsy 451 +Gypsy6_I-int LTR Gypsy 6746 Gypsy6_LTR LTR Gypsy 484 -Gypsy12_I-int LTR Gypsy 9627 -BLASTOPIA_LTR LTR Gypsy 478 -Bica_LTR LTR Gypsy 125 +Gypsy6A_LTR LTR Gypsy 573 +Gypsy7_I-int LTR Gypsy 1009 +Gypsy7_LTR LTR Gypsy 87 +Gypsy8_I-int LTR Gypsy 4083 Gypsy8_LTR LTR Gypsy 1241 -NINJA_I-int LTR Pao 4503 -PROTOP_B DNA P 8285 -PROTOP_A DNA P 3384 +Gypsy9_I-int LTR Gypsy 474 +Gypsy9_LTR LTR Gypsy 42 +HELENA_RT LINE Jockey 627 +Helitron1_DM RC Helitron 6 +HETA LINE Jockey 24397 +HMSBEAGLE_I-int LTR Gypsy 5908 +HOBO DNA hAT-hobo 4404 +I_DM LINE I 7013 +IDEFIX_I-int LTR Gypsy 5547 +IDEFIX_LTR LTR Gypsy 1844 +Invader1_I-int LTR Gypsy 1672 +Invader1_LTR LTR Gypsy 1931 +Invader2_I-int LTR Gypsy 5510 +Invader2_LTR LTR Gypsy 472 +Invader3_I-int LTR Gypsy 3722 Invader3_LTR LTR Gypsy 608 -Chimpo_LTR LTR Gypsy 120 -Invader2_LTR LTR Gypsy 472 -BLASTOPIA_I-int LTR Gypsy 9540 -FROGGER_LTR LTR Copia 54 +Invader4_I-int LTR Gypsy 1219 +Invader4_LTR LTR Gypsy 1228 +Invader5_I-int LTR Gypsy 335 +Invader5_LTR LTR Gypsy 64 +Invader6_I-int LTR Gypsy 6701 +Invader6_LTR LTR Gypsy 588 +IVK_DM LINE I 2921 +Jockey2 LINE Jockey 1588 +LINEJ1_DM LINE Jockey 6329 +LmeSINE1c SINE tRNA-Deu-L2 1414 +LOOPER1_DM DNA PiggyBac 589 +LSU-rRNA_Cel rRNA rRNA 326925 +LSU-rRNA_Dme rRNA rRNA 3078755 +LSU-rRNA_Hsa rRNA rRNA 0 +M4DM DNA CMC-Transib 1650 +Mariner2_DM DNA TcMar-Tc1 1591 +MAX_I-int LTR Pao 9201 +MAX_LTR LTR Pao 753 +MDG1_I-int LTR Gypsy 13740 +MDG1_LTR LTR Gypsy 582 +MDG3_I-int LTR Gypsy 4971 +MDG3_LTR LTR Gypsy 848 +MICROPIA_I-int LTR Gypsy 10355 +MICROPIA_LTR LTR Gypsy 863 +MINOS DNA TcMar-Tc1 226 +MuDR-1_DEl DNA MULE-NOF 9 +NINJA_I-int LTR Pao 4503 +NINJA_LTR LTR Pao 406 +NOF_FB DNA MULE-NOF 960 NOMAD_I-int LTR Gypsy 11594 +NOMAD_LTR LTR Gypsy 822 +NTS_DM Other Other 36205 +P-1_DY DNA P 2 +PLACW_DM DNA P 127 +POGO DNA TcMar-Pogo 2492 +POGON1 DNA TcMar-Pogo 403 +PROTOP DNA P 4353 +PROTOP_A DNA P 3384 +PROTOP_B DNA P 8285 +QUASIMODO_I-int LTR Gypsy 13018 QUASIMODO_LTR LTR Gypsy 1174 -TABOR_LTR LTR Gypsy 273 -Stalker2_LTR LTR Gypsy 672 -MICROPIA_LTR LTR Gypsy 863 -Gypsy9_I-int LTR Gypsy 474 -STALKER4_I-int LTR Gypsy 5741 -TRANSIB1 DNA CMC-Transib 2116 -DOC LINE Jockey 16414 -TRANSIB3 DNA CMC-Transib 1132 -Copia_I-int LTR Copia 26733 -TRANSIB4 DNA CMC-Transib 571 -Gypsy10_LTR LTR Gypsy 368 -Invader3_I-int LTR Gypsy 3722 -Invader1_I-int LTR Gypsy 1672 -BS3_DM LINE Jockey 877 -Gypsy2-LTR_DM LTR Gypsy 690 -LSU-rRNA_Hsa rRNA rRNA 0 -NOMAD_LTR LTR Gypsy 822 -Helitron1_DM RC Helitron 6 -LINEJ1_DM LINE Jockey 6329 -Invader4_LTR LTR Gypsy 1228 -MDG3_I-int LTR Gypsy 4971 -LmeSINE1c SINE tRNA-Deu-L2 1414 +QUASIMODO2-I_DM LTR Gypsy 2225 +QUASIMODO2-LTR_DM LTR Gypsy 200 +R1_DM LINE R1 5407 +R1-2_DM LINE R1 177 +R2_DM LINE R2 8407 +ROO_I-int LTR Pao 28034 +ROO_LTR LTR Pao 1851 +ROOA_I-int LTR Pao 4589 +ROOA_LTR LTR Pao 483 +ROVER-I_DM LTR Gypsy 5589 ROVER-LTR_DM LTR Gypsy 415 S_DM DNA TcMar-Tc1 3476 -Invader6_I-int LTR Gypsy 6701 -ROVER-I_DM LTR Gypsy 5589 -QUASIMODO_I-int LTR Gypsy 13018 -Chouto_I-int LTR Gypsy 1304 -NTS_DM Other Other 36205 -Gypsy3_LTR LTR Gypsy 447 +S2_DM DNA TcMar-Tc1 733 SSU-rRNA_Cel rRNA rRNA 2183 -MINOS DNA TcMar-Tc1 226 -DOC4_DM LINE Jockey 830 -ZAM_LTR LTR Gypsy 225 -QUASIMODO2-LTR_DM LTR Gypsy 200 -Gypsy2-I_DM LTR Gypsy 3896 -TRANSPAC_I-int LTR Gypsy 14982 -Bica_I-int LTR Gypsy 1390 -BS2 LINE Jockey 4991 -BLOOD_I-int LTR Gypsy 17222 -DMCR1A LINE CR1 17957 -QUASIMODO2-I_DM LTR Gypsy 2225 -HMSBEAGLE_I-int LTR Gypsy 5908 -DMLTR5 LTR Gypsy 160 -Gypsy7_LTR LTR Gypsy 87 -G5A_DM LINE Jockey 1595 -MDG1_I-int LTR Gypsy 13740 -Gypsy2_I-int LTR Gypsy 3453 -BARI1 DNA TcMar-Tc1 322 -Invader5_LTR LTR Gypsy 64 -DM176_LTR LTR Gypsy 872 -DOC3_DM LINE Jockey 10659 -Copia1-LTR_DM LTR Copia 566 -TOM_I-int LTR Gypsy 2311 -NOF_FB DNA MULE-NOF 960 -Chimpo_I-int LTR Gypsy 1060 -DIVER_I-int LTR Pao 15627 +SSU-rRNA_Dme rRNA rRNA 4153 +SSU-rRNA_Hsa rRNA rRNA 172100 +Stalker2_I-int LTR Gypsy 12474 +Stalker2_LTR LTR Gypsy 672 +Stalker3_LTR LTR Gypsy 439 +STALKER4_I-int LTR Gypsy 5741 +STALKER4_LTR LTR Gypsy 1210 +TABOR_I-int LTR Gypsy 3081 +TABOR_LTR LTR Gypsy 273 +TAHRE LINE Jockey 3914 +TART_B1 LINE Jockey 21513 +TART-A LINE Jockey 3408 +TC1_DM DNA TcMar-Tc1 1960 +TC1-2_DM DNA TcMar-Tc1 3948 TIRANT_I-int LTR Gypsy 8559 -Gypsy2_LTR LTR Gypsy 485 -FB4_DM DNA TcMar-Tc1 6939 -GTWIN_LTR LTR Gypsy 467 -Invader6_LTR LTR Gypsy 588 -Gypsy8_I-int LTR Gypsy 4083 -G_DM LINE Jockey 8035 -TRANSPAC_LTR LTR Gypsy 555 -FUSHI_DM Unknown Unknown 0 +TIRANT_LTR LTR Gypsy 1279 +TLD2 LTR Gypsy 17 +TOM_I-int LTR Gypsy 2311 +Transib-N1_DM DNA CMC-Transib 371 +TRANSIB1 DNA CMC-Transib 2116 +TRANSIB2 DNA CMC-Transib 3076 +TRANSIB3 DNA CMC-Transib 1132 +TRANSIB4 DNA CMC-Transib 571 Transib5 DNA CMC-Transib 965 -MuDR-1_DEl DNA MULE-NOF 9 -Mariner2_DM DNA TcMar-Tc1 1591 -DOC5_DM LINE Jockey 2183 -TC1_DM DNA TcMar-Tc1 1960 -Gypsy9_LTR LTR Gypsy 42 -DMRP1 Unknown Unknown 227 -Gypsy10_I-int LTR Gypsy 1930 -Gypsy4_LTR LTR Gypsy 194 -DM297_LTR LTR Gypsy 1478 -ACCORD2_I-int LTR Gypsy 2458 -Invader1_LTR LTR Gypsy 1931 -BEL_LTR LTR Pao 858 -IVK_DM LINE I 2921 -M4DM DNA CMC-Transib 1650 -FW2_DM LINE Jockey 13847 -Copia2_I-int LTR Copia 3455 -MDG1_LTR LTR Gypsy 582 -Gypsy12_LTR LTR Gypsy 5934 -Gypsy7_I-int LTR Gypsy 1009 -FROGGER_I-int LTR Copia 1361 -Gypsy_I-int LTR Gypsy 5634 -5S_DM RNA RNA 10392 -GTWIN_I-int LTR Gypsy 5054 -CIRCE LTR Gypsy 3323 -DIVER2_LTR LTR Pao 535 -POGO DNA TcMar-Pogo 2492 -Gypsy6A_LTR LTR Gypsy 573 -MAX_I-int LTR Pao 9201 -ROOA_LTR LTR Pao 483 -DM176_I-int LTR Gypsy 2813 -Copia2_LTR_DM LTR Copia 486 -DM297_I-int LTR Gypsy 11530 -IDEFIX_I-int LTR Gypsy 5547 -Jockey2 LINE Jockey 1588 -TC1-2_DM DNA TcMar-Tc1 3948 -DMRPR Unknown Unknown 187 +TRANSPAC_I-int LTR Gypsy 14982 +TRANSPAC_LTR LTR Gypsy 555 +XDMR Unknown Unknown 1440 +XDMR_DM Unknown Unknown 4328 +ZAM_I-int LTR Gypsy 4426 +ZAM_LTR LTR Gypsy 225
--- 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 @@ -1,210 +1,210 @@ -LSU-rRNA_Dme rRNA rRNA 3659329 -FW3_DM LINE Jockey 831 -DMTOM1_LTR LTR Gypsy 1004 -R1_DM LINE R1 7343 -TAHRE LINE Jockey 4560 -G4_DM LINE Jockey 3668 -BS LINE Jockey 7296 -Stalker2_I-int LTR Gypsy 12252 -Stalker3_LTR LTR Gypsy 593 -TABOR_I-int LTR Gypsy 3947 -G7_DM LINE Jockey 162 -BEL_I-int LTR Pao 23757 -Gypsy6_I-int LTR Gypsy 7489 +5S_DM RNA RNA 6317 ACCORD_I-int LTR Gypsy 2723 -DM412B_LTR LTR Gypsy 3078 -G2_DM LINE Jockey 1328 -SSU-rRNA_Hsa rRNA rRNA 318045 -TART_B1 LINE Jockey 25248 -S2_DM DNA TcMar-Tc1 765 -LOOPER1_DM DNA PiggyBac 821 -HOBO DNA hAT-hobo 5031 +ACCORD_LTR LTR Gypsy 295 +ACCORD2_I-int LTR Gypsy 2934 +ACCORD2_LTR LTR Gypsy 235 +ALA_DM Unknown Unknown 5 ARS406_DM Unknown Unknown 563 -G6_DM LINE Jockey 4827 -DOC2_DM LINE Jockey 4438 Baggins1 LINE LOA 5136 -NINJA_LTR LTR Pao 491 -TRANSIB2 DNA CMC-Transib 3197 -Gypsy5_LTR LTR Gypsy 651 -MDG3_LTR LTR Gypsy 1037 -Gypsy12A_LTR LTR Gypsy 3059 -Gypsy_LTR LTR Gypsy 1306 -TIRANT_LTR LTR Gypsy 1371 -I_DM LINE I 7987 -DIVER2_I-int LTR Pao 6679 -P-1_DY DNA P 8 -Invader2_I-int LTR Gypsy 6823 -DOC6_DM LINE Jockey 1259 -BURDOCK_LTR LTR Gypsy 287 -SSU-rRNA_Dme rRNA rRNA 7113 -MAX_LTR LTR Pao 1017 -STALKER4_LTR LTR Gypsy 1292 -XDMR_DM Unknown Unknown 3317 BARI_DM DNA TcMar-Tc1 990 -Transib-N1_DM DNA CMC-Transib 308 -Gypsy5_I-int LTR Gypsy 2448 -XDMR Unknown Unknown 1249 -ACCORD2_LTR LTR Gypsy 235 -POGON1 DNA TcMar-Pogo 331 +BARI1 DNA TcMar-Tc1 395 +BATUMI_I-int LTR Pao 6395 +BATUMI_LTR LTR Pao 554 +BEL_I-int LTR Pao 23757 +BEL_LTR LTR Pao 875 +Bica_I-int LTR Gypsy 1852 +Bica_LTR LTR Gypsy 140 +BLASTOPIA_I-int LTR Gypsy 10309 +BLASTOPIA_LTR LTR Gypsy 550 +BLOOD_I-int LTR Gypsy 22330 +BLOOD_LTR LTR Gypsy 748 +BS LINE Jockey 7296 +BS2 LINE Jockey 5595 +BS3_DM LINE Jockey 1252 BS4_DM LINE Jockey 34 -ALA_DM Unknown Unknown 5 -Gypsy1-I_DM LTR Gypsy 8160 -ACCORD_LTR LTR Gypsy 295 BURDOCK_I-int LTR Gypsy 3119 -ZAM_I-int LTR Gypsy 5129 -Invader5_I-int LTR Gypsy 416 -G3_DM LINE Jockey 797 -ROOA_I-int LTR Pao 4985 -Gypsy1-LTR_DM LTR Gypsy 1042 +BURDOCK_LTR LTR Gypsy 287 +Chimpo_I-int LTR Gypsy 1288 +Chimpo_LTR LTR Gypsy 94 +Chouto_I-int LTR Gypsy 1690 +Chouto_LTR LTR Gypsy 299 +CIRCE LTR Gypsy 3767 +Copia_I-int LTR Copia 27612 +Copia_LTR LTR Copia 1408 +Copia1-I_DM LTR Copia 3588 +Copia1-LTR_DM LTR Copia 771 +Copia2_I-int LTR Copia 4218 +Copia2_LTR_DM LTR Copia 891 +DIVER_I-int LTR Pao 13178 +DIVER_LTR LTR Pao 469 +DIVER2_I-int LTR Pao 6679 +DIVER2_LTR LTR Pao 793 DM1731_I-int LTR Copia 5180 -ROO_I-int LTR Pao 31793 +DM1731_LTR LTR Copia 577 +DM176_I-int LTR Gypsy 3627 +DM176_LTR LTR Gypsy 899 +DM297_I-int LTR Gypsy 11837 +DM297_LTR LTR Gypsy 1489 DM412 LTR Gypsy 24086 -PROTOP DNA P 4942 -TART-A LINE Jockey 3697 -ROO_LTR LTR Pao 1639 -DIVER_LTR LTR Pao 469 -Gypsy3_I-int LTR Gypsy 3399 -BATUMI_LTR LTR Pao 554 -IDEFIX_LTR LTR Gypsy 2191 -G5_DM LINE Jockey 2601 -HETA LINE Jockey 23025 -Gypsy11_I-int LTR Gypsy 671 -R1-2_DM LINE R1 267 -Gypsy11_LTR LTR Gypsy 134 -HELENA_RT LINE Jockey 653 -FTZ_DM Unknown Unknown 0 -MICROPIA_I-int LTR Gypsy 10149 -Invader4_I-int LTR Gypsy 1439 -PLACW_DM DNA P 149 -BLOOD_LTR LTR Gypsy 748 -R2_DM LINE R2 15327 -Copia1-I_DM LTR Copia 3588 -Gypsy4_I-int LTR Gypsy 12113 -Chouto_LTR LTR Gypsy 299 -BATUMI_I-int LTR Pao 6395 -DNAREP1_DM RC Helitron 67821 +DM412B_LTR LTR Gypsy 3078 +DMCR1A LINE CR1 20380 +DMLTR5 LTR Gypsy 161 +DMRP1 Unknown Unknown 262 +DMRPR Unknown Unknown 128 +DMRT1A LINE R1 4456 DMRT1B LINE R1 9706 DMRT1C LINE R1 2530 -TLD2 LTR Gypsy 65 -DMRT1A LINE R1 4456 -DM1731_LTR LTR Copia 577 -LSU-rRNA_Cel rRNA rRNA 520168 -Copia_LTR LTR Copia 1408 +DMTOM1_LTR LTR Gypsy 1004 +DNAREP1_DM RC Helitron 67821 +DOC LINE Jockey 17883 +DOC2_DM LINE Jockey 4438 +DOC3_DM LINE Jockey 11941 +DOC4_DM LINE Jockey 813 +DOC5_DM LINE Jockey 3037 +DOC6_DM LINE Jockey 1259 +FB4_DM DNA TcMar-Tc1 7149 +FROGGER_I-int LTR Copia 1611 +FROGGER_LTR LTR Copia 41 +FTZ_DM Unknown Unknown 0 +FUSHI_DM Unknown Unknown 0 +FW2_DM LINE Jockey 14234 +FW3_DM LINE Jockey 831 +G_DM LINE Jockey 8905 +G2_DM LINE Jockey 1328 +G3_DM LINE Jockey 797 +G4_DM LINE Jockey 3668 +G5_DM LINE Jockey 2601 +G5A_DM LINE Jockey 1804 +G6_DM LINE Jockey 4827 +G7_DM LINE Jockey 162 +GTWIN_I-int LTR Gypsy 5448 +GTWIN_LTR LTR Gypsy 598 +Gypsy_I-int LTR Gypsy 6822 +Gypsy_LTR LTR Gypsy 1306 +Gypsy1-I_DM LTR Gypsy 8160 +Gypsy1-LTR_DM LTR Gypsy 1042 +Gypsy10_I-int LTR Gypsy 2258 +Gypsy10_LTR LTR Gypsy 314 +Gypsy11_I-int LTR Gypsy 671 +Gypsy11_LTR LTR Gypsy 134 +Gypsy12_I-int LTR Gypsy 9778 +Gypsy12_LTR LTR Gypsy 6292 +Gypsy12A_LTR LTR Gypsy 3059 +Gypsy2_I-int LTR Gypsy 3190 +Gypsy2_LTR LTR Gypsy 479 +Gypsy2-I_DM LTR Gypsy 4606 +Gypsy2-LTR_DM LTR Gypsy 966 +Gypsy3_I-int LTR Gypsy 3399 +Gypsy3_LTR LTR Gypsy 566 +Gypsy4_I-int LTR Gypsy 12113 +Gypsy4_LTR LTR Gypsy 274 +Gypsy5_I-int LTR Gypsy 2448 +Gypsy5_LTR LTR Gypsy 651 +Gypsy6_I-int LTR Gypsy 7489 Gypsy6_LTR LTR Gypsy 428 -Gypsy12_I-int LTR Gypsy 9778 -BLASTOPIA_LTR LTR Gypsy 550 -Bica_LTR LTR Gypsy 140 +Gypsy6A_LTR LTR Gypsy 617 +Gypsy7_I-int LTR Gypsy 1256 +Gypsy7_LTR LTR Gypsy 112 +Gypsy8_I-int LTR Gypsy 4809 Gypsy8_LTR LTR Gypsy 1311 -NINJA_I-int LTR Pao 5274 -PROTOP_B DNA P 8690 -PROTOP_A DNA P 3533 +Gypsy9_I-int LTR Gypsy 504 +Gypsy9_LTR LTR Gypsy 51 +HELENA_RT LINE Jockey 653 +Helitron1_DM RC Helitron 3 +HETA LINE Jockey 23025 +HMSBEAGLE_I-int LTR Gypsy 7239 +HOBO DNA hAT-hobo 5031 +I_DM LINE I 7987 +IDEFIX_I-int LTR Gypsy 6193 +IDEFIX_LTR LTR Gypsy 2191 +Invader1_I-int LTR Gypsy 1832 +Invader1_LTR LTR Gypsy 3346 +Invader2_I-int LTR Gypsy 6823 +Invader2_LTR LTR Gypsy 492 +Invader3_I-int LTR Gypsy 4667 Invader3_LTR LTR Gypsy 657 -Chimpo_LTR LTR Gypsy 94 -Invader2_LTR LTR Gypsy 492 -BLASTOPIA_I-int LTR Gypsy 10309 -FROGGER_LTR LTR Copia 41 +Invader4_I-int LTR Gypsy 1439 +Invader4_LTR LTR Gypsy 1420 +Invader5_I-int LTR Gypsy 416 +Invader5_LTR LTR Gypsy 69 +Invader6_I-int LTR Gypsy 6931 +Invader6_LTR LTR Gypsy 649 +IVK_DM LINE I 3349 +Jockey2 LINE Jockey 1770 +LINEJ1_DM LINE Jockey 7025 +LmeSINE1c SINE tRNA-Deu-L2 599 +LOOPER1_DM DNA PiggyBac 821 +LSU-rRNA_Cel rRNA rRNA 520168 +LSU-rRNA_Dme rRNA rRNA 3659329 +LSU-rRNA_Hsa rRNA rRNA 5 +M4DM DNA CMC-Transib 1727 +Mariner2_DM DNA TcMar-Tc1 2011 +MAX_I-int LTR Pao 12395 +MAX_LTR LTR Pao 1017 +MDG1_I-int LTR Gypsy 16315 +MDG1_LTR LTR Gypsy 690 +MDG3_I-int LTR Gypsy 5392 +MDG3_LTR LTR Gypsy 1037 +MICROPIA_I-int LTR Gypsy 10149 +MICROPIA_LTR LTR Gypsy 797 +MINOS DNA TcMar-Tc1 173 +MuDR-1_DEl DNA MULE-NOF 6 +NINJA_I-int LTR Pao 5274 +NINJA_LTR LTR Pao 491 +NOF_FB DNA MULE-NOF 1272 NOMAD_I-int LTR Gypsy 16469 +NOMAD_LTR LTR Gypsy 619 +NTS_DM Other Other 65954 +P-1_DY DNA P 8 +PLACW_DM DNA P 149 +POGO DNA TcMar-Pogo 2427 +POGON1 DNA TcMar-Pogo 331 +PROTOP DNA P 4942 +PROTOP_A DNA P 3533 +PROTOP_B DNA P 8690 +QUASIMODO_I-int LTR Gypsy 14906 QUASIMODO_LTR LTR Gypsy 1332 -TABOR_LTR LTR Gypsy 384 -Stalker2_LTR LTR Gypsy 726 -MICROPIA_LTR LTR Gypsy 797 -Gypsy9_I-int LTR Gypsy 504 -STALKER4_I-int LTR Gypsy 6207 -TRANSIB1 DNA CMC-Transib 2082 -DOC LINE Jockey 17883 -TRANSIB3 DNA CMC-Transib 1184 -Copia_I-int LTR Copia 27612 -TRANSIB4 DNA CMC-Transib 635 -Gypsy10_LTR LTR Gypsy 314 -Invader3_I-int LTR Gypsy 4667 -Invader1_I-int LTR Gypsy 1832 -BS3_DM LINE Jockey 1252 -Gypsy2-LTR_DM LTR Gypsy 966 -LSU-rRNA_Hsa rRNA rRNA 5 -NOMAD_LTR LTR Gypsy 619 -Helitron1_DM RC Helitron 3 -LINEJ1_DM LINE Jockey 7025 -Invader4_LTR LTR Gypsy 1420 -MDG3_I-int LTR Gypsy 5392 -LmeSINE1c SINE tRNA-Deu-L2 599 +QUASIMODO2-I_DM LTR Gypsy 2717 +QUASIMODO2-LTR_DM LTR Gypsy 313 +R1_DM LINE R1 7343 +R1-2_DM LINE R1 267 +R2_DM LINE R2 15327 +ROO_I-int LTR Pao 31793 +ROO_LTR LTR Pao 1639 +ROOA_I-int LTR Pao 4985 +ROOA_LTR LTR Pao 400 +ROVER-I_DM LTR Gypsy 6513 ROVER-LTR_DM LTR Gypsy 564 S_DM DNA TcMar-Tc1 3612 -Invader6_I-int LTR Gypsy 6931 -ROVER-I_DM LTR Gypsy 6513 -QUASIMODO_I-int LTR Gypsy 14906 -Chouto_I-int LTR Gypsy 1690 -NTS_DM Other Other 65954 -Gypsy3_LTR LTR Gypsy 566 +S2_DM DNA TcMar-Tc1 765 SSU-rRNA_Cel rRNA rRNA 3463 -MINOS DNA TcMar-Tc1 173 -DOC4_DM LINE Jockey 813 -ZAM_LTR LTR Gypsy 259 -QUASIMODO2-LTR_DM LTR Gypsy 313 -Gypsy2-I_DM LTR Gypsy 4606 -TRANSPAC_I-int LTR Gypsy 9674 -Bica_I-int LTR Gypsy 1852 -BS2 LINE Jockey 5595 -BLOOD_I-int LTR Gypsy 22330 -DMCR1A LINE CR1 20380 -QUASIMODO2-I_DM LTR Gypsy 2717 -HMSBEAGLE_I-int LTR Gypsy 7239 -DMLTR5 LTR Gypsy 161 -Gypsy7_LTR LTR Gypsy 112 -G5A_DM LINE Jockey 1804 -MDG1_I-int LTR Gypsy 16315 -Gypsy2_I-int LTR Gypsy 3190 -BARI1 DNA TcMar-Tc1 395 -Invader5_LTR LTR Gypsy 69 -DM176_LTR LTR Gypsy 899 -DOC3_DM LINE Jockey 11941 -Copia1-LTR_DM LTR Copia 771 -TOM_I-int LTR Gypsy 2563 -NOF_FB DNA MULE-NOF 1272 -Chimpo_I-int LTR Gypsy 1288 -DIVER_I-int LTR Pao 13178 +SSU-rRNA_Dme rRNA rRNA 7113 +SSU-rRNA_Hsa rRNA rRNA 318045 +Stalker2_I-int LTR Gypsy 12252 +Stalker2_LTR LTR Gypsy 726 +Stalker3_LTR LTR Gypsy 593 +STALKER4_I-int LTR Gypsy 6207 +STALKER4_LTR LTR Gypsy 1292 +TABOR_I-int LTR Gypsy 3947 +TABOR_LTR LTR Gypsy 384 +TAHRE LINE Jockey 4560 +TART_B1 LINE Jockey 25248 +TART-A LINE Jockey 3697 +TC1_DM DNA TcMar-Tc1 1840 +TC1-2_DM DNA TcMar-Tc1 3807 TIRANT_I-int LTR Gypsy 10917 -Gypsy2_LTR LTR Gypsy 479 -FB4_DM DNA TcMar-Tc1 7149 -GTWIN_LTR LTR Gypsy 598 -Invader6_LTR LTR Gypsy 649 -Gypsy8_I-int LTR Gypsy 4809 -G_DM LINE Jockey 8905 -TRANSPAC_LTR LTR Gypsy 538 -FUSHI_DM Unknown Unknown 0 +TIRANT_LTR LTR Gypsy 1371 +TLD2 LTR Gypsy 65 +TOM_I-int LTR Gypsy 2563 +Transib-N1_DM DNA CMC-Transib 308 +TRANSIB1 DNA CMC-Transib 2082 +TRANSIB2 DNA CMC-Transib 3197 +TRANSIB3 DNA CMC-Transib 1184 +TRANSIB4 DNA CMC-Transib 635 Transib5 DNA CMC-Transib 1123 -MuDR-1_DEl DNA MULE-NOF 6 -Mariner2_DM DNA TcMar-Tc1 2011 -DOC5_DM LINE Jockey 3037 -TC1_DM DNA TcMar-Tc1 1840 -Gypsy9_LTR LTR Gypsy 51 -DMRP1 Unknown Unknown 262 -Gypsy10_I-int LTR Gypsy 2258 -Gypsy4_LTR LTR Gypsy 274 -DM297_LTR LTR Gypsy 1489 -ACCORD2_I-int LTR Gypsy 2934 -Invader1_LTR LTR Gypsy 3346 -BEL_LTR LTR Pao 875 -IVK_DM LINE I 3349 -M4DM DNA CMC-Transib 1727 -FW2_DM LINE Jockey 14234 -Copia2_I-int LTR Copia 4218 -MDG1_LTR LTR Gypsy 690 -Gypsy12_LTR LTR Gypsy 6292 -Gypsy7_I-int LTR Gypsy 1256 -FROGGER_I-int LTR Copia 1611 -Gypsy_I-int LTR Gypsy 6822 -5S_DM RNA RNA 6317 -GTWIN_I-int LTR Gypsy 5448 -CIRCE LTR Gypsy 3767 -DIVER2_LTR LTR Pao 793 -POGO DNA TcMar-Pogo 2427 -Gypsy6A_LTR LTR Gypsy 617 -MAX_I-int LTR Pao 12395 -ROOA_LTR LTR Pao 400 -DM176_I-int LTR Gypsy 3627 -Copia2_LTR_DM LTR Copia 891 -DM297_I-int LTR Gypsy 11837 -IDEFIX_I-int LTR Gypsy 6193 -Jockey2 LINE Jockey 1770 -TC1-2_DM DNA TcMar-Tc1 3807 -DMRPR Unknown Unknown 128 +TRANSPAC_I-int LTR Gypsy 9674 +TRANSPAC_LTR LTR Gypsy 538 +XDMR Unknown Unknown 1249 +XDMR_DM Unknown Unknown 3317 +ZAM_I-int LTR Gypsy 5129 +ZAM_LTR LTR Gypsy 259
--- 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 @@ -1,210 +1,210 @@ -LSU-rRNA_Dme rRNA rRNA 4126525 -FW3_DM LINE Jockey 376 -DMTOM1_LTR LTR Gypsy 458 -R1_DM LINE R1 6019 -TAHRE LINE Jockey 1417 -G4_DM LINE Jockey 1225 -BS LINE Jockey 4135 -Stalker2_I-int LTR Gypsy 4814 -Stalker3_LTR LTR Gypsy 235 -TABOR_I-int LTR Gypsy 3691 -G7_DM LINE Jockey 418 -BEL_I-int LTR Pao 15192 -Gypsy6_I-int LTR Gypsy 3763 +5S_DM RNA RNA 4146 ACCORD_I-int LTR Gypsy 2031 -DM412B_LTR LTR Gypsy 3001 -G2_DM LINE Jockey 764 -SSU-rRNA_Hsa rRNA rRNA 301813 -TART_B1 LINE Jockey 5089 -S2_DM DNA TcMar-Tc1 205 -LOOPER1_DM DNA PiggyBac 31 -HOBO DNA hAT-hobo 2119 +ACCORD_LTR LTR Gypsy 344 +ACCORD2_I-int LTR Gypsy 1200 +ACCORD2_LTR LTR Gypsy 76 +ALA_DM Unknown Unknown 0 ARS406_DM Unknown Unknown 230 -G6_DM LINE Jockey 786 -DOC2_DM LINE Jockey 2052 Baggins1 LINE LOA 1832 -NINJA_LTR LTR Pao 114 -TRANSIB2 DNA CMC-Transib 1484 -Gypsy5_LTR LTR Gypsy 326 -MDG3_LTR LTR Gypsy 454 -Gypsy12A_LTR LTR Gypsy 1077 -Gypsy_LTR LTR Gypsy 1737 -TIRANT_LTR LTR Gypsy 1596 -I_DM LINE I 11149 -DIVER2_I-int LTR Pao 2668 -P-1_DY DNA P 4 -Invader2_I-int LTR Gypsy 3157 -DOC6_DM LINE Jockey 768 -BURDOCK_LTR LTR Gypsy 193 -SSU-rRNA_Dme rRNA rRNA 3822 -MAX_LTR LTR Pao 343 -STALKER4_LTR LTR Gypsy 803 -XDMR_DM Unknown Unknown 1587 BARI_DM DNA TcMar-Tc1 522 -Transib-N1_DM DNA CMC-Transib 130 -Gypsy5_I-int LTR Gypsy 1036 -XDMR Unknown Unknown 903 -ACCORD2_LTR LTR Gypsy 76 -POGON1 DNA TcMar-Pogo 256 +BARI1 DNA TcMar-Tc1 125 +BATUMI_I-int LTR Pao 1842 +BATUMI_LTR LTR Pao 169 +BEL_I-int LTR Pao 15192 +BEL_LTR LTR Pao 605 +Bica_I-int LTR Gypsy 618 +Bica_LTR LTR Gypsy 67 +BLASTOPIA_I-int LTR Gypsy 12045 +BLASTOPIA_LTR LTR Gypsy 919 +BLOOD_I-int LTR Gypsy 13280 +BLOOD_LTR LTR Gypsy 542 +BS LINE Jockey 4135 +BS2 LINE Jockey 2086 +BS3_DM LINE Jockey 453 BS4_DM LINE Jockey 23 -ALA_DM Unknown Unknown 0 -Gypsy1-I_DM LTR Gypsy 22753 -ACCORD_LTR LTR Gypsy 344 BURDOCK_I-int LTR Gypsy 2232 -ZAM_I-int LTR Gypsy 2892 -Invader5_I-int LTR Gypsy 117 -G3_DM LINE Jockey 250 -ROOA_I-int LTR Pao 2579 -Gypsy1-LTR_DM LTR Gypsy 576 +BURDOCK_LTR LTR Gypsy 193 +Chimpo_I-int LTR Gypsy 370 +Chimpo_LTR LTR Gypsy 33 +Chouto_I-int LTR Gypsy 518 +Chouto_LTR LTR Gypsy 159 +CIRCE LTR Gypsy 1570 +Copia_I-int LTR Copia 87220 +Copia_LTR LTR Copia 3075 +Copia1-I_DM LTR Copia 1946 +Copia1-LTR_DM LTR Copia 389 +Copia2_I-int LTR Copia 1892 +Copia2_LTR_DM LTR Copia 460 +DIVER_I-int LTR Pao 11751 +DIVER_LTR LTR Pao 328 +DIVER2_I-int LTR Pao 2668 +DIVER2_LTR LTR Pao 240 DM1731_I-int LTR Copia 6873 -ROO_I-int LTR Pao 22941 +DM1731_LTR LTR Copia 321 +DM176_I-int LTR Gypsy 2298 +DM176_LTR LTR Gypsy 330 +DM297_I-int LTR Gypsy 42705 +DM297_LTR LTR Gypsy 2516 DM412 LTR Gypsy 23508 -PROTOP DNA P 2059 -TART-A LINE Jockey 1825 -ROO_LTR LTR Pao 1453 -DIVER_LTR LTR Pao 328 -Gypsy3_I-int LTR Gypsy 2258 -BATUMI_LTR LTR Pao 169 -IDEFIX_LTR LTR Gypsy 1012 -G5_DM LINE Jockey 1300 -HETA LINE Jockey 10327 -Gypsy11_I-int LTR Gypsy 168 -R1-2_DM LINE R1 68 -Gypsy11_LTR LTR Gypsy 48 -HELENA_RT LINE Jockey 416 -FTZ_DM Unknown Unknown 0 -MICROPIA_I-int LTR Gypsy 3327 -Invader4_I-int LTR Gypsy 1180 -PLACW_DM DNA P 204 -BLOOD_LTR LTR Gypsy 542 -R2_DM LINE R2 15128 -Copia1-I_DM LTR Copia 1946 -Gypsy4_I-int LTR Gypsy 5348 -Chouto_LTR LTR Gypsy 159 -BATUMI_I-int LTR Pao 1842 -DNAREP1_DM RC Helitron 36953 +DM412B_LTR LTR Gypsy 3001 +DMCR1A LINE CR1 8072 +DMLTR5 LTR Gypsy 94 +DMRP1 Unknown Unknown 144 +DMRPR Unknown Unknown 136 +DMRT1A LINE R1 1235 DMRT1B LINE R1 4115 DMRT1C LINE R1 670 -TLD2 LTR Gypsy 1 -DMRT1A LINE R1 1235 -DM1731_LTR LTR Copia 321 -LSU-rRNA_Cel rRNA rRNA 251671 -Copia_LTR LTR Copia 3075 +DMTOM1_LTR LTR Gypsy 458 +DNAREP1_DM RC Helitron 36953 +DOC LINE Jockey 21700 +DOC2_DM LINE Jockey 2052 +DOC3_DM LINE Jockey 5205 +DOC4_DM LINE Jockey 658 +DOC5_DM LINE Jockey 752 +DOC6_DM LINE Jockey 768 +FB4_DM DNA TcMar-Tc1 3348 +FROGGER_I-int LTR Copia 546 +FROGGER_LTR LTR Copia 57 +FTZ_DM Unknown Unknown 0 +FUSHI_DM Unknown Unknown 0 +FW2_DM LINE Jockey 8864 +FW3_DM LINE Jockey 376 +G_DM LINE Jockey 4582 +G2_DM LINE Jockey 764 +G3_DM LINE Jockey 250 +G4_DM LINE Jockey 1225 +G5_DM LINE Jockey 1300 +G5A_DM LINE Jockey 582 +G6_DM LINE Jockey 786 +G7_DM LINE Jockey 418 +GTWIN_I-int LTR Gypsy 2930 +GTWIN_LTR LTR Gypsy 938 +Gypsy_I-int LTR Gypsy 11161 +Gypsy_LTR LTR Gypsy 1737 +Gypsy1-I_DM LTR Gypsy 22753 +Gypsy1-LTR_DM LTR Gypsy 576 +Gypsy10_I-int LTR Gypsy 927 +Gypsy10_LTR LTR Gypsy 162 +Gypsy11_I-int LTR Gypsy 168 +Gypsy11_LTR LTR Gypsy 48 +Gypsy12_I-int LTR Gypsy 2466 +Gypsy12_LTR LTR Gypsy 2680 +Gypsy12A_LTR LTR Gypsy 1077 +Gypsy2_I-int LTR Gypsy 1552 +Gypsy2_LTR LTR Gypsy 250 +Gypsy2-I_DM LTR Gypsy 2658 +Gypsy2-LTR_DM LTR Gypsy 385 +Gypsy3_I-int LTR Gypsy 2258 +Gypsy3_LTR LTR Gypsy 212 +Gypsy4_I-int LTR Gypsy 5348 +Gypsy4_LTR LTR Gypsy 218 +Gypsy5_I-int LTR Gypsy 1036 +Gypsy5_LTR LTR Gypsy 326 +Gypsy6_I-int LTR Gypsy 3763 Gypsy6_LTR LTR Gypsy 760 -Gypsy12_I-int LTR Gypsy 2466 -BLASTOPIA_LTR LTR Gypsy 919 -Bica_LTR LTR Gypsy 67 +Gypsy6A_LTR LTR Gypsy 219 +Gypsy7_I-int LTR Gypsy 742 +Gypsy7_LTR LTR Gypsy 39 +Gypsy8_I-int LTR Gypsy 1247 Gypsy8_LTR LTR Gypsy 486 -NINJA_I-int LTR Pao 1146 -PROTOP_B DNA P 4300 -PROTOP_A DNA P 1988 +Gypsy9_I-int LTR Gypsy 188 +Gypsy9_LTR LTR Gypsy 8 +HELENA_RT LINE Jockey 416 +Helitron1_DM RC Helitron 0 +HETA LINE Jockey 10327 +HMSBEAGLE_I-int LTR Gypsy 4079 +HOBO DNA hAT-hobo 2119 +I_DM LINE I 11149 +IDEFIX_I-int LTR Gypsy 3286 +IDEFIX_LTR LTR Gypsy 1012 +Invader1_I-int LTR Gypsy 1768 +Invader1_LTR LTR Gypsy 1903 +Invader2_I-int LTR Gypsy 3157 +Invader2_LTR LTR Gypsy 213 +Invader3_I-int LTR Gypsy 2022 Invader3_LTR LTR Gypsy 227 -Chimpo_LTR LTR Gypsy 33 -Invader2_LTR LTR Gypsy 213 -BLASTOPIA_I-int LTR Gypsy 12045 -FROGGER_LTR LTR Copia 57 +Invader4_I-int LTR Gypsy 1180 +Invader4_LTR LTR Gypsy 679 +Invader5_I-int LTR Gypsy 117 +Invader5_LTR LTR Gypsy 23 +Invader6_I-int LTR Gypsy 3298 +Invader6_LTR LTR Gypsy 146 +IVK_DM LINE I 1769 +Jockey2 LINE Jockey 760 +LINEJ1_DM LINE Jockey 15939 +LmeSINE1c SINE tRNA-Deu-L2 653 +LOOPER1_DM DNA PiggyBac 31 +LSU-rRNA_Cel rRNA rRNA 251671 +LSU-rRNA_Dme rRNA rRNA 4126525 +LSU-rRNA_Hsa rRNA rRNA 11 +M4DM DNA CMC-Transib 918 +Mariner2_DM DNA TcMar-Tc1 926 +MAX_I-int LTR Pao 3905 +MAX_LTR LTR Pao 343 +MDG1_I-int LTR Gypsy 8043 +MDG1_LTR LTR Gypsy 281 +MDG3_I-int LTR Gypsy 3770 +MDG3_LTR LTR Gypsy 454 +MICROPIA_I-int LTR Gypsy 3327 +MICROPIA_LTR LTR Gypsy 149 +MINOS DNA TcMar-Tc1 93 +MuDR-1_DEl DNA MULE-NOF 4 +NINJA_I-int LTR Pao 1146 +NINJA_LTR LTR Pao 114 +NOF_FB DNA MULE-NOF 63 NOMAD_I-int LTR Gypsy 8154 +NOMAD_LTR LTR Gypsy 277 +NTS_DM Other Other 21753 +P-1_DY DNA P 4 +PLACW_DM DNA P 204 +POGO DNA TcMar-Pogo 1032 +POGON1 DNA TcMar-Pogo 256 +PROTOP DNA P 2059 +PROTOP_A DNA P 1988 +PROTOP_B DNA P 4300 +QUASIMODO_I-int LTR Gypsy 8000 QUASIMODO_LTR LTR Gypsy 528 -TABOR_LTR LTR Gypsy 88 -Stalker2_LTR LTR Gypsy 356 -MICROPIA_LTR LTR Gypsy 149 -Gypsy9_I-int LTR Gypsy 188 -STALKER4_I-int LTR Gypsy 3132 -TRANSIB1 DNA CMC-Transib 289 -DOC LINE Jockey 21700 -TRANSIB3 DNA CMC-Transib 741 -Copia_I-int LTR Copia 87220 -TRANSIB4 DNA CMC-Transib 153 -Gypsy10_LTR LTR Gypsy 162 -Invader3_I-int LTR Gypsy 2022 -Invader1_I-int LTR Gypsy 1768 -BS3_DM LINE Jockey 453 -Gypsy2-LTR_DM LTR Gypsy 385 -LSU-rRNA_Hsa rRNA rRNA 11 -NOMAD_LTR LTR Gypsy 277 -Helitron1_DM RC Helitron 0 -LINEJ1_DM LINE Jockey 15939 -Invader4_LTR LTR Gypsy 679 -MDG3_I-int LTR Gypsy 3770 -LmeSINE1c SINE tRNA-Deu-L2 653 +QUASIMODO2-I_DM LTR Gypsy 1811 +QUASIMODO2-LTR_DM LTR Gypsy 105 +R1_DM LINE R1 6019 +R1-2_DM LINE R1 68 +R2_DM LINE R2 15128 +ROO_I-int LTR Pao 22941 +ROO_LTR LTR Pao 1453 +ROOA_I-int LTR Pao 2579 +ROOA_LTR LTR Pao 276 +ROVER-I_DM LTR Gypsy 3069 ROVER-LTR_DM LTR Gypsy 168 S_DM DNA TcMar-Tc1 2041 -Invader6_I-int LTR Gypsy 3298 -ROVER-I_DM LTR Gypsy 3069 -QUASIMODO_I-int LTR Gypsy 8000 -Chouto_I-int LTR Gypsy 518 -NTS_DM Other Other 21753 -Gypsy3_LTR LTR Gypsy 212 +S2_DM DNA TcMar-Tc1 205 SSU-rRNA_Cel rRNA rRNA 1817 -MINOS DNA TcMar-Tc1 93 -DOC4_DM LINE Jockey 658 -ZAM_LTR LTR Gypsy 118 -QUASIMODO2-LTR_DM LTR Gypsy 105 -Gypsy2-I_DM LTR Gypsy 2658 -TRANSPAC_I-int LTR Gypsy 16760 -Bica_I-int LTR Gypsy 618 -BS2 LINE Jockey 2086 -BLOOD_I-int LTR Gypsy 13280 -DMCR1A LINE CR1 8072 -QUASIMODO2-I_DM LTR Gypsy 1811 -HMSBEAGLE_I-int LTR Gypsy 4079 -DMLTR5 LTR Gypsy 94 -Gypsy7_LTR LTR Gypsy 39 -G5A_DM LINE Jockey 582 -MDG1_I-int LTR Gypsy 8043 -Gypsy2_I-int LTR Gypsy 1552 -BARI1 DNA TcMar-Tc1 125 -Invader5_LTR LTR Gypsy 23 -DM176_LTR LTR Gypsy 330 -DOC3_DM LINE Jockey 5205 -Copia1-LTR_DM LTR Copia 389 -TOM_I-int LTR Gypsy 3390 -NOF_FB DNA MULE-NOF 63 -Chimpo_I-int LTR Gypsy 370 -DIVER_I-int LTR Pao 11751 +SSU-rRNA_Dme rRNA rRNA 3822 +SSU-rRNA_Hsa rRNA rRNA 301813 +Stalker2_I-int LTR Gypsy 4814 +Stalker2_LTR LTR Gypsy 356 +Stalker3_LTR LTR Gypsy 235 +STALKER4_I-int LTR Gypsy 3132 +STALKER4_LTR LTR Gypsy 803 +TABOR_I-int LTR Gypsy 3691 +TABOR_LTR LTR Gypsy 88 +TAHRE LINE Jockey 1417 +TART_B1 LINE Jockey 5089 +TART-A LINE Jockey 1825 +TC1_DM DNA TcMar-Tc1 1485 +TC1-2_DM DNA TcMar-Tc1 2287 TIRANT_I-int LTR Gypsy 12728 -Gypsy2_LTR LTR Gypsy 250 -FB4_DM DNA TcMar-Tc1 3348 -GTWIN_LTR LTR Gypsy 938 -Invader6_LTR LTR Gypsy 146 -Gypsy8_I-int LTR Gypsy 1247 -G_DM LINE Jockey 4582 -TRANSPAC_LTR LTR Gypsy 979 -FUSHI_DM Unknown Unknown 0 +TIRANT_LTR LTR Gypsy 1596 +TLD2 LTR Gypsy 1 +TOM_I-int LTR Gypsy 3390 +Transib-N1_DM DNA CMC-Transib 130 +TRANSIB1 DNA CMC-Transib 289 +TRANSIB2 DNA CMC-Transib 1484 +TRANSIB3 DNA CMC-Transib 741 +TRANSIB4 DNA CMC-Transib 153 Transib5 DNA CMC-Transib 328 -MuDR-1_DEl DNA MULE-NOF 4 -Mariner2_DM DNA TcMar-Tc1 926 -DOC5_DM LINE Jockey 752 -TC1_DM DNA TcMar-Tc1 1485 -Gypsy9_LTR LTR Gypsy 8 -DMRP1 Unknown Unknown 144 -Gypsy10_I-int LTR Gypsy 927 -Gypsy4_LTR LTR Gypsy 218 -DM297_LTR LTR Gypsy 2516 -ACCORD2_I-int LTR Gypsy 1200 -Invader1_LTR LTR Gypsy 1903 -BEL_LTR LTR Pao 605 -IVK_DM LINE I 1769 -M4DM DNA CMC-Transib 918 -FW2_DM LINE Jockey 8864 -Copia2_I-int LTR Copia 1892 -MDG1_LTR LTR Gypsy 281 -Gypsy12_LTR LTR Gypsy 2680 -Gypsy7_I-int LTR Gypsy 742 -FROGGER_I-int LTR Copia 546 -Gypsy_I-int LTR Gypsy 11161 -5S_DM RNA RNA 4146 -GTWIN_I-int LTR Gypsy 2930 -CIRCE LTR Gypsy 1570 -DIVER2_LTR LTR Pao 240 -POGO DNA TcMar-Pogo 1032 -Gypsy6A_LTR LTR Gypsy 219 -MAX_I-int LTR Pao 3905 -ROOA_LTR LTR Pao 276 -DM176_I-int LTR Gypsy 2298 -Copia2_LTR_DM LTR Copia 460 -DM297_I-int LTR Gypsy 42705 -IDEFIX_I-int LTR Gypsy 3286 -Jockey2 LINE Jockey 760 -TC1-2_DM DNA TcMar-Tc1 2287 -DMRPR Unknown Unknown 136 +TRANSPAC_I-int LTR Gypsy 16760 +TRANSPAC_LTR LTR Gypsy 979 +XDMR Unknown Unknown 903 +XDMR_DM Unknown Unknown 1587 +ZAM_I-int LTR Gypsy 2892 +ZAM_LTR LTR Gypsy 118
--- 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 @@ -1,210 +1,210 @@ -LSU-rRNA_Dme rRNA rRNA 5583038 -FW3_DM LINE Jockey 647 -DMTOM1_LTR LTR Gypsy 1403 -R1_DM LINE R1 15424 -TAHRE LINE Jockey 3806 -G4_DM LINE Jockey 2223 -BS LINE Jockey 5200 -Stalker2_I-int LTR Gypsy 10966 -Stalker3_LTR LTR Gypsy 543 -TABOR_I-int LTR Gypsy 5504 -G7_DM LINE Jockey 1949 -BEL_I-int LTR Pao 29338 -Gypsy6_I-int LTR Gypsy 11381 +5S_DM RNA RNA 6331 ACCORD_I-int LTR Gypsy 4103 -DM412B_LTR LTR Gypsy 5607 -G2_DM LINE Jockey 1235 -SSU-rRNA_Hsa rRNA rRNA 563673 -TART_B1 LINE Jockey 13382 -S2_DM DNA TcMar-Tc1 716 -LOOPER1_DM DNA PiggyBac 220 -HOBO DNA hAT-hobo 4375 +ACCORD_LTR LTR Gypsy 790 +ACCORD2_I-int LTR Gypsy 2286 +ACCORD2_LTR LTR Gypsy 213 +ALA_DM Unknown Unknown 9 ARS406_DM Unknown Unknown 755 -G6_DM LINE Jockey 2874 -DOC2_DM LINE Jockey 4511 Baggins1 LINE LOA 5500 -NINJA_LTR LTR Pao 297 -TRANSIB2 DNA CMC-Transib 3357 -Gypsy5_LTR LTR Gypsy 502 -MDG3_LTR LTR Gypsy 926 -Gypsy12A_LTR LTR Gypsy 2436 -Gypsy_LTR LTR Gypsy 3771 -TIRANT_LTR LTR Gypsy 3225 -I_DM LINE I 11479 -DIVER2_I-int LTR Pao 6446 -P-1_DY DNA P 13 -Invader2_I-int LTR Gypsy 5970 -DOC6_DM LINE Jockey 1718 -BURDOCK_LTR LTR Gypsy 543 -SSU-rRNA_Dme rRNA rRNA 9958 -MAX_LTR LTR Pao 958 -STALKER4_LTR LTR Gypsy 2040 -XDMR_DM Unknown Unknown 4049 BARI_DM DNA TcMar-Tc1 1117 -Transib-N1_DM DNA CMC-Transib 366 -Gypsy5_I-int LTR Gypsy 2834 -XDMR Unknown Unknown 1771 -ACCORD2_LTR LTR Gypsy 213 -POGON1 DNA TcMar-Pogo 641 +BARI1 DNA TcMar-Tc1 370 +BATUMI_I-int LTR Pao 4723 +BATUMI_LTR LTR Pao 348 +BEL_I-int LTR Pao 29338 +BEL_LTR LTR Pao 927 +Bica_I-int LTR Gypsy 1561 +Bica_LTR LTR Gypsy 123 +BLASTOPIA_I-int LTR Gypsy 13780 +BLASTOPIA_LTR LTR Gypsy 1038 +BLOOD_I-int LTR Gypsy 27362 +BLOOD_LTR LTR Gypsy 1269 +BS LINE Jockey 5200 +BS2 LINE Jockey 5214 +BS3_DM LINE Jockey 851 BS4_DM LINE Jockey 8 -ALA_DM Unknown Unknown 9 -Gypsy1-I_DM LTR Gypsy 36962 -ACCORD_LTR LTR Gypsy 790 BURDOCK_I-int LTR Gypsy 5190 -ZAM_I-int LTR Gypsy 6896 -Invader5_I-int LTR Gypsy 191 -G3_DM LINE Jockey 480 -ROOA_I-int LTR Pao 4103 -Gypsy1-LTR_DM LTR Gypsy 1432 +BURDOCK_LTR LTR Gypsy 543 +Chimpo_I-int LTR Gypsy 1366 +Chimpo_LTR LTR Gypsy 107 +Chouto_I-int LTR Gypsy 1231 +Chouto_LTR LTR Gypsy 162 +CIRCE LTR Gypsy 3676 +Copia_I-int LTR Copia 50888 +Copia_LTR LTR Copia 2612 +Copia1-I_DM LTR Copia 4100 +Copia1-LTR_DM LTR Copia 600 +Copia2_I-int LTR Copia 3614 +Copia2_LTR_DM LTR Copia 747 +DIVER_I-int LTR Pao 24742 +DIVER_LTR LTR Pao 547 +DIVER2_I-int LTR Pao 6446 +DIVER2_LTR LTR Pao 648 DM1731_I-int LTR Copia 18829 -ROO_I-int LTR Pao 34023 +DM1731_LTR LTR Copia 1274 +DM176_I-int LTR Gypsy 4726 +DM176_LTR LTR Gypsy 560 +DM297_I-int LTR Gypsy 82387 +DM297_LTR LTR Gypsy 6128 DM412 LTR Gypsy 43689 -PROTOP DNA P 4775 -TART-A LINE Jockey 5092 -ROO_LTR LTR Pao 2219 -DIVER_LTR LTR Pao 547 -Gypsy3_I-int LTR Gypsy 5766 -BATUMI_LTR LTR Pao 348 -IDEFIX_LTR LTR Gypsy 2538 -G5_DM LINE Jockey 2714 -HETA LINE Jockey 22459 -Gypsy11_I-int LTR Gypsy 487 -R1-2_DM