Mercurial > repos > iuc > isoformswitchanalyzer

comparison IsoformSwitchAnalyzeR.R @ 2:2b0a6af4b85e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
author iuc
date Wed, 24 May 2023 06:06:54 +0000
parents 2c4e879a81cf
children 02a77166b29a
comparison
equal deleted inserted replaced
1:2c4e879a81cf 2:2b0a6af4b85e
32 parser$add_argument("--readLength", 32 parser$add_argument("--readLength",
33 required = FALSE, 33 required = FALSE,
34 type = "integer", 34 type = "integer",
35 help = "Read length (required for stringtie)") 35 help = "Read length (required for stringtie)")
36 parser$add_argument("--annotation", required = FALSE, help = "Annotation") 36 parser$add_argument("--annotation", required = FALSE, help = "Annotation")
37 parser$add_argument("--stringtieAnnotation", required = FALSE, help = "Stringtie annotation")
37 parser$add_argument("--transcriptome", required = FALSE, help = "Transcriptome") 38 parser$add_argument("--transcriptome", required = FALSE, help = "Transcriptome")
38 parser$add_argument( 39 parser$add_argument(
39 "--fixStringTieAnnotationProblem", 40 "--fixStringTieAnnotationProblem",
40 action = "store_true", 41 action = "store_true",
41 required = FALSE, 42 required = FALSE,
101 parser$add_argument( 102 parser$add_argument(
102 "--overwriteIFvalues", 103 "--overwriteIFvalues",
103 required = FALSE, 104 required = FALSE,
104 action = "store_true", 105 action = "store_true",
105 help = "Overwrite IF values" 106 help = "Overwrite IF values"
107 )
108 parser$add_argument(
109 "--removeNonConvensionalChr",
110 required = FALSE,
111 action = "store_true",
112 help = "Remove non-conventional chromosomes"
106 ) 113 )
107 parser$add_argument( 114 parser$add_argument(
108 "--reduceToSwitchingGenes", 115 "--reduceToSwitchingGenes",
109 required = FALSE, 116 required = FALSE,
110 action = "store_true", 117 action = "store_true",
346 colnames(quantificationData$abundance)[-1] 353 colnames(quantificationData$abundance)[-1]
347 ) 354 )
348 ) 355 )
349 356
350 if (args$toolSource == "stringtie") { 357 if (args$toolSource == "stringtie") {
351 SwitchList <- importRdata( 358 if (!is.null(args$stringtieAnnotation)) {
352 isoformCountMatrix = quantificationData$counts, 359 SwitchList <- importRdata(
353 isoformRepExpression = quantificationData$abundance, 360 isoformCountMatrix = quantificationData$counts,
354 designMatrix = myDesign, 361 isoformRepExpression = quantificationData$abundance,
355 isoformExonAnnoation = args$annotation, 362 designMatrix = myDesign,
356 isoformNtFasta = args$transcriptome, 363 removeNonConvensionalChr = args$removeNonConvensionalChr,
357 showProgress = TRUE, 364 isoformExonAnnoation = args$stringtieAnnotation,
358 fixStringTieAnnotationProblem = args$fixStringTieAnnotationProblem 365 isoformNtFasta = args$transcriptome,
359 ) 366 addAnnotatedORFs = FALSE,
367 showProgress = TRUE,
368 fixStringTieAnnotationProblem = args$fixStringTieAnnotationProblem
369 )
370
371 SwitchList <- addORFfromGTF(
372 SwitchList,
373 removeNonConvensionalChr = args$removeNonConvensionalChr,
374 pathToGTF = args$annotation
375 )
376
377 } else {
378 SwitchList <- importRdata(
379 isoformCountMatrix = quantificationData$counts,
380 isoformRepExpression = quantificationData$abundance,
381 designMatrix = myDesign,
382 removeNonConvensionalChr = args$removeNonConvensionalChr,
383 isoformNtFasta = args$transcriptome,
384 isoformExonAnnoation = args$annotation,
385 showProgress = TRUE,
386 fixStringTieAnnotationProblem = args$fixStringTieAnnotationProblem
387 )
388 }
389
360 } else { 390 } else {
361 SwitchList <- importRdata( 391 SwitchList <- importRdata(
362 isoformCountMatrix = quantificationData$counts, 392 isoformCountMatrix = quantificationData$counts,
363 isoformRepExpression = quantificationData$abundance, 393 isoformRepExpression = quantificationData$abundance,
364 designMatrix = myDesign, 394 designMatrix = myDesign,
395 removeNonConvensionalChr = args$removeNonConvensionalChr,
365 isoformExonAnnoation = args$annotation, 396 isoformExonAnnoation = args$annotation,
366 isoformNtFasta = args$transcriptome, 397 isoