Mercurial > repos > fubar > microsatbed
diff seqrequester/README.md @ 1:1085e094cf5f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
| author | fubar |
|---|---|
| date | Sat, 13 Jul 2024 12:39:06 +0000 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqrequester/README.md Sat Jul 13 12:39:06 2024 +0000 @@ -0,0 +1,221 @@ +# seqrequester + +This is 'seqrequester', a tool for summarizing, extracting, generating and +modifying DNA sequences. + +## Installation +### Dependency +* GCC (tested with 11.3.0) +* git 2.25.1 or higher + +### Make +``` +git clone https://github.com/marbl/seqrequester.git +cd seqrequester/src +make -j 12 +``` + +## Summarizing + +The summarize mode will generate a table of Nx lengths, a lovely ASCII +plot of the histogram of sequence lengths, report GC content, and di- +and tri-nucleotide frequencies. + +It can optionally split sequences at N's before computing the length of a sequence. + +You can also get a simple histogram of the sequence lengths and the number of sequences +at each length, or just a simple list of all sequence lengths. + +It will, of course, read FASTA and FASTQ, uncompressed or compressed with +gzip, bzip2 or xz. + +Only one report is generated, regardless of how many sequence files are supplied. + + +``` +% seqrequester summarize +usage: seqrequester [mode] [options] [sequence_file ...] + +OPTIONS for summarize mode: + -size base size to use for N50 statistics + -1x limit NG table to 1x coverage + + -split-n split sequences at N bases before computing length + -simple output a simple 'length numSequences' histogram + -lengths output a list of the sequence lengths + + -assequences load data as complete sequences (for testing) + -asbases load data as blocks of bases (for testing) +``` + +``` +% seqrequester summarize /archive/mothra/FLX/*gz + +G=6462464889 sum of || length num +NG length index lengths || range seqs +----- ------------ --------- ------------ || ------------------- ------- +00010 652 801160 646246790 || 42-112 4768|- +00020 582 1862887 1292493013 || 113-183 16961|- +00030 555 3002684 1938739802 || 184-254 89381|-- +00040 538 4186751 2584986254 || 255-325 536862|-------- +00050 523 5405461 3231232945 || 326-396 1463599|-------------------- +00060 509 6657839 3877479295 || 397-467 1960924|--------------------------- +00070 488 7952426 4523725460 || 468-538 4616863|--------------------------------------------------------------- +00080 447 9329218 5169971940 || 539-609 2858982|---------------------------------------- +00090 389 10872299 5816218777 || 610-680 625376|--------- +00100 42 12803136 6462464889 || 681-751 252454|---- +001.000x 12803137 6462464889 || 752-822 134849|-- + || 823-893 78435|-- + || 894-964 47976|- + || 965-1035 30852|- + || 1036-1106 21127|- + || 1107-1177 14817|- + || 1178-1248 28461|- + || 1249-1319 4930|- + || 1320-1390 3655|- + || 1391-1461 2657|- + || 1462-1532 2120|- + || 1533-1603 1597|- + || 1604-1674 1268|- + || 1675-1745 953|- + || 1746-1816 766|- + || 1817-1887 573|- + || 1888-1958 443|- + || 1959-2029 344|- + || 2030-2100 1022|- + || 2101-2171 21|- + || 2172-2242 23|- + || 2243-2313 20|- + || 2314-2384 17|- + || 2385-2455 8|- + || 2456-2526 9|- + || 2527-2597 4|- + || 2598-2668 2|- + || 2669-2739 6|- + || 2740-2810 2|- + || 2811-2881 6|- + || 2882-2952 1|- + || 2953-3023 0| + || 3024-3094 0| + || 3095-3165 1|- + || 3166-3236 0| + || 3237-3307 0| + || 3308-3378 0| + || 3379-3449 1|- + || 3450-3520 0| + || 3521-3591 1|- + +--------------------- --------------------- ---------------------------------------------------------------------------------------------- + mononucleotide dinucleotide trinucleotide +--------------------- --------------------- ---------------------------------------------------------------------------------------------- + 1959571306 0.3032 A 665030151 0.1031 AA 237235545 0.0369 AAA 132268487 0.0205 AAC 136675399 0.0212 AAG 158473516 0.0246 AAT + 1247489432 0.1930 C 389352138 0.0604 AC 115665542 0.0180 ACA 87346626 0.0136 ACC 70986769 0.0110 ACG 114582435 0.0178 ACT + 1345011807 0.2081 G 397219280 0.0616 AG 121659180 0.0189 AGA 65811037 0.0102 AGC 102037062 0.0159 AGG 106854671 0.0166 AGT + 