LINE R1 184 -Gypsy11_LTR LTR Gypsy 159 -HELENA_RT LINE Jockey 934 -FTZ_DM Unknown Unknown 0 -MICROPIA_I-int LTR Gypsy 6941 -Invader4_I-int LTR Gypsy 1888 -PLACW_DM DNA P 277 -BLOOD_LTR LTR Gypsy 1269 -R2_DM LINE R2 54042 -Copia1-I_DM LTR Copia 4100 -Gypsy4_I-int LTR Gypsy 13114 -Chouto_LTR LTR Gypsy 162 -BATUMI_I-int LTR Pao 4723 -DNAREP1_DM RC Helitron 76851 +DM412B_LTR LTR Gypsy 5607 +DMCR1A LINE CR1 17489 +DMLTR5 LTR Gypsy 189 +DMRP1 Unknown Unknown 295 +DMRPR Unknown Unknown 221 +DMRT1A LINE R1 3797 DMRT1B LINE R1 9003 DMRT1C LINE R1 1907 -TLD2 LTR Gypsy 33 -DMRT1A LINE R1 3797 -DM1731_LTR LTR Copia 1274 -LSU-rRNA_Cel rRNA rRNA 363697 -Copia_LTR LTR Copia 2612 +DMTOM1_LTR LTR Gypsy 1403 +DNAREP1_DM RC Helitron 76851 +DOC LINE Jockey 29082 +DOC2_DM LINE Jockey 4511 +DOC3_DM LINE Jockey 11067 +DOC4_DM LINE Jockey 1030 +DOC5_DM LINE Jockey 1793 +DOC6_DM LINE Jockey 1718 +FB4_DM DNA TcMar-Tc1 7840 +FROGGER_I-int LTR Copia 1075 +FROGGER_LTR LTR Copia 85 +FTZ_DM Unknown Unknown 0 +FUSHI_DM Unknown Unknown 0 +FW2_DM LINE Jockey 17723 +FW3_DM LINE Jockey 647 +G_DM LINE Jockey 10948 +G2_DM LINE Jockey 1235 +G3_DM LINE Jockey 480 +G4_DM LINE Jockey 2223 +G5_DM LINE Jockey 2714 +G5A_DM LINE Jockey 1578 +G6_DM LINE Jockey 2874 +G7_DM LINE Jockey 1949 +GTWIN_I-int LTR Gypsy 7568 +GTWIN_LTR LTR Gypsy 2533 +Gypsy_I-int LTR Gypsy 24082 +Gypsy_LTR LTR Gypsy 3771 +Gypsy1-I_DM LTR Gypsy 36962 +Gypsy1-LTR_DM LTR Gypsy 1432 +Gypsy10_I-int LTR Gypsy 2236 +Gypsy10_LTR LTR Gypsy 363 +Gypsy11_I-int LTR Gypsy 487 +Gypsy11_LTR LTR Gypsy 159 +Gypsy12_I-int LTR Gypsy 5002 +Gypsy12_LTR LTR Gypsy 7572 +Gypsy12A_LTR LTR Gypsy 2436 +Gypsy2_I-int LTR Gypsy 4226 +Gypsy2_LTR LTR Gypsy 869 +Gypsy2-I_DM LTR Gypsy 7374 +Gypsy2-LTR_DM LTR Gypsy 1155 +Gypsy3_I-int LTR Gypsy 5766 +Gypsy3_LTR LTR Gypsy 681 +Gypsy4_I-int LTR Gypsy 13114 +Gypsy4_LTR LTR Gypsy 390 +Gypsy5_I-int LTR Gypsy 2834 +Gypsy5_LTR LTR Gypsy 502 +Gypsy6_I-int LTR Gypsy 11381 Gypsy6_LTR LTR Gypsy 1423 -Gypsy12_I-int LTR Gypsy 5002 -BLASTOPIA_LTR LTR Gypsy 1038 -Bica_LTR LTR Gypsy 123 +Gypsy6A_LTR LTR Gypsy 793 +Gypsy7_I-int LTR Gypsy 1162 +Gypsy7_LTR LTR Gypsy 80 +Gypsy8_I-int LTR Gypsy 4176 Gypsy8_LTR LTR Gypsy 1467 -NINJA_I-int LTR Pao 3676 -PROTOP_B DNA P 9371 -PROTOP_A DNA P 4465 +Gypsy9_I-int LTR Gypsy 429 +Gypsy9_LTR LTR Gypsy 62 +HELENA_RT LINE Jockey 934 +Helitron1_DM RC Helitron 0 +HETA LINE Jockey 22459 +HMSBEAGLE_I-int LTR Gypsy 7863 +HOBO DNA hAT-hobo 4375 +I_DM LINE I 11479 +IDEFIX_I-int LTR Gypsy 7222 +IDEFIX_LTR LTR Gypsy 2538 +Invader1_I-int LTR Gypsy 2993 +Invader1_LTR LTR Gypsy 2525 +Invader2_I-int LTR Gypsy 5970 +Invader2_LTR LTR Gypsy 417 +Invader3_I-int LTR Gypsy 4411 Invader3_LTR LTR Gypsy 506 -Chimpo_LTR LTR Gypsy 107 -Invader2_LTR LTR Gypsy 417 -BLASTOPIA_I-int LTR Gypsy 13780 -FROGGER_LTR LTR Copia 85 +Invader4_I-int LTR Gypsy 1888 +Invader4_LTR LTR Gypsy 1624 +Invader5_I-int LTR Gypsy 191 +Invader5_LTR LTR Gypsy 47 +Invader6_I-int LTR Gypsy 6566 +Invader6_LTR LTR Gypsy 312 +IVK_DM LINE I 3025 +Jockey2 LINE Jockey 1823 +LINEJ1_DM LINE Jockey 24891 +LmeSINE1c SINE tRNA-Deu-L2 627 +LOOPER1_DM DNA PiggyBac 220 +LSU-rRNA_Cel rRNA rRNA 363697 +LSU-rRNA_Dme rRNA rRNA 5583038 +LSU-rRNA_Hsa rRNA rRNA 15 +M4DM DNA CMC-Transib 1880 +Mariner2_DM DNA TcMar-Tc1 1096 +MAX_I-int LTR Pao 8914 +MAX_LTR LTR Pao 958 +MDG1_I-int LTR Gypsy 16306 +MDG1_LTR LTR Gypsy 650 +MDG3_I-int LTR Gypsy 7857 +MDG3_LTR LTR Gypsy 926 +MICROPIA_I-int LTR Gypsy 6941 +MICROPIA_LTR LTR Gypsy 460 +MINOS DNA TcMar-Tc1 273 +MuDR-1_DEl DNA MULE-NOF 32 +NINJA_I-int LTR Pao 3676 +NINJA_LTR LTR Pao 297 +NOF_FB DNA MULE-NOF 228 NOMAD_I-int LTR Gypsy 11614 +NOMAD_LTR LTR Gypsy 757 +NTS_DM Other Other 56043 +P-1_DY DNA P 13 +PLACW_DM DNA P 277 +POGO DNA TcMar-Pogo 2909 +POGON1 DNA TcMar-Pogo 641 +PROTOP DNA P 4775 +PROTOP_A DNA P 4465 +PROTOP_B DNA P 9371 +QUASIMODO_I-int LTR Gypsy 17910 QUASIMODO_LTR LTR Gypsy 1625 -TABOR_LTR LTR Gypsy 443 -Stalker2_LTR LTR Gypsy 790 -MICROPIA_LTR LTR Gypsy 460 -Gypsy9_I-int LTR Gypsy 429 -STALKER4_I-int LTR Gypsy 7287 -TRANSIB1 DNA CMC-Transib 1229 -DOC LINE Jockey 29082 -TRANSIB3 DNA CMC-Transib 1802 -Copia_I-int LTR Copia 50888 -TRANSIB4 DNA CMC-Transib 364 -Gypsy10_LTR LTR Gypsy 363 -Invader3_I-int LTR Gypsy 4411 -Invader1_I-int LTR Gypsy 2993 -BS3_DM LINE Jockey 851 -Gypsy2-LTR_DM LTR Gypsy 1155 -LSU-rRNA_Hsa rRNA rRNA 15 -NOMAD_LTR LTR Gypsy 757 -Helitron1_DM RC Helitron 0 -LINEJ1_DM LINE Jockey 24891 -Invader4_LTR LTR Gypsy 1624 -MDG3_I-int LTR Gypsy 7857 -LmeSINE1c SINE tRNA-Deu-L2 627 +QUASIMODO2-I_DM LTR Gypsy 3977 +QUASIMODO2-LTR_DM LTR Gypsy 298 +R1_DM LINE R1 15424 +R1-2_DM LINE R1 184 +R2_DM LINE R2 54042 +ROO_I-int LTR Pao 34023 +ROO_LTR LTR Pao 2219 +ROOA_I-int LTR Pao 4103 +ROOA_LTR LTR Pao 435 +ROVER-I_DM LTR Gypsy 6947 ROVER-LTR_DM LTR Gypsy 415 S_DM DNA TcMar-Tc1 4974 -Invader6_I-int LTR Gypsy 6566 -ROVER-I_DM LTR Gypsy 6947 -QUASIMODO_I-int LTR Gypsy 17910 -Chouto_I-int LTR Gypsy 1231 -NTS_DM Other Other 56043 -Gypsy3_LTR LTR Gypsy 681 +S2_DM DNA TcMar-Tc1 716 SSU-rRNA_Cel rRNA rRNA 3855 -MINOS DNA TcMar-Tc1 273 -DOC4_DM LINE Jockey 1030 -ZAM_LTR LTR Gypsy 377 -QUASIMODO2-LTR_DM LTR Gypsy 298 -Gypsy2-I_DM LTR Gypsy 7374 -TRANSPAC_I-int LTR Gypsy 28474 -Bica_I-int LTR Gypsy 1561 -BS2 LINE Jockey 5214 -BLOOD_I-int LTR Gypsy 27362 -DMCR1A LINE CR1 17489 -QUASIMODO2-I_DM LTR Gypsy 3977 -HMSBEAGLE_I-int LTR Gypsy 7863 -DMLTR5 LTR Gypsy 189 -Gypsy7_LTR LTR Gypsy 80 -G5A_DM LINE Jockey 1578 -MDG1_I-int LTR Gypsy 16306 -Gypsy2_I-int LTR Gypsy 4226 -BARI1 DNA TcMar-Tc1 370 -Invader5_LTR LTR Gypsy 47 -DM176_LTR LTR Gypsy 560 -DOC3_DM LINE Jockey 11067 -Copia1-LTR_DM LTR Copia 600 -TOM_I-int LTR Gypsy 6929 -NOF_FB DNA MULE-NOF 228 -Chimpo_I-int LTR Gypsy 1366 -DIVER_I-int LTR Pao 24742 +SSU-rRNA_Dme rRNA rRNA 9958 +SSU-rRNA_Hsa rRNA rRNA 563673 +Stalker2_I-int LTR Gypsy 10966 +Stalker2_LTR LTR Gypsy 790 +Stalker3_LTR LTR Gypsy 543 +STALKER4_I-int LTR Gypsy 7287 +STALKER4_LTR LTR Gypsy 2040 +TABOR_I-int LTR Gypsy 5504 +TABOR_LTR LTR Gypsy 443 +TAHRE LINE Jockey 3806 +TART_B1 LINE Jockey 13382 +TART-A LINE Jockey 5092 +TC1_DM DNA TcMar-Tc1 2618 +TC1-2_DM DNA TcMar-Tc1 4438 TIRANT_I-int LTR Gypsy 23165 -Gypsy2_LTR LTR Gypsy 869 -FB4_DM DNA TcMar-Tc1 7840 -GTWIN_LTR LTR Gypsy 2533 -Invader6_LTR LTR Gypsy 312 -Gypsy8_I-int LTR Gypsy 4176 -G_DM LINE Jockey 10948 -TRANSPAC_LTR LTR Gypsy 1457 -FUSHI_DM Unknown Unknown 0 +TIRANT_LTR LTR Gypsy 3225 +TLD2 LTR Gypsy 33 +TOM_I-int LTR Gypsy 6929 +Transib-N1_DM DNA CMC-Transib 366 +TRANSIB1 DNA CMC-Transib 1229 +TRANSIB2 DNA CMC-Transib 3357 +TRANSIB3 DNA CMC-Transib 1802 +TRANSIB4 DNA CMC-Transib 364 Transib5 DNA CMC-Transib 973 -MuDR-1_DEl DNA MULE-NOF 32 -Mariner2_DM DNA TcMar-Tc1 1096 -DOC5_DM LINE Jockey 1793 -TC1_DM DNA TcMar-Tc1 2618 -Gypsy9_LTR LTR Gypsy 62 -DMRP1 Unknown Unknown 295 -Gypsy10_I-int LTR Gypsy 2236 -Gypsy4_LTR LTR Gypsy 390 -DM297_LTR LTR Gypsy 6128 -ACCORD2_I-int LTR Gypsy 2286 -Invader1_LTR LTR Gypsy 2525 -BEL_LTR LTR Pao 927 -IVK_DM LINE I 3025 -M4DM DNA CMC-Transib 1880 -FW2_DM LINE Jockey 17723 -Copia2_I-int LTR Copia 3614 -MDG1_LTR LTR Gypsy 650 -Gypsy12_LTR LTR Gypsy 7572 -Gypsy7_I-int LTR Gypsy 1162 -FROGGER_I-int LTR Copia 1075 -Gypsy_I-int LTR Gypsy 24082 -5S_DM RNA RNA 6331 -GTWIN_I-int LTR Gypsy 7568 -CIRCE LTR Gypsy 3676 -DIVER2_LTR LTR Pao 648 -POGO DNA TcMar-Pogo 2909 -Gypsy6A_LTR LTR Gypsy 793 -MAX_I-int LTR Pao 8914 -ROOA_LTR LTR Pao 435 -DM176_I-int LTR Gypsy 4726 -Copia2_LTR_DM LTR Copia 747 -DM297_I-int LTR Gypsy 82387 -IDEFIX_I-int LTR Gypsy 7222 -Jockey2 LINE Jockey 1823 -TC1-2_DM DNA TcMar-Tc1 4438 -DMRPR Unknown Unknown 221 +TRANSPAC_I-int LTR Gypsy 28474 +TRANSPAC_LTR LTR Gypsy 1457 +XDMR Unknown Unknown 1771 +XDMR_DM Unknown Unknown 4049 +ZAM_I-int LTR Gypsy 6896 +ZAM_LTR LTR Gypsy 377
--- 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 @@ -1,211 +1,211 @@ Tag Mutant_1 Mutant_2 Wildtype_1 Wildtype_2 -LSU-rRNA_Dme 218650.181450173 354466.098949349 157455.221275418 149201.031867455 -FW3_DM 25.3386538652006 32.2981814492716 35.756634311884 44.2453336153694 -DMTOM1_LTR 54.9461072223747 39.3419337866127 43.2005545717588 49.0430203929395 -R1_DM 604.054709763298 517.028601444589 315.957840856997 262.031236427494 -TAHRE 149.055512536249 121.719476366005 196.209690086873 189.678242903128 -G4_DM 87.0600116574048 105.226787966377 157.828320885669 165.108271224056 -BS 203.649150075801 355.194096523239 313.935504138996 242.355874491196 -Stalker2_I-int 429.46472687139 413.519801853174 527.184456786045 604.508533973842 -Stalker3_LTR 21.2656708636846 20.1863634057947 25.5158653994552 21.2745908621546 -TABOR_I-int 215.554792695617 317.054754599099 169.833255871247 149.309827895896 -G7_DM 76.3292679803337 35.9059570366902 6.97060741098101 4.74922529496845 -BEL_I-int 1148.97283940843 1304.98396962057 1022.22666828812 1059.36800967358 -Gypsy6_I-int 445.717495579363 323.23951274896 322.239993215042 326.921161631196 +5S_DM 247.942840217287 356.138990129468 271.810660587451 503.611727197063 ACCORD_I-int 160.687012069425 174.461719477315 117.166444321613 104.919109832721 -DM412B_LTR 219.588612399041 257.784155662936 132.441540808639 141.022914371002 -G2_DM 48.3666731430026 65.6271559235199 57.1417693937208 54.8583983051458 -SSU-rRNA_Hsa 22075.2937251301 25925.561270609 13684.9804569472 8340.22115575582 -TART_B1 524.083255060455 437.142142008891 1086.38207353363 1042.55187521078 -S2_DM 28.0409214335141 17.6093808433528 32.9167572185214 35.52226674706 -LOOPER1_DM 8.61592558013002 2.66288198118994 35.3263499037988 28.5438132524124 -HOBO 171.339429150313 182.020868327145 216.476085707688 213.42436937797 +ACCORD_LTR 30.9390054922851 29.5494000493336 12.6933900385148 10.6615261723782 +ACCORD2_I-int 89.5272994371693 103.079302497675 126.245445332212 119.118324235025 +ACCORD2_LTR 8.34178249348953 6.52835582485276 10.1116835900033 9.30460465953003 +ALA_DM 0.352469682823501 0 0.215142204042624 0.290768895610313 ARS406_DM 29.5682900590826 19.7568663120544 24.2250121751994 34.8438059906359 -G6_DM 112.555318714971 67.5169431359773 207.698283782749 168.30672907577 -DOC2_DM 176.665637690757 176.265607271025 190.960220308233 219.9182080466 Baggins1 215.398139503251 157.367735146451 220.994071992583 188.660551768492 -NINJA_LTR 11.6314995331755 9.79253373727915 21.1269644369856 19.6753619362979 -TRANSIB2 131.471191693166 127.474737422125 137.561925264854 149.067520482887 -Gypsy5_LTR 19.6599756419331 28.0032105118684 28.0115149663496 21.8561286533752 -MDG3_LTR 36.2652140327291 38.9983361116205 44.6204931184401 41.0953372462576 -Gypsy12A_LTR 95.4017941508943 92.5136739916635 131.624000433277 108.650643993054 -Gypsy_LTR 147.684797103047 149.207290365385 56.1951436959333 44.4391795457762 -TIRANT_LTR 126.301636345088 137.095472321908 58.9919923484874 61.9822362475985 -I_DM 449.55549879233 957.692619622151 343.668156737687 339.860377485855 -DIVER2_I-int 252.44661949781 229.179649219831 287.386956160137 272.692762599872 -P-1_DY 0.509122875189502 0.343597674992251 0.344227526468198 0.0969229652034378 -Invader2_I-int 233.804889606256 271.184464987634 293.583051636564 267.022769135471 -DOC6_DM 67.2825461211972 65.9707535985121 54.1728069779326 60.0922384261314 +BARI_DM 43.7454039682056 44.8394965864887 42.5981564004395 43.7122573067505 +BARI1 14.490420293855 10.7374273435078 16.9962341193673 15.6045973977535 +BATUMI_I-int 184.968256886155 158.226729333931 275.166878970516 232.082040179632 +BATUMI_LTR 13.628827735842 14.5170017684226 23.8377562079227 19.5299774884927 +BEL_I-int 1148.97283940843 1304.98396962057 1022.22666828812 1059.36800967358 +BEL_LTR 36.3043773308206 51.9691483425779 37.6498857074591 41.5799520722748 +Bica_I-int 61.1339083208317 53.0858407863027 79.6886723773878 67.3614608163893 +Bica_LTR 4.81708566525451 5.7552610561202 6.02398171319346 6.05768532521486 +BLASTOPIA_I-int 539.670247700872 1034.65849882041 443.580196295081 462.322544020398 +BLASTOPIA_LTR 40.6515034189771 78.9415658294696 23.6656424446886 23.1645886836216 +BLOOD_I-int 1071.58616237963 1140.74428097427 960.825083254357 834.603653366803 +BLOOD_LTR 49.6982252781136 46.55748496145 32.1852737247765 36.1522660208823 +BS 203.649150075801 355.194096523239 313.935504138996 242.355874491196 +BS2 204.197436249082 179.186187508459 240.744126323696 241.871259665179 +BS3_DM 33.3279666758666 38.9124366928724 53.871607892273 42.5007202417075 +BS4_DM 0.313306384732001 1.97568663120544 1.46296698748984 1.0176911346361 +BURDOCK_I-int 203.257517094886 191.727502645676 134.205706881789 161.473660028927 BURDOCK_LTR 21.2656708636846 16.5785878183761 12.3491625120466 17.930748562636 -SSU-rRNA_Dme 389.988122395158 328.307578455096 306.061299471036 201.260537244939 -MAX_LTR 37.5184395716571 29.4635006305855 43.7599243022696 36.4914963990943 -STALKER4_LTR 79.8931281066602 68.9772332546943 55.5927455246139 58.6383939480799 -XDMR_DM 158.572193972484 136.322377553175 142.725338161877 209.741296700239 -BARI_DM 43.7454039682056 44.8394965864887 42.5981564004395 43.7122573067505 -Transib-N1_DM 14.333767101489 11.1669244372481 13.2527597690256 17.9792100452377 -Gypsy5_I-int 110.988786791311 88.9917978229929 105.333623099269 105.936800967358 -XDMR 69.3582009200467 77.5671751295006 53.7425225698474 69.7845349464752 -ACCORD2_LTR 8.34178249348953 6.52835582485276 10.1116835900033 9.30460465953003 -POGON1 25.1036740766516 21.990251199504 14.2424139076217 19.5299774884927 -BS4_DM 0.313306384732001 1.97568663120544 1.46296698748984 1.0176911346361 -ALA_DM 0.352469682823501 0 0.215142204042624 0.290768895610313 -Gypsy1-I_DM 1447.55382405803 1954.46947477467 351.112076997562 305.161955943024 -ACCORD_LTR 30.9390054922851 29.5494000493336 12.6933900385148 10.6615261723782 -BURDOCK_I-int 203.257517094886 191.727502645676 134.205706881789 161.473660028927 -ZAM_I-int 270.070103638985 248.421119019397 220.692872906923 214.490521995208 -Invader5_I-int 7.48018993547652 10.0502319935233 17.8998313763463 16.2345966715758 -G3_DM 18.7983830839201 21.4748546870157 34.2936673243942 26.9445843265557 -ROOA_I-int 160.687012069425 221.534600951254 214.496777430496 222.389743659288 -Gypsy1-LTR_DM 56.0818428670282 49.4780651988841 44.8356353224828 38.5268786683665 +Chimpo_I-int 53.4970651929892 31.7827849367832 55.4206317613798 51.369171557822 +Chimpo_LTR 4.19047289579051 2.83468081868607 4.04467343600132 5.81537791220627 +Chouto_I-int 48.2100199506366 44.4958989114965 72.7180649664068 63.1937733126415 +Chouto_LTR 6.34445429082302 13.658007580942 12.8655038017489 13.617676611083 +CIRCE 143.964283784354 134.862087434458 162.088136525713 161.037506685512 +Copia_I-int 1992.94191328026 7492.14730320603 1188.10130760498 1295.52081439175 +Copia_LTR 102.294534614998 264.140712650293 60.5840446584028 54.7130138573406 +Copia1-I_DM 160.56952217515 167.16026888373 154.386045620987 170.487495792847 +Copia1-LTR_DM 23.4979788549001 33.4148738929964 33.1749278633726 27.4291991525729 +Copia2_I-int 141.536159302681 162.521700271335 181.493963330357 167.434422388939 +Copia2_LTR_DM 29.2549836743506 39.5137326241088 38.3383407603955 23.5522805444354 +DIVER_I-int 968.978321379896 1009.40406970848 567.028792974739 757.307588617061 +DIVER_LTR 21.4223240560506 28.1750093493646 20.1803387391981 20.7899760361374 +DIVER2_I-int 252.44661949781 229.179649219831 287.386956160137 272.692762599872 +DIVER2_LTR 25.3778171632921 20.615860499535 34.1215535611601 25.9268931919196 DM1731_I-int 737.405739764856 590.386705055435 222.887323388158 236.54049657899 -ROO_I-int 1332.45289096711 1970.61856549931 1368.00321862543 1358.56920325659 +DM1731_LTR 49.8940417685711 27.5737134181281 24.8274103465188 21.3230523447563 +DM176_I-int 185.08574678043 197.396864283048 156.064154812519 136.322150558635 +DM176_LTR 21.9314469312401 28.3468081868607 38.6825682868637 42.2584128286989 +DM297_I-int 3226.54663986442 3668.33467763602 509.327653850507 558.760894397819 +DM297_LTR 239.992690704713 216.122937570126 64.0693483638933 71.6260712853405 DM412 1711.00533031955 2019.32353592946 1036.38302531413 1142.04329899211 -PROTOP 187.004748386913 176.866903202261 212.646554475729 210.952833765282 -TART-A 199.419513881919 156.766439215214 159.076145669116 165.156732706658 -ROO_LTR 86.9033584650388 124.811855440935 70.523614485172 89.7022042957817 -DIVER_LTR 21.4223240560506 28.1750093493646 20.1803387391981 20.7899760361374 -Gypsy3_I-int 225.81557679559 193.960887533126 146.253670308176 133.414461602532 -BATUMI_LTR 13.628827735842 14.5170017684226 23.8377562079227 19.5299774884927 -IDEFIX_LTR 99.3964505562273 86.9302117730394 94.2753138114777 89.3629739175697 -G5_DM 106.289191020331 111.669244372481 111.916974542973 123.625242116985 -HETA 879.568511837001 887.083297411243 990.729849616282 1182.31479103414 -Gypsy11_I-int 19.0725261705606 14.4311023496745 28.8720837825201 27.1384302569626 -R1-2_DM 7.20604684883602 5.84116047486826 11.4885936958761 8.57768242050425 -Gypsy11_LTR 6.22696439654852 4.12317209990701 5.76581106834231 7.22076090765612 -HELENA_RT 36.5785204174611 35.7341581991941 28.0975718479666 30.3853495912778 -FTZ_DM 0 0 0 0 -MICROPIA_I-int 271.832452053102 285.787366174805 436.695645765717 501.818652340799 -Invader4_I-int 73.9403067967522 101.361314122714 61.9179263234671 59.0745472914953 -PLACW_DM 10.8482335713455 17.5234814246048 6.41123768047018 6.1546082904183 -BLOOD_LTR 49.6982252781136 46.55748496145 32.1852737247765 36.1522660208823 -R2_DM 2116.46295546085 1299.48640682069 659.496912272258 407.415684232651 -Copia1-I_DM 160.56952217515 167.16026888373 154.386045620987 170.487495792847 -Gypsy4_I-int 513.587491171932 459.390091464639 521.20350351366 487.328669042885 -Chouto_LTR 6.34445429082302 13.658007580942 12.8655038017489 13.617676611083 -BATUMI_I-int 184.968256886155 158.226729333931 275.166878970516 232.082040179632 -DNAREP1_DM 3009.73862162988 3174.24122099716 2918.23188407496 3099.30565831033 +DM412B_LTR 219.588612399041 257.784155662936 132.441540808639 141.022914371002 +DMCR1A 684.926920322246 693.380108134362 876.919623677734 870.222843079066 +DMLTR5 7.40186333929352 8.07454536231789 6.92757897017248 7.75383721627503 +DMRP1 11.5531729369925 12.369516299721 11.2734514918335 11.0007565505902 +DMRPR 8.65508887822152 11.6823209497365 5.50764042349117 9.06229724652144 +DMRT1A 148.703042853426 106.085782153857 191.734732242786 171.553648410085 DMRT1B 352.587172717776 353.476108148278 417.634046487541 344.997294641637 DMRT1C 74.6844094604907 57.552610561202 108.861955245568 101.139114189787 -TLD2 1.2923888370195 0.0858994187480627 2.79684865255411 0.823845204229221 -DMRT1A 148.703042853426 106.085782153857 191.734732242786 171.553648410085 -DM1731_LTR 49.8940417685711 27.5737134181281 24.8274103465188 21.3230523447563 -LSU-rRNA_Cel 14243.5740259843 21618.3926157437 22382.0179984887 15843.270199567 -Copia_LTR 102.294534614998 264.140712650293 60.5840446584028 54.7130138573406 +DMTOM1_LTR 54.9461072223747 39.3419337866127 43.2005545717588 49.0430203929395 +DNAREP1_DM 3009.73862162988 3174.24122099716 2918.23188407496 3099.30565831033 +DOC 1138.94703509701 1864.01738683296 769.477606978848 795.446775424614 +DOC2_DM 176.665637690757 176.265607271025 190.960220308233 219.9182080466 +DOC3_DM 433.420219978632 447.106474583666 513.802611694594 516.550943051722 +DOC4_DM 40.3381970342451 56.5218175362252 34.9821223773306 40.2230305594267 +DOC5_DM 70.2197934780597 64.5963628985431 130.67737473549 105.791416519552 +DOC6_DM 67.2825461211972 65.9707535985121 54.1728069779326 60.0922384261314 +FB4_DM 307.040257037361 287.591253968514 307.610323340143 336.274227773327 +FROGGER_I-int 42.1005454483626 46.9010826364422 69.3188181425333 65.9560778209394 +FROGGER_LTR 3.32888033777751 4.89626686863957 1.76416607314951 2.61692006049282 +FTZ_DM 0 0 0 0 +FUSHI_DM 0 0 0 0 +FW2_DM 694.091132075657 761.412447782827 612.466826468541 671.046149586002 +FW3_DM 25.3386538652006 32.2981814492716 35.756634311884 44.2453336153694 +G_DM 428.759787505743 393.591136703623 383.168265399913 389.388012704811 +G2_DM 48.3666731430026 65.6271559235199 57.1417693937208 54.8583983051458 +G3_DM 18.7983830839201 21.4748546870157 34.2936673243942 26.9445843265557 +G4_DM 87.0600116574048 105.226787966377 157.828320885669 165.108271224056 +G5_DM 