Mercurial > repos > iuc > pairtools_sort
changeset 2:0f35bc206bbb draft
planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
| author | iuc |
|---|---|
| date | Fri, 05 Apr 2024 10:29:00 +0000 |
| parents | ad73120a6ed7 |
| children | d392cfd963f4 |
| files | test-data/output_pairs_split.bam test-data/output_pairs_split.pairs |
| diffstat | 2 files changed, 842 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_pairs_split.pairs Fri Apr 05 10:29:00 2024 +0000 @@ -0,0 +1,842 @@ +## pairs format v1.0.0 +#sorted: chr1-chr2-pos1-pos2 +#shape: upper triangle +#genome_assembly: unknown +#chromsize: chrI 230218 +#chromsize: chrII 813184 +#chromsize: chrIII 316620 +#chromsize: chrIV 1531933 +#chromsize: chrV 576874 +#chromsize: chrVI 270161 +#chromsize: chrVII 1090940 +#chromsize: chrVIII 562643 +#chromsize: chrIX 439888 +#chromsize: chrX 745751 +#chromsize: chrXI 666816 +#chromsize: chrXII 1078177 +#chromsize: chrXIII 924431 +#chromsize: chrXIV 784333 +#chromsize: chrXV 1091291 +#chromsize: chrXVI 948066 +#chromsize: chrM 85779 +#samheader: @SQ SN:chrI LN:230218 +#samheader: @SQ SN:chrII LN:813184 +#samheader: @SQ SN:chrIII LN:316620 +#samheader: @SQ SN:chrIV LN:1531933 +#samheader: @SQ SN:chrIX LN:439888 +#samheader: @SQ SN:chrM LN:85779 +#samheader: @SQ SN:chrV LN:576874 +#samheader: @SQ SN:chrVI LN:270161 +#samheader: @SQ SN:chrVII LN:1090940 +#samheader: @SQ SN:chrVIII LN:562643 +#samheader: @SQ SN:chrX LN:745751 +#samheader: @SQ SN:chrXI LN:666816 +#samheader: @SQ SN:chrXII LN:1078177 +#samheader: @SQ SN:chrXIII LN:924431 +#samheader: @SQ SN:chrXIV LN:784333 +#samheader: @SQ SN:chrXV LN:1091291 +#samheader: @SQ SN:chrXVI LN:948066 +#samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz +#samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa VN:1.0.2 +#samheader: @PG ID:pairtools_sort-1.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-1.2 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-1.3 VN:1.0.2 +#samheader: @PG ID:pairtools_split-1.5 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpnt_hb134/files/7/4/2/dataset_7420fb9f-e3dd-4326-8cef-1e023c2b5e85.dat --output-pairs /tmp/tmpnt_hb134/job_working_directory/000/2/outputs/dataset_ba891b58-22e9-49f5-83f9-063b56eda346.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-1.4 VN:1.0.3 +#samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz +#samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-2CCE5976 VN:1.0.2 +#samheader: @PG ID:pairtools_sort-2.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-2.2 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-2.3 VN:1.0.2 +#samheader: @PG ID:pairtools_split-2.5 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpnt_hb134/files/7/4/2/dataset_7420fb9f-e3dd-4326-8cef-1e023c2b5e85.dat --output-pairs /tmp/tmpnt_hb134/job_working_directory/000/2/outputs/dataset_ba891b58-22e9-49f5-83f9-063b56eda346.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-2.4 VN:1.0.3 +#samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz +#samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-3CAFD9D9 VN:1.0.2 +#samheader: @PG ID:pairtools_sort-3.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-3.2 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-3.3 VN:1.0.2 +#samheader: @PG ID:pairtools_split-3.5 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpnt_hb134/files/7/4/2/dataset_7420fb9f-e3dd-4326-8cef-1e023c2b5e85.dat --output-pairs /tmp/tmpnt_hb134/job_working_directory/000/2/outputs/dataset_ba891b58-22e9-49f5-83f9-063b56eda346.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-3.4 VN:1.0.3 +#samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz +#samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam +#samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:samtools VN:1.0.2 +#samheader: @PG ID:pairtools_sort-4.4 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-4.3 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-4.4 VN:1.0.2 +#samheader: @PG ID:pairtools_split-4.6 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpnt_hb134/files/7/4/2/dataset_7420fb9f-e3dd-4326-8cef-1e023c2b5e85.dat --output-pairs /tmp/tmpnt_hb134/job_working_directory/000/2/outputs/dataset_ba891b58-22e9-49f5-83f9-063b56eda346.