1910392344 0.2956 T 507072196 0.0786 AT 152454159 0.0237 ATA 89877335 0.0140 ATC 106195089 0.0165 ATG 158544503 0.0246 ATT + 380831936 0.0590 CA 132169383 0.0205 CAA 76839888 0.0119 CAC 67197045 0.0104 CAG 104566859 0.0162 CAT + --GC-- --AT-- 281892951 0.0437 CC 86178881 0.0134 CCA 65022575 0.0101 CCC 50576089 0.0079 CCG 79660170 0.0124 CCT + 40.12% 59.88% 208535008 0.0323 CG 60164341 0.0093 CGA 27649662 0.0043 CGC 52322022 0.0081 CGG 67296554 0.0105 CGT + 374626420 0.0581 CT 95122699 0.0148 CTA 75643338 0.0118 CTC 74304266 0.0115 CTG 129554475 0.0201 CTT + 383528854 0.0595 GA 128291282 0.0199 GAA 70244915 0.0109 GAC 88104990 0.0137 GAG 96746854 0.0150 GAT + 218253748 0.0338 GC 72696062 0.0113 GCA 51118632 0.0079 GCC 27797659 0.0043 GCG 66512705 0.0103 GCT + 361154273 0.0560 GG 87662449 0.0136 GGA 51591104 0.0080 GGC 124820908 0.0194 GGG 89162545 0.0139 GGT + 371793122 0.0576 GT 112773785 0.0175 GTA 61960408 0.0096 GTC 66540524 0.0103 GTG 130508651 0.0203 GTT + 526153182 0.0816 TA 165978181 0.0258 TAA 109335141 0.0170 TAC 104450634 0.0162 TAG 146068463 0.0227 TAT + 355583693 0.0551 TC 105474843 0.0164 TCA 77928750 0.0121 TCC 58773061 0.0091 TCG 113158614 0.0176 TCT + 375551419 0.0582 TG 113251416 0.0176 TGA 72683975 0.0113 TGC 81429936 0.0127 TGG 107781308 0.0167 TGT + 653083381 0.1013 TT 164899014 0.0256 TTA 127390884 0.0198 TTC 127703170 0.0198 TTG 233082150 0.0362 TTT +``` + +# Extracting + +``` +% seqrequester extract +usage: ./FreeBSD-amd64/bin/seqrequester [mode] [options] [sequence_file ...] + +OPTIONS for extract mode: + -bases baselist extract bases as specified in the 'list' from each sequence + -sequences seqlist extract ordinal sequences as specified in the 'list' + + -reverse reverse the bases in the sequence + -complement complement the bases in the sequence + -rc alias for -reverse -complement + + -compress compress homopolymer runs to one base + + -upcase + -downcase + + -length min-max print sequence if it is at least 'min' bases and at most 'max' bases long + + a 'baselist' is a set of integers formed from any combination + of the following, seperated by a comma: + num a single number + bgn-end a range of numbers: bgn <= end + bases are spaced-based; -bases 0-2,4 will print the bases between + the first two spaces (the first two bases) and the base after the + fourth space (the fifth base). + + a 'seqlist' is a set of integers formed from any combination + of the following, seperated by a comma: + num a single number + bgn-end a range of numbers: bgn <= end + sequences are 1-based; -sequences 1,3-5 will print the first, third, + fourth and fifth sequences. +``` + +# Sampling + +``` +% seqrequester sample +usage: ./FreeBSD-amd64/bin/seqrequester [mode] [options] [sequence_file ...] + +OPTIONS for sample mode: + -paired treat inputs as paired sequences; the first two files form the + first pair, and so on. + + -copies C write C different copies of the sampling (without replacement). + -output O write output sequences to file O. If paired, two files must be supplied. + + -coverage C output C coverage of sequences, based on genome size G. + -genomesize G + + -bases B output B bases. + + -reads R output R reads. + -pairs P output P pairs (only if -paired). + + -fraction F output fraction F of the input bases. + +``` + +# Generating + +Undocumented. + +# Simulating + +``` +seqrequester simulate +usage: ./FreeBSD-amd64/bin/seqrequester [mode] [options] [sequence_file ...] + +OPTIONS for simulate mode: + -genome G sample reads from these sequences + -circular treat the sequences in G as circular + + -genomesize g genome size to use for deciding coverage below + -coverage c generate approximately c coverage of output + -nreads n generate exactly n reads of output + -nbases n generate approximately n bases of output + + -distribution F generate read length by sampling the distribution in file F + one column - each line is the length of a sequence + two columns - each line has the 'length' and 'number of sequences' + + if file F doesn't exist, use a built-in distribution + ultra-long-nanopore + pacbio + pacbio-hifi + + -length min[-max] (not implemented) + -output x.fasta (not implemented) +```