106.289191020331 111.669244372481 111.916974542973 123.625242116985 +G5A_DM 61.7996843883872 49.9934617113725 77.6233072185786 77.2960647497417 +G6_DM 112.555318714971 67.5169431359773 207.698283782749 168.30672907577 +G7_DM 76.3292679803337 35.9059570366902 6.97060741098101 4.74922529496845 +GTWIN_I-int 296.387839956473 251.685296931824 234.418945524843 244.924333069087 +GTWIN_LTR 99.2006340657698 80.5736547856828 25.7310076034978 22.6315123750027 +Gypsy_I-int 943.130544639506 958.723412647127 293.540023195756 273.031992978084 +Gypsy_LTR 147.684797103047 149.207290365385 56.1951436959333 44.4391795457762 +Gypsy1-I_DM 1447.55382405803 1954.46947477467 351.112076997562 305.161955943024 +Gypsy1-LTR_DM 56.0818428670282 49.4780651988841 44.8356353224828 38.5268786683665 +Gypsy10_I-int 87.5691345325943 79.6287611794541 97.1582193456488 93.5306614213175 +Gypsy10_LTR 14.2162772072145 13.9157058371862 13.5109304138768 17.8338255974326 +Gypsy11_I-int 19.0725261705606 14.4311023496745 28.8720837825201 27.1384302569626 +Gypsy11_LTR 6.22696439654852 4.12317209990701 5.76581106834231 7.22076090765612 +Gypsy12_I-int 195.894817053684 211.827966632723 420.732094225755 466.538693006748 +Gypsy12_LTR 296.544493148839 230.210442244808 270.734949567238 287.5704377586 +Gypsy12A_LTR 95.4017941508943 92.5136739916635 131.624000433277 108.650643993054 +Gypsy2_I-int 165.50409773468 133.315897896993 137.260726179194 167.337499423735 +Gypsy2_LTR 34.0329060415136 21.4748546870157 20.6106231472833 23.5038190618337 +Gypsy2-I_DM 288.790160126722 228.320655032351 198.188998364065 188.805936216297 +Gypsy2-LTR_DM 45.2336092956826 33.0712762180041 41.5654738210349 33.438422995186 +Gypsy3_I-int 225.81557679559 193.960887533126 146.253670308176 133.414461602532 +Gypsy3_LTR 26.6702060003116 18.2106767745893 24.354097497625 21.6622827229683 +Gypsy4_I-int 513.587491171932 459.390091464639 521.20350351366 487.328669042885 +Gypsy4_LTR 15.273686255685 18.7260732870777 11.7897927815358 9.40152762473347 +Gypsy5_I-int 110.988786791311 88.9917978229929 105.333623099269 105.936800967358 +Gypsy5_LTR 19.6599756419331 28.0032105118684 28.0115149663496 21.8561286533752 +Gypsy6_I-int 445.717495579363 323.23951274896 322.239993215042 326.921161631196 Gypsy6_LTR 55.7293731842047 65.2835582485276 18.4161726660486 23.455357579232 -Gypsy12_I-int 195.894817053684 211.827966632723 420.732094225755 466.538693006748 -BLASTOPIA_LTR 40.6515034189771 78.9415658294696 23.6656424446886 23.1645886836216 -Bica_LTR 4.81708566525451 5.7552610561202 6.02398171319346 6.05768532521486 +Gypsy6A_LTR 31.0564953865596 18.8119727058257 26.5485479788598 27.7684295307849 +Gypsy7_I-int 45.5077523823231 63.7373687110625 54.0437216555071 48.8976359451344 +Gypsy7_LTR 3.13306384732001 3.35007733117444 4.81918537055477 4.21614898634954 +Gypsy8_I-int 163.545932830104 107.116575178834 206.923771848195 197.868233462818 Gypsy8_LTR 57.4525583002307 41.7471175115585 56.4102858999759 60.1406999087332 -NINJA_I-int 143.964283784354 98.4407338852798 226.931996824159 218.22205615554 -PROTOP_B 366.999266415448 369.367500616669 373.91715062608 401.503383355241 -PROTOP_A 174.864125978548 170.768044471149 152.019481376518 163.993657124217 +Gypsy9_I-int 16.8010548812535 16.1490907246358 21.6863341674965 22.9707427532148 +Gypsy9_LTR 2.42812448167301 0.687195349984501 2.19445048123476 2.03538226927219 +HELENA_RT 36.5785204174611 35.7341581991941 28.0975718479666 30.3853495912778 +Helitron1_DM 0 0 0.129085322425574 0.290768895610313 +HETA 879.568511837001 887.083297411243 990.729849616282 1182.31479103414 +HMSBEAGLE_I-int 307.941012893465 350.383729073348 311.48288301291 286.310439210955 +HOBO 171.339429150313 182.020868327145 216.476085707688 213.42436937797 +I_DM 449.55549879233 957.692619622151 343.668156737687 339.860377485855 +IDEFIX_I-int 282.837338816814 282.265490006134 266.475133927194 268.815843991735 +IDEFIX_LTR 99.3964505562273 86.9302117730394 94.2753138114777 89.3629739175697 +Invader1_I-int 117.21575118786 151.870172346575 78.8281035612173 81.027598910074 +Invader1_LTR 98.8873276810378 163.466593877563 143.973162945324 93.5791229039192 +Invader2_I-int 233.804889606256 271.184464987634 293.583051636564 267.022769135471 +Invader2_LTR 16.3310953041555 18.2965761933373 21.1699928777942 22.8738197880113 +Invader3_I-int 172.749307881607 173.688624708583 200.813733253385 180.373638243598 Invader3_LTR 19.8166288342991 19.4991680558102 28.2696856112007 29.4645814218451 -Chimpo_LTR 4.19047289579051 2.83468081868607 4.04467343600132 5.81537791220627 -Invader2_LTR 16.3310953041555 18.2965761933373 21.1699928777942 22.8738197880113 -BLASTOPIA_I-int 539.670247700872 1034.65849882041 443.580196295081 462.322544020398 -FROGGER_LTR 3.32888033777751 4.89626686863957 1.76416607314951 2.61692006049282 +Invader4_I-int 73.9403067967522 101.361314122714 61.9179263234671 59.0745472914953 +Invader4_LTR 63.6011961005962 58.3257053299346 61.1003859481051 59.5107006349108 +Invader5_I-int 7.48018993547652 10.0502319935233 17.8998313763463 16.2345966715758 +Invader5_LTR 1.84067501030051 1.97568663120544 2.96896241578821 3.10153488651001 +Invader6_I-int 257.14621526879 283.296283031111 298.230123243885 324.740394914118 +Invader6_LTR 12.218949004548 12.5413151372172 27.9254580847325 28.4953517698107 +IVK_DM 118.468976726788 151.956071765323 144.102248267749 141.555990679621 +Jockey2 71.3946924208047 65.2835582485276 76.1603402310888 76.9568343715296 +LINEJ1_DM 974.813652795529 1369.15083542537 302.274796679886 306.712723386279 +LmeSINE1c 24.5553879033706 56.0923204424849 25.7740360443063 68.5245363988305 +LOOPER1_DM 8.61592558013002 2.66288198118994 35.3263499037988 28.5438132524124 +LSU-rRNA_Cel 14243.5740259843 21618.3926157437 22382.0179984887 15843.270199567 +LSU-rRNA_Dme 218650.181450173 354466.098949349 157455.221275418 149201.031867455 +LSU-rRNA_Hsa 0.587449471372502 0.944893606228689 0.215142204042624 0 +M4DM 73.6270004120202 78.8556664107215 74.3101172763222 79.9614462928362 +Mariner2_DM 42.9229747082841 79.542861760706 86.5301944659432 77.1022188193348 +MAX_I-int 349.101639187632 335.437230211185 533.337523821664 445.894101418416 +MAX_LTR 37.5184395716571 29.4635006305855 43.7599243022696 36.4914963990943 +MDG1_I-int 638.596738680001 690.889024990668 702.009011791081 665.860770947618 +MDG1_LTR 25.4561437594751 24.1377366682056 29.6896241578821 28.2045828742004 +MDG3_I-int 307.706033104916 323.840808680196 232.009352839565 240.902030013145 +MDG3_LTR 36.2652140327291 38.9983361116205 44.6204931184401 41.0953372462576 +MICROPIA_I-int 271.832452053102 285.787366174805 436.695645765717 501.818652340799 +MICROPIA_LTR 18.0151171220901 12.7990133934613 34.2936673243942 41.8222594852834 +MINOS 10.6915803789795 7.98864594356983 7.44392025987478 10.9522950679885 +MuDR-1_DEl 1.253225538928 0.343597674992251 0.258170644851148 0.43615334341547 +NINJA_I-int 143.964283784354 98.4407338852798 226.931996824159 218.22205615554 +NINJA_LTR 11.6314995331755 9.79253373727915 21.1269644369856 19.6753619362979 +NOF_FB 8.92923196486203 5.41166338112795 54.7321767084434 46.5230232976501 NOMAD_I-int 454.842544034682 700.423860471703 708.635391675594 561.862429284329 +NOMAD_LTR 29.6466166552656 23.7941389932134 26.6346048604768 39.8353386986129 +NTS_DM 2194.82871494194 1868.57005602661 2837.89778508544 1754.54797759523 +P-1_DY 0.509122875189502 0.343597674992251 0.344227526468198 0.0969229652034378 +PLACW_DM 10.8482335713455 17.5234814246048 6.41123768047018 6.1546082904183 +POGO 113.926034148174 88.6482001480007 104.43002584229 120.766014643484 +POGON1 25.1036740766516 21.990251199504 14.2424139076217 19.5299774884927 +PROTOP 187.004748386913 176.866903202261 212.646554475729 210.952833765282 +PROTOP_A 174.864125978548 170.768044471149 152.019481376518 163.993657124217 +PROTOP_B 366.999266415448 369.367500616669 373.91715062608 401.503383355241 +QUASIMODO_I-int 701.414668818767 687.195349984501 641.38193869187 630.871580509177 QUASIMODO_LTR 63.6403593986877 45.3548930989771 57.3138831569549 56.893780574418 -TABOR_LTR 17.3493410545346 7.55914884982952 16.5229212704735 13.2299847502693 -Stalker2_LTR 30.9390054922851 30.5801930743103 31.238648026989 32.5661163083551 -MICROPIA_LTR 18.0151171220901 12.7990133934613 34.2936673243942 41.8222594852834 -Gypsy9_I-int 16.8010548812535 16.1490907246358 21.6863341674965 22.9707427532148 -STALKER4_I-int 285.382953192761 269.036979518932 267.077532098513 278.217371616468 -TRANSIB1 48.1316933544536 24.8249320181901 89.5852137633485 102.544497185237 -DOC 1138.94703509701 1864.01738683296 769.477606978848 795.446775424614 -TRANSIB3 70.5722631608832 63.6514692923144 50.9456739172933 54.8583983051458 -Copia_I-int 1992.94191328026 7492.14730320603 1188.10130760498 1295.52081439175 -TRANSIB4 14.255440505306 13.1426110684536 27.3230599134132 27.6715065655815 -Gypsy10_LTR 14.2162772072145 13.9157058371862 13.5109304138768 17.8338255974326 -Invader3_I-int 172.749307881607 173.688624708583 200.813733253385 180.373638243598 -Invader1_I-int 117.21575118786 151.870172346575 78.8281035612173 81.027598910074 -BS3_DM 33.3279666758666 38.9124366928724 53.871607892273 42.5007202417075 -Gypsy2-LTR_DM 45.2336092956826 33.0712762180041 41.5654738210349 33.438422995186 -LSU-rRNA_Hsa 0.587449471372502 0.944893606228689 0.215142204042624 0 -NOMAD_LTR 29.6466166552656 23.7941389932134 26.6346048604768 39.8353386986129 -Helitron1_DM 0 0 0.129085322425574 0.290768895610313 -LINEJ1_DM 974.813652795529 1369.15083542537 302.274796679886 306.712723386279 -Invader4_LTR 63.6011961005962 58.3257053299346 61.1003859481051 59.5107006349108 -MDG3_I-int 307.706033104916 323.840808680196 232.009352839565 240.902030013145 -LmeSINE1c 24.5553879033706 56.0923204424849 25.7740360443063 68.5245363988305 +QUASIMODO2-I_DM 155.752436509896 155.563847352742 116.908273676762 107.826798788825 +QUASIMODO2-LTR_DM 11.670662831267 9.01943896854658 13.4679019730682 9.69229652034378 +R1_DM 604.054709763298 517.028601444589 315.957840856997 262.031236427494 +R1-2_DM 7.20604684883602 5.84116047486826 11.4885936958761 8.57768242050425 +R2_DM 