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Re: [MUMmer-help] mapview fails to generate output
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From: John F W. <jwo...@bi...> - 2014-05-22 19:56:01
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Thank you for the prompt reply. Since I am aligning contigs from draft assemblies, it looks like mummerplot may do the job nicely. Thank you for the help. On Thu, May 22, 2014 at 2:33 PM, Adam Phillippy <aph...@gm...>wrote: > Hi John, > Sorry, the developer of MapView moved on long ago and I can no longer > offer support for it. I plan on removing it from the next release. As for > your current version, it's provided as is, but I'd suggest looking for > alternative visualization options such as mummerplot; or if you're doing > read mapping, maybe an assembly viewer like Tablet or IGV. > > Best, > -Adam > > > > On Thu, May 22, 2014 at 12:17 PM, John F Wolters <jwo...@bi...>wrote: > >> Hello, >> >> I've been using mapview to generate files to visualize the alignments in >> the following manner: >> >> mapview -n 1 -f pdf filename.coords >> >> However, in several recent instances, mapview produces no messages, and >> produces no output files. >> >> Nothing appears in response to running the command at all. >> >> Any help would be greatly appreciated. >> >> Here is an example of a coords file used that causes this problem: >> >> /import/linux/home/jwolter1/Strains/C2/Assembly/Mira_PcBio_CCS/Quiver/Joining_unitigs/C2_joined.fasta >> /import/linux/home/jwolter1/Strains/C2/Assembly/Mira_PcBio_CCS/Quiver/Joining_unitigs/C2.polished_assembly.fasta >> NUCMER >> >> [S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] >> | [LEN R] [LEN Q] | [COV R] [COV Q] | [TAGS] >> >> =============================================================================================================================== >> 1 17884 | 17910 1 | 17884 17910 | 99.83 >> | 76481 70521 | 23.38 25.40 | S.cerevisiae unitig_1|quiver >> 8075 10672 | 1 2600 | 2598 2600 | 99.69 >> | 76481 5150 | 3.40 50.49 | S.cerevisiae unitig_3|quiver >> 8131 10669 | 5150 2609 | 2539 2542 | 99.45 >> | 76481 5150 | 3.32 49.36 | S.cerevisiae unitig_3|quiver >> 8935 9164 | 6863 7101 | 230 239 | 84.43 >> | 76481 15910 | 0.30 1.50 | S.cerevisiae unitig_0|quiver >> 9012 9509 | 42308 42800 | 498 493 | 82.58 >> | 76481 70521 | 0.65 0.70 | S.cerevisiae unitig_1|quiver >> 9016 9436 | 8918 9335 | 421 418 | 85.25 >> | 76481 15910 | 0.55 2.63 | S.cerevisiae unitig_0|quiver >> 14381 25322 | 13325 2386 | 10942 10940 | 99.60 >> | 76481 15910 | 14.31 68.76 | S.cerevisiae unitig_0|quiver >> 14442 16994 | 13365 15910 | 2553 2546 | 98.87 >> | 76481 15910 | 3.34 16.00 | S.cerevisiae unitig_0|quiver >> 18185 18722 | 48779 49345 | 538 567 | 83.42 >> | 76481 70521 | 0.70 0.80 | S.cerevisiae unitig_1|quiver >> 18371 18787 | 8469 8886 | 417 418 | 85.19 >> | 76481 70521 | 0.55 0.59 | S.cerevisiae unitig_1|quiver >> 18371 18787 | 1361 944 | 417 418 | 85.19 >> | 76481 5150 | 0.55 8.12 | S.cerevisiae unitig_3|quiver >> 18371 18787 | 3847 4264 | 417 418 | 85.19 >> | 76481 5150 | 0.55 8.12 | S.cerevisiae unitig_3|quiver >> 20602 20836 | 8738 8960 | 235 223 | 84.45 >> | 76481 70521 | 0.31 0.32 | S.cerevisiae unitig_1|quiver >> 20602 20836 | 1092 870 | 235 223 | 84.45 >> | 76481 5150 | 0.31 4.33 | S.cerevisiae unitig_3|quiver >> 20602 20836 | 4116 4338 | 235 223 | 84.45 >> | 76481 5150 | 0.31 4.33 | S.cerevisiae unitig_3|quiver >> 20603 20836 | 49255 49485 | 234 231 | 84.03 >> | 76481 70521 | 0.31 0.33 | S.cerevisiae unitig_1|quiver >> 22865 25314 | 1 2451 | 2450 2451 | 99.96 >> | 76481 15910 | 3.20 15.41 | S.cerevisiae unitig_0|quiver >> 23744 27089 | 1 3351 | 3346 3351 | 99.85 >> | 76481 3351 | 4.37 100.00 | S.cerevisiae unitig_2|quiver >> 25448 71629 | 68349 22100 | 46182 46250 | 99.77 >> | 76481 70521 | 60.38 65.58 | S.cerevisiae unitig_1|quiver >> 25524 27721 | 68323 70521 | 2198 2199 | 98.55 >> | 76481 70521 | 2.87 3.12 | S.cerevisiae unitig_1|quiver >> 44253 44984 | 8814 9521 | 732 708 | 82.75 >> | 76481 15910 | 0.96 4.45 | S.cerevisiae unitig_0|quiver >> 50957 51450 | 8392 8890 | 494 499 | 82.78 >> | 76481 70521 | 0.65 0.71 | S.cerevisiae unitig_1|quiver >> 50957 51450 | 1438 940 | 494 499 | 82.78 >> | 76481 5150 | 0.65 9.69 | S.cerevisiae unitig_3|quiver >> 50957 51450 | 3770 4268 | 494 499 | 82.78 >> | 76481 5150 | 0.65 9.69 | S.cerevisiae unitig_3|quiver >> 70145 72606 | 1 2466 | 2462 2466 | 99.68 >> | 76481 4897 | 3.22 50.36 | S.cerevisiae unitig_6|quiver >> 70155 72611 | 4897 2440 | 2457 2458 | 99.55 >> | 76481 4897 | 3.21 50.19 | S.cerevisiae unitig_6|quiver >> 73234 76481 | 21163 17910 | 3248 3254 | 98.22 >> | 76481 70521 | 4.25 4.61 | S.cerevisiae unitig_1|quiver >> 73293 75543 | 3908 1658 | 2251 2251 | 99.60 >> | 76481 3908 | 2.94 57.60 | S.cerevisiae unitig_4|quiver >> 73355 75773 | 4813 2399 | 2419 2415 | 99.50 >> | 76481 4813 | 3.16 50.18 | S.cerevisiae unitig_5|quiver >> 73358 75773 | 1 2414 | 2416 2414 | 99.55 >> | 76481 4813 | 3.16 50.16 | S.cerevisiae unitig_5|quiver >> 73850 75526 | 1 1683 | 1677 1683 | 98.40 >> | 76481 3908 | 2.19 43.07 | S.cerevisiae unitig_4|quiver >> 74500 74961 | 20981 21367 | 462 387 | 81.90 >> | 76481 70521 | 0.60 0.55 | S.cerevisiae unitig_1|quiver >> >> >> >> ------------------------------------------------------------------------------ >> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE >> Instantly run your Selenium tests across 300+ browser/OS combos. >> Get unparalleled scalability from the best Selenium testing platform >> available >> Simple to use. 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