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-4.5 VN:1.0.3 +#columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type +HWI-ST560:29:B0A7LABXX:2:1101:15566:24141 chrI 3199 chrI 3399 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:18861:21891 chrI 35431 chrI 35703 + - UU +HWUSI-EAS1533_0033_FC:1:1:2785:5545 chrI 50947 chrI 51201 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:19121:14576 chrI 85708 chrI 85934 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:14350:22419 chrI 94155 chrI 94554 - + UU +HWUSI-EAS1533_0033_FC:1:1:1548:16444 chrI 119190 chrI 121691 + - UU +HWUSI-EAS1533_0033_FC:1:1:2382:14559 chrI 133796 chrI 153772 + - UU +HWUSI-EAS1533_0033_FC:1:1:1160:9629 chrI 10807 chrX 448620 + + UU +HWI-ST560:29:B0A7LABXX:2:1101:1226:5768 chrI 34588 chrX 518111 - + UU +HWUSI-EAS1533_0033_FC:1:1:2020:12833 chrI 79395 chrXV 383129 - + UU +HWUSI-EAS1533_0033_FC:1:1:1238:11260 chrII 11700 chrII 42692 - - UU +HWUSI-EAS1533_0033_FC:1:1:1585:7670 chrII 20403 chrII 26681 + + UU +HWI-ST560:29:B0A7LABXX:2:1101:4374:5551 chrII 22903 chrII 23092 + - UU +HWUSI-EAS1533_0033_FC:1:1:1502:18166 chrII 53074 chrII 53324 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:2416:5458 chrII 55526 chrII 55730 + - UU +HWUSI-EAS1533_0033_FC:1:1:2229:14691 chrII 56528 chrII 56789 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:9983:2230 chrII 69562 chrII 91521 - - UU +HWUSI-EAS1533_0033_FC:1:1:2771:20227 chrII 84449 chrII 114125 - - UU +HWUSI-EAS1533_0033_FC:1:1:1515:8375 chrII 126897 chrII 136056 - + UU +HWUSI-EAS1533_0033_FC:1:1:2262:14069 chrII 147635 chrII 147883 + - UU +HWUSI-EAS1533_0033_FC:1:1:2148:13704 chrII 178555 chrII 191157 - - UU +HWUSI-EAS1533_0033_FC:1:1:2951:12833 chrII 188963 chrII 189298 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:10119:22809 chrII 212558 chrII 212771 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:17198:12556 chrII 236553 chrII 236829 + - UU +HWUSI-EAS1533_0033_FC:1:1:2544:2469 chrII 250592 chrII 250768 + - UU +HWUSI-EAS1533_0033_FC:1:1:3025:9231 chrII 274855 chrII 283930 - + UU +HWUSI-EAS1533_0033_FC:1:1:1868:10767 chrII 276112 chrII 276329 + - UU +HWUSI-EAS1533_0033_FC:1:1:1410:21133 chrII 319176 chrII 319379 + - UU +HWUSI-EAS1533_0033_FC:1:1:1760:17314 chrII 327789 chrII 328642 - + UU +HWUSI-EAS1533_0033_FC:1:1:3052:7878 chrII 329706 chrII 396585 - - UU +HWUSI-EAS1533_0033_FC:1:1:2308:7870 chrII 364961 chrII 365268 - - UU +HWUSI-EAS1533_0033_FC:1:1:1151:13110 chrII 401039 chrII 401275 + - UU +HWUSI-EAS1533_0033_FC:1:1:1955:14706 chrII 408741 chrII 408965 + - UU +HWUSI-EAS1533_0033_FC:1:1:2734:12933 chrII 428609 chrII 428916 + - UU +HWUSI-EAS1533_0033_FC:1:1:1776:7586 chrII 446926 chrII 447223 + - UU +HWUSI-EAS1533_0033_FC:1:1:2208:18926 chrII 469836 chrII 470147 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:9546:17730 chrII 482953 chrII 483180 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:18138:24479 chrII 493570 chrII 493844 + - UU +HWUSI-EAS1533_0033_FC:1:1:1831:12134 chrII 513405 chrII 513670 + - UU +HWUSI-EAS1533_0033_FC:1:1:2294:6569 chrII 556786 chrII 557020 + - UU +HWUSI-EAS1533_0033_FC:1:1:1513:12716 chrII 557332 chrII 557570 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:5620:23491 chrII 571962 chrII 572560 - + UU +HWUSI-EAS1533_0033_FC:1:1:2421:18479 chrII 594392 chrII 594631 + - UU +HWUSI-EAS1533_0033_FC:1:1:2741:20996 chrII 615832 chrII 616146 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:5221:14370 chrII 688819 chrII 691365 - - UU +HWI-ST560:29:B0A7LABXX:2:1101:20922:4151 chrII 736016 chrII 736278 + - UU +HWUSI-EAS1533_0033_FC:1:1:2796:9905 chrII 747450 chrII 783460 + - UU +HWUSI-EAS1533_0033_FC:1:1:2239:7598 chrII 768757 chrII 769022 + - UU +HWUSI-EAS1533_0033_FC:1:1:2507:2555 chrII 783305 chrII 783561 + - UU +HWUSI-EAS1533_0033_FC:1:1:2502:3756 chrII 784470 chrII 784699 + - UU +HWUSI-EAS1533_0033_FC:1:1:1596:14420 chrII 799994 chrII 800209 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:1565:22796 chrII 201163 chrIV 438170 - + UU +HWUSI-EAS1533_0033_FC:1:1:2343:7694 chrII 245030 chrIV 434994 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:13461:15948 chrII 342115 chrIV 773721 - + UU +HWUSI-EAS1533_0033_FC:1:1:2985:19319 chrII 624951 chrIV 125181 + + UU +HWI-ST560:29:B0A7LABXX:2:1101:19802:11576 chrII 52352 chrVII 288874 - + UU +HWUSI-EAS1533_0033_FC:1:1:1985:16682 chrII 57830 chrVII 289181 + - UU +HWUSI-EAS1533_0033_FC:1:1:1213:3863 chrII 187593 chrVII 105286 - + UU +HWUSI-EAS1533_0033_FC:1:1:2206:19226 chrII 303839 chrVII 733162 - - UU +HWUSI-EAS1533_0033_FC:1:1:2371:7513 chrII 743995 chrVII 97752 - + UU +HWUSI-EAS1533_0033_FC:1:1:1131:20871 chrII 772130 chrVIII 530331 + + UU +HWI-ST560:29:B0A7LABXX:2:1101:2317:19439 chrII 792092 chrX 177292 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:5417:14518 chrII 588576 chrXI 395885 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:11007:18781 chrII 99101 chrXIII 574066 - - UU +HWUSI-EAS1533_0033_FC:1:1:1395:5659 chrII 321669 chrXIII 710492 - - UU +HWUSI-EAS1533_0033_FC:1:1:2818:12967 chrII 556147 chrXIII 902866 - + UU +HWUSI-EAS1533_0033_FC:1:1:1785:1587 chrII 285155 chrXIV 365651 + - UU +HWUSI-EAS1533_0033_FC:1:1:1455:21045 chrII 515072 chrXIV 404330 - - UU +HWUSI-EAS1533_0033_FC:1:1:2276:7938 chrII 554117 chrXIV 779544 - - UU +HWI-ST560:29:B0A7LABXX:2:1101:13476:19994 chrII 565574 chrXIV 317889 + + UU +HWUSI-EAS1533_0033_FC:1:1:1326:21359 chrII 365178 chrXV 1030461 - - UU +HWUSI-EAS1533_0033_FC:1:1:1142:11756 chrII 565844 chrXV 328639 - - UU +HWUSI-EAS1533_0033_FC:1:1:1792:19745 chrII 280505 chrXVI 486977 - - UU +HWUSI-EAS1533_0033_FC:1:1:2530:4893 chrII 535816 chrXVI 428211 + - UU +HWUSI-EAS1533_0033_FC:1:1:2896:17270 chrII 605856 chrXVI 716198 - + UU +HWUSI-EAS1533_0033_FC:1:1:2501:6790 chrII 766938 chrXVI 473396 - - UU +HWUSI-EAS1533_0033_FC:1:1:2940:16409 chrIII 38831 chrIII 39104 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:2688:4346 chrIII 80421 chrIII 80656 + - UU +HWUSI-EAS1533_0033_FC:1:1:2557:18598 chrIII 123083 chrIII 123413 + - UU +HWUSI-EAS1533_0033_FC:1:1:2012:7457 chrIII 130481 chrIII 130777 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:14807:25132 chrIII 159701 chrIII 159947 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:9017:24534 chrIII 163831 chrIII 164111 + - UU +HWUSI-EAS1533_0033_FC:1:1:1090:13307 chrIII 174236 chrIII 174422 + - UU +HWUSI-EAS1533_0033_FC:1:1:2228:15729 chrIII 188089 chrIII 191523 + + UU +HWUSI-EAS1533_0033_FC:1:1:1723:8895 chrIII 195801 chrIII 196051 + - UU +HWUSI-EAS1533_0033_FC:1:1:2422:8313 chrIII 240411 chrIII 240608 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:10131:14407 chrIII 273871 chrIII 274141 + - UU +HWUSI-EAS1533_0033_FC:1:1:2377:16350 chrIII 285418 chrIII 285677 + - UU +HWI-ST560:29:B0A7LABXX:2:1101:11438:10695 chrIII 103251 chrV 106007 + - UU +HWUSI-EAS1533_0033_FC:1:1:2834:12779 chrIII 197857 chrV 257881 - + UU +HWUSI-EAS1533_0033_FC:1:1:1446:15290 chrIII 266982 chrVIII 288886 - + UU +HWUSI-EAS1533_0033_FC:1:1:1491:11863 chrIII 103479 chrX 431261 - + UU +HWUSI-EAS1533_0033_FC:1:1:1300:9019 chrIII 238125 chrX 34984 + + UU +HWI-ST560:29:B0A7LABXX:2:1101:10436:21845 chrIII 150902 chrXIII 131933 - - UU +HWI-ST560:29:B0A7LABXX:2:1101:14317:17406 chrIV 32639 chrIV 1252439 - - UU +HWUSI-EAS1533_0033_FC:1:1:2633:2423 chrIV 52140 chrIV 83162 + - UU 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