2116.46295546085 1299.48640682069 659.496912272258 407.415684232651 +ROO_I-int 1332.45289096711 1970.61856549931 1368.00321862543 1358.56920325659 +ROO_LTR 86.9033584650388 124.811855440935 70.523614485172 89.7022042957817 +ROOA_I-int 160.687012069425 221.534600951254 214.496777430496 222.389743659288 +ROOA_LTR 17.0360346698026 23.7082395744653 17.2113763234099 23.4068960966302 +ROVER-I_DM 272.067431841651 263.625316137804 280.244234985922 270.851226261007 ROVER-LTR_DM 16.2527687079725 14.4311023496745 24.2680406160079 20.1115152797133 S_DM 194.798244707122 175.320713664796 155.418728200391 168.452113523575 -Invader6_I-int 257.14621526879 283.296283031111 298.230123243885 324.740394914118 -ROVER-I_DM 272.067431841651 263.625316137804 280.244234985922 270.851226261007 -QUASIMODO_I-int 701.414668818767 687.195349984501 641.38193869187 630.871580509177 -Chouto_I-int 48.2100199506366 44.4958989114965 72.7180649664068 63.1937733126415 -NTS_DM 2194.82871494194 1868.57005602661 2837.89778508544 1754.54797759523 -Gypsy3_LTR 26.6702060003116 18.2106767745893 24.354097497625 21.6622827229683 +S2_DM 28.0409214335141 17.6093808433528 32.9167572185214 35.52226674706 SSU-rRNA_Cel 150.974514142733 156.07924386523 149.007490519921 105.791416519552 -MINOS 10.6915803789795 7.98864594356983 7.44392025987478 10.9522950679885 -DOC4_DM 40.3381970342451 56.5218175362252 34.9821223773306 40.2230305594267 -ZAM_LTR 14.7645633804955 10.1361314122714 11.1443661694079 10.9038335853868 -QUASIMODO2-LTR_DM 11.670662831267 9.01943896854658 13.4679019730682 9.69229652034378 -Gypsy2-I_DM 288.790160126722 228.320655032351 198.188998364065 188.805936216297 -TRANSPAC_I-int 1115.13574985737 1439.67425821753 416.257136381668 726.049932338953 -Bica_I-int 61.1339083208317 53.0858407863027 79.6886723773878 67.3614608163893 -BS2 204.197436249082 179.186187508459 240.744126323696 241.871259665179 -BLOOD_I-int 1071.58616237963 1140.74428097427 960.825083254357 834.603653366803 -DMCR1A 684.926920322246 693.380108134362 876.919623677734 870.222843079066 -QUASIMODO2-I_DM 155.752436509896 155.563847352742 116.908273676762 107.826798788825 -HMSBEAGLE_I-int 307.941012893465 350.383729073348 311.48288301291 286.310439210955 -DMLTR5 7.40186333929352 8.07454536231789 6.92757897017248 7.75383721627503 -Gypsy7_LTR 3.13306384732001 3.35007733117444 4.81918537055477 4.21614898634954 -G5A_DM 61.7996843883872 49.9934617113725 77.6233072185786 77.2960647497417 -MDG1_I-int 638.596738680001 690.889024990668 702.009011791081 665.860770947618 -Gypsy2_I-int 165.50409773468 133.315897896993 137.260726179194 167.337499423735 -BARI1 14.490420293855 10.7374273435078 16.9962341193673 15.6045973977535 -Invader5_LTR 1.84067501030051 1.97568663120544 2.96896241578821 3.10153488651001 -DM176_LTR 21.9314469312401 28.3468081868607 38.6825682868637 42.2584128286989 -DOC3_DM 433.420219978632 447.106474583666 513.802611694594 516.550943051722 -Copia1-LTR_DM 23.4979788549001 33.4148738929964 33.1749278633726 27.4291991525729 -TOM_I-int 271.362492476004 291.199029555932 110.281893792249 111.994486292572 -NOF_FB 8.92923196486203 5.41166338112795 54.7321767084434 46.5230232976501 -Chimpo_I-int 53.4970651929892 31.7827849367832 55.4206317613798 51.369171557822 -DIVER_I-int 968.978321379896 1009.40406970848 567.028792974739 757.307588617061 +SSU-rRNA_Dme 389.988122395158 328.307578455096 306.061299471036 201.260537244939 +SSU-rRNA_Hsa 22075.2937251301 25925.561270609 13684.9804569472 8340.22115575582 +Stalker2_I-int 429.46472687139 413.519801853174 527.184456786045 604.508533973842 +Stalker2_LTR 30.9390054922851 30.5801930743103 31.238648026989 32.5661163083551 +Stalker3_LTR 21.2656708636846 20.1863634057947 25.5158653994552 21.2745908621546 +STALKER4_I-int 285.382953192761 269.036979518932 267.077532098513 278.217371616468 +STALKER4_LTR 79.8931281066602 68.9772332546943 55.5927455246139 58.6383939480799 +TABOR_I-int 215.554792695617 317.054754599099 169.833255871247 149.309827895896 +TABOR_LTR 17.3493410545346 7.55914884982952 16.5229212704735 13.2299847502693 +TAHRE 149.055512536249 121.719476366005 196.209690086873 189.678242903128 +TART_B1 524.083255060455 437.142142008891 1086.38207353363 1042.55187521078 +TART-A 199.419513881919 156.766439215214 159.076145669116 165.156732706658 +TC1_DM 102.529514403547 127.560636840873 79.1723310876855 94.9845058993691 +TC1-2_DM 173.806716930078 196.451970676819 163.809274158054 191.325933311586 TIRANT_I-int 907.2178002896 1093.32780182534 469.741488306664 414.781829588112 -Gypsy2_LTR 34.0329060415136 21.4748546870157 20.6106231472833 23.5038190618337 -FB4_DM 307.040257037361 287.591253968514 307.610323340143 336.274227773327 -GTWIN_LTR 99.2006340657698 80.5736547856828 25.7310076034978 22.6315123750027 -Invader6_LTR 12.218949004548 12.5413151372172 27.9254580847325 28.4953517698107 -Gypsy8_I-int 163.545932830104 107.116575178834 206.923771848195 197.868233462818 -G_DM 428.759787505743 393.591136703623 383.168265399913 389.388012704811 -TRANSPAC_LTR 57.0609253193157 84.0955309543534 23.1493011549863 26.896122843954 -FUSHI_DM 0 0 0 0 +TIRANT_LTR 126.301636345088 137.095472321908 58.9919923484874 61.9822362475985 +TLD2 1.2923888370195 0.0858994187480627 2.79684865255411 0.823845204229221 +TOM_I-int 271.362492476004 291.199029555932 110.281893792249 111.994486292572 +Transib-N1_DM 14.333767101489 11.1669244372481 13.2527597690256 17.9792100452377 +TRANSIB1 48.1316933544536 24.8249320181901 89.5852137633485 102.544497185237 +TRANSIB2 131.471191693166 127.474737422125 137.561925264854 149.067520482887 +TRANSIB3 70.5722631608832 63.6514692923144 50.9456739172933 54.8583983051458 +TRANSIB4 14.255440505306 13.1426110684536 27.3230599134132 27.6715065655815 Transib5 38.1058890430296 28.1750093493646 48.3209390279733 46.7653307106587 -MuDR-1_DEl 1.253225538928 0.343597674992251 0.258170644851148 0.43615334341547 -Mariner2_DM 42.9229747082841 79.542861760706 86.5301944659432 77.1022188193348 -DOC5_DM 70.2197934780597 64.5963628985431 130.67737473549 105.791416519552 -TC1_DM 102.529514403547 127.560636840873 79.1723310876855 94.9845058993691 -Gypsy9_LTR 2.42812448167301 0.687195349984501 2.19445048123476 2.03538226927219 -DMRP1 11.5531729369925 12.369516299721 11.2734514918335 11.0007565505902 -Gypsy10_I-int 87.5691345325943 79.6287611794541 97.1582193456488 93.5306614213175 -Gypsy4_LTR 15.273686255685 18.7260732870777 11.7897927815358 9.40152762473347 -DM297_LTR 239.992690704713 216.122937570126 64.0693483638933 71.6260712853405 -ACCORD2_I-int 89.5272994371693 103.079302497675 126.245445332212 119.118324235025 -Invader1_LTR 98.8873276810378 163.466593877563 143.973162945324 93.5791229039192 -BEL_LTR 36.3043773308206 51.9691483425779 37.6498857074591 41.5799520722748 -IVK_DM 118.468976726788 151.956071765323 144.102248267749 141.555990679621 -M4DM 73.6270004120202 78.8556664107215 74.3101172763222 79.9614462928362 -FW2_DM 694.091132075657 761.412447782827 612.466826468541 671.046149586002 -Copia2_I-int 141.536159302681 162.521700271335 181.493963330357 167.434422388939 -MDG1_LTR 25.4561437594751 24.1377366682056 29.6896241578821 28.2045828742004 -Gypsy12_LTR 296.544493148839 230.210442244808 270.734949567238 287.5704377586 -Gypsy7_I-int 45.5077523823231 63.7373687110625 54.0437216555071 48.8976359451344 -FROGGER_I-int 42.1005454483626 46.9010826364422 69.3188181425333 65.9560778209394 -Gypsy_I-int 943.130544639506 958.723412647127 293.540023195756 273.031992978084 -5S_DM 247.942840217287 356.138990129468 271.810660587451 503.611727197063 -GTWIN_I-int 296.387839956473 251.685296931824 234.418945524843 244.924333069087 -CIRCE 143.964283784354 134.862087434458 162.088136525713 161.037506685512 -DIVER2_LTR 25.3778171632921 20.615860499535 34.1215535611601 25.9268931919196 -POGO 113.926034148174 88.6482001480007 104.43002584229 120.766014643484 -Gypsy6A_LTR 31.0564953865596 18.8119727058257 26.5485479788598 27.7684295307849 -MAX_I-int 349.101639187632 335.437230211185 533.337523821664 445.894101418416 -ROOA_LTR 17.0360346698026 23.7082395744653 17.2113763234099 23.4068960966302 -DM176_I-int 185.08574678043 197.396864283048 156.064154812519 136.322150558635 -Copia2_LTR_DM 29.2549836743506 39.5137326241088 38.3383407603955 23.5522805444354 -DM297_I-int 3226.54663986442 3668.33467763602 509.327653850507 558.760894397819 -IDEFIX_I-int 282.837338816814 282.265490006134 266.475133927194 268.815843991735 -Jockey2 71.3946924208047 65.2835582485276 76.1603402310888 76.9568343715296 -TC1-2_DM 173.806716930078 196.451970676819 163.809274158054 191.325933311586 -DMRPR 8.65508887822152 11.6823209497365 5.50764042349117 9.06229724652144 +TRANSPAC_I-int 1115.13574985737 1439.67425821753 416.257136381668 726.049932338953 +TRANSPAC_LTR 57.0609253193157 84.0955309543534 23.1493011549863 26.896122843954 +XDMR 69.3582009200467 77.5671751295006 53.7425225698474 69.7845349464752 +XDMR_DM 158.572193972484 136.322377553175 142.725338161877 209.741296700239 +ZAM_I-int 270.070103638985 248.421119019397 220.692872906923 214.490521995208 +ZAM_LTR 14.7645633804955 10.1361314122714 11.1443661694079 10.9038335853868
--- 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 @@ -1,3 +1,3 @@ Low_complexity 2.0 +Simple_repeat 121.0 rRNA 111.0 -Simple_repeat 121.0
--- 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 @@ -1,3 +1,3 @@ Low_complexity 2.0 +Simple_repeat 121.0 rRNA 111.0 -Simple_repeat 121.0
--- 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 @@ -1,3 +1,3 @@ Low_complexity 0.0 +Simple_repeat 98.0 rRNA 772.0 -Simple_repeat 98.0
--- 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 @@ -1,3 +1,3 @@ Low_complexity 0.0 +Simple_repeat 98.0 rRNA 772.0 -Simple_repeat 98.0
--- 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 @@ -1,1 +1,2 @@ +# Total reads aligned to repeated sequences 15862067
--- 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 @@ -1,1 +1,2 @@ +# Total reads aligned to repeated sequences 28421096
--- 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 @@ -1,1 +1,2 @@ +# Total reads aligned to repeated sequences 10808170
--- 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 @@ -1,1 +1,2 @@ +# Total reads aligned to repeated sequences 29256707
--- 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 @@ -1,1 +1,3 @@ +# Total reads aligned to repeated sequences + 2510
--- 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 @@ -52,9 +52,9 @@ TAHRE -0.509503033739914 0.0198535740576507 LINE Jockey Gypsy8_I-int -0.578276897527121 0.0248976847994314 LTR Gypsy BLASTOPIA_I-int 0.796987753936179 0.0301824235833205 LTR Gypsy -Gypsy11_I-int -0.734634622561586 0.0432538714324547 LTR Gypsy +DM176_LTR -0.691384671506076 0.0432538714324547 LTR Gypsy DMRT1A -0.509608409844153 0.0432538714324547 LINE R1 -DM176_LTR -0.691384671506076 0.0432538714324547 LTR Gypsy +Gypsy11_I-int -0.734634622561586 0.0432538714324547 LTR Gypsy QUASIMODO2-I_DM 0.470057940126177 0.044414105251971 LTR Gypsy MuDR-1_DEl 1.35524442785064 0.0532319546519159 DNA MULE-NOF DM1731_LTR 0.752238181600754 0.0540130070646644 LTR Copia @@ -71,14 +71,14 @@ BATUMI_LTR -0.625598883331715 0.112325719453317 LTR Pao Gypsy2-I_DM 0.418860685191156 0.127538985839499 LTR Gypsy Invader3_LTR -0.553726127316243 0.130228544874336 LTR Gypsy +MDG3_I-int 0.417195433411295 0.130837858091619 LTR Gypsy SSU-rRNA_Dme 0.50182621141568 0.130837858091619 rRNA rRNA -MDG3_I-int 0.417195433411295 0.130837858091619 LTR Gypsy G5A_DM -0.468375220785066 0.142388172856184 LINE Jockey S2_DM -0.576444154651051 0.154380925206633 DNA TcMar-Tc1 Stalker2_I-int -0.424817076156048 0.157921464286182 LTR Gypsy -R1-2_DM -0.611853226580459 0.158635278613665 LINE R1 BLOOD_LTR 0.494999752604753 0.158635278613665 LTR Gypsy Invader5_LTR -0.675984091871337 0.158635278613665 LTR Gypsy +R1-2_DM -0.611853226580459 0.158635278613665 LINE R1 Transib5 -0.51646991193603 0.158635278613665 DNA CMC-Transib TLD2 -1.24823548505769 0.158665416598185 LTR Gypsy TC1_DM 0.400572910860442 0.167626897114732 DNA TcMar-Tc1 @@ -92,53 +92,53 @@ POGON1 0.482507112501569 0.255779427421414 DNA TcMar-Pogo HOBO -0.283220815078204 0.273166685685814 DNA hAT-hobo BS3_DM -0.418041606433149 0.277910060681416 LINE Jockey +Gypsy9_I-int -0.437336296478435 0.280951304168472 LTR Gypsy P-1_DY 0.969417874734635 0.280951304168472 DNA P -Gypsy9_I-int -0.437336296478435 0.280951304168472 LTR Gypsy Bica_I-int -0.363151852276854 0.287621291763315 LTR Gypsy DMCR1A -0.342108879038489 0.320538100201906 LINE CR1 Mariner2_DM -0.422114252836712 0.320538100201906 DNA TcMar-Tc1 +Gypsy7_LTR -0.484940393339899 0.322658401361327 LTR Gypsy TRANSIB3 0.344232145502121 0.322658401361327 DNA CMC-Transib -Gypsy7_LTR -0.484940393339899 0.322658401361327 LTR Gypsy DMRPR 0.474671090698546 0.369600785239272 Unknown Unknown DIVER2_LTR -0.381362071713278 0.384462351162869 LTR Pao Gypsy1-LTR_DM 0.341547880045558 0.384860099197221 LTR Gypsy +DOC4_DM 0.362114244909638 0.389414554540185 LINE Jockey SSU-rRNA_Cel 0.268693361351043 0.389414554540185 rRNA rRNA -DOC4_DM 0.362114244909638 0.389414554540185 LINE Jockey ZAM_I-int 0.25296287202699 0.397202788288282 LTR Gypsy XDMR_DM -0.256211211677393 0.408914532732159 Unknown Unknown Chimpo_LTR -0.460515218470088 0.409319591327129 LTR Gypsy +5S_DM -0.36064468671157 0.412039231991319 RNA RNA +BLOOD_I-int 0.301193505006723 0.412039231991319 LTR Gypsy +CIRCE -0.21220098912431 0.412039231991319 LTR Gypsy DOC2_DM -0.219218822289782 0.412039231991319 LINE Jockey -PROTOP -0.21894181311432 0.412039231991319 DNA P -HETA -0.298692871636692 0.412039231991319 LINE Jockey HELENA_RT 0.306716860759321 0.412039231991319 LINE Jockey +HETA -0.298692871636692 0.412039231991319 LINE Jockey Invader2_LTR -0.349451178427879 0.412039231991319 LTR Gypsy -BLOOD_I-int 0.301193505006723 0.412039231991319 LTR Gypsy -5S_DM -0.36064468671157 0.412039231991319 RNA RNA -CIRCE -0.21220098912431 0.412039231991319 LTR Gypsy +PROTOP -0.21894181311432 0.412039231991319 DNA P ACCORD2_LTR -0.373877436518785 0.415323684742582 LTR Gypsy BARI1 -0.361825471165769 0.439062969216072 DNA TcMar-Tc1 Copia2_I-int -0.199651272204726 0.454016393978291 LTR Copia Chouto_LTR -0.42256718750228 0.457631460799645 LTR Gypsy S_DM 0.193275098711318 0.466588891242574 DNA TcMar-Tc1 +Chimpo_I-int -0.3198026895528 0.469668398060595 LTR Gypsy +Gypsy2_LTR 0.337405927915915 0.469668398060595 LTR Gypsy Gypsy6_I-int 0.244887845096584 0.469668398060595 LTR Gypsy NOMAD_LTR -0.310707505731374 0.469668398060595 LTR Gypsy -Chimpo_I-int -0.3198026895528 0.469668398060595 LTR Gypsy -Gypsy2_LTR 0.337405927915915 0.469668398060595 LTR Gypsy DIVER2_I-int -0.217400353167491 0.482143273163041 LTR Pao DOC3_DM -0.226748306440889 0.495640056965812 LINE Jockey XDMR 0.249633734746355 0.503551868695532 Unknown Unknown ROO_I-int 0.276608752749181 0.50509162020251 LTR Pao BURDOCK_LTR 0.32676718204459 0.510777537217992 LTR Gypsy BEL_I-int 0.237362494177496 0.533794803142695 LTR Pao +Invader6_I-int -0.205266937253198 0.533794803142695 LTR Gypsy ROOA_I-int -0.194233478923581 0.533794803142695 LTR Pao -Invader6_I-int -0.205266937253198 0.533794803142695 LTR Gypsy +DIVER_LTR 0.271030983517942 0.536617484807809 LTR Pao DOC6_DM 0.222079405295424 0.536617484807809 LINE Jockey -DIVER_LTR 0.271030983517942 0.536617484807809 LTR Pao GTWIN_I-int 0.193808394449743 0.536617484807809 LTR Gypsy MAX_LTR -0.257749452683052 0.540151898310569 LTR Pao -Transib-N1_DM -0.285359544492984 0.568470618173646 DNA CMC-Transib +Gypsy10_I-int -0.188834668589015 0.568470618173646 LTR Gypsy Gypsy11_LTR -0.304519901682671 0.568470618173646 LTR Gypsy -Gypsy10_I-int -0.188834668589015 0.568470618173646 LTR Gypsy +Transib-N1_DM -0.285359544492984 0.568470618173646 DNA CMC-Transib Gypsy8_LTR -0.22930840819102 0.572155988619062 LTR Gypsy MDG1_LTR -0.222278232633914 0.598330807400594 LTR Gypsy ARS406_DM -0.253969785738388 0.616310720408007 Unknown Unknown @@ -146,48 +146,48 @@ Invader3_I-int -0.138005789457227 0.63087021446348 LTR Gypsy FW2_DM 0.18134923098773 0.631976090641453 LINE Jockey Gypsy9_LTR -0.341386719736692 0.637388403082853 LTR Gypsy +PROTOP_A 0.129470019526978 0.641582941744779 DNA P TART-A 0.137000662462686 0.641582941744779 LINE Jockey -PROTOP_A 0.129470019526978 0.641582941744779 DNA P +Invader2_I-int -0.151224307192946 0.653366733778121 LTR Gypsy MDG3_LTR -0.188668582948884 0.653366733778121 LTR Gypsy -Invader2_I-int -0.151224307192946 0.653366733778121 LTR Gypsy Jockey2 -0.162959614427421 0.6545684300628 LINE Jockey POGO -0.150727724968995 0.655487951511946 DNA TcMar-Pogo Baggins1 -0.134826103211095 0.693165877070164 LINE LOA -Stalker3_LTR -0.174018068430168 0.707635948527852 LTR Gypsy Bica_LTR -0.203027970314789 0.707635948527852 LTR Gypsy HMSBEAGLE_I-int 0.13884460350775 0.707635948527852 LTR Gypsy +Stalker3_LTR -0.174018068430168 0.707635948527852 LTR Gypsy +NTS_DM -0.176552072990723 0.7126900116144 Other Other TABOR_LTR -0.243243320673685 0.7126900116144 LTR Gypsy -NTS_DM -0.176552072990723 0.7126900116144 Other Other ZAM_LTR 0.185889162361338 0.717882303973929 LTR Gypsy G5_DM -0.112256553949312 0.728328879400999 LINE Jockey -QUASIMODO_I-int 0.126271255526405 0.756425760962704 LTR Gypsy +BEL_LTR 0.152542861711851 0.756425760962704 LTR Pao FB4_DM -0.114616335459739 0.756425760962704 DNA TcMar-Tc1 Invader1_LTR 0.141219962488351 0.756425760962704 LTR Gypsy -BEL_LTR 0.152542861711851 0.756425760962704 LTR Pao +QUASIMODO_I-int 0.126271255526405 0.756425760962704 LTR Gypsy DMRT1B -0.111235216287692 0.760051744799183 LINE R1 NOMAD_I-int -0.137546703453753 0.760051744799183 LTR Gypsy LmeSINE1c -0.228543531933743 0.760296029745035 SINE tRNA-Deu-L2 +Copia2_LTR_DM 0.147979193864449 0.76240178289376 LTR Copia Gypsy10_LTR -0.154651074858764 0.76240178289376 LTR Gypsy QUASIMODO2-LTR_DM -0.155430480903998 0.76240178289376 LTR Gypsy -Copia2_LTR_DM 0.147979193864449 0.76240178289376 LTR Copia BS4_DM -0.253251631796478 0.81092436860891 LINE Jockey G_DM 0.0902785903431559 0.81092436860891 LINE Jockey IVK_DM -0.0807211765160779 0.818709085450591 LINE I +Gypsy12_LTR -0.0832045482918072 0.835273508731359 LTR Gypsy Gypsy5_I-int -0.0774807293903186 0.835273508731359 LTR Gypsy -Gypsy12_LTR -0.0832045482918072 0.835273508731359 LTR Gypsy Gypsy6A_LTR -0.116239966704279 0.835273508731359 LTR Gypsy IDEFIX_I-int 0.0781972363147815 0.835273508731359 LTR Gypsy +DMRP1 0.100504519100353 0.846311908195535 Unknown Unknown PROTOP_B -0.0745501769371703 0.846311908195535 DNA P -DMRP1 0.100504519100353 0.846311908195535 Unknown Unknown Copia1-LTR_DM -0.0961752276665428 0.850550157756311 LTR Copia TC1-2_DM 0.0595720035046981 0.853067020850826 DNA TcMar-Tc1 +Gypsy7_I-int 0.0826410967604942 0.861339242519926 LTR Gypsy LSU-rRNA_Cel -0.0920825033469626 0.861339242519926 rRNA rRNA -Gypsy7_I-int 0.0826410967604942 0.861339242519926 LTR Gypsy -Gypsy5_LTR -0.0710979993807782 0.905487490633946 LTR Gypsy +DMLTR5 0.0726894766496021 0.905487490633946 LTR Gypsy +Gypsy2-LTR_DM 0.0652192786223383 0.905487490633946 LTR Gypsy Gypsy4_I-int -0.0516274039610208 0.905487490633946 LTR Gypsy +Gypsy5_LTR -0.0710979993807782 0.905487490633946 LTR Gypsy QUASIMODO_LTR -0.0643467685962964 0.905487490633946 LTR Gypsy -Gypsy2-LTR_DM 0.0652192786223383 0.905487490633946 LTR Gypsy -DMLTR5 0.0726894766496021 0.905487490633946 LTR Gypsy Stalker2_LTR -0.0523210063310555 0.917308330496379 LTR Gypsy ROVER-I_DM -0.0408110836395496 0.922716163337686 LTR Gypsy MDG1_I-int -0.0411424164719924 0.937452811422426 LTR Gypsy @@ -196,10 +196,10 @@ BARI_DM 0.0372716083617889 0.949850971355763 DNA TcMar-Tc1 Gypsy2_I-int -0.0261599267227275 0.951965771983562 LTR Gypsy DMTOM1_LTR 0.0349640382618226 0.953829042793374 LTR Gypsy +Gypsy3_LTR -0.0298883238815861 0.957715681080923 LTR Gypsy IDEFIX_LTR 0.0219961145617681 0.957715681080923 LTR Gypsy +MINOS 0.0330479824589295 0.957715681080923 DNA TcMar-Tc1 STALKER4_I-int 0.0241275307638275 0.957715681080923 LTR Gypsy -Gypsy3_LTR -0.0298883238815861 0.957715681080923 LTR Gypsy -MINOS 0.0330479824589295 0.957715681080923 DNA TcMar-Tc1 G2_DM 0.0226097987515835 0.962242582647045 LINE Jockey Copia1-I_DM 0.0124236833262227 0.963045943681341 LTR Copia Invader4_LTR 0.016495431966038 0.963045943681341 LTR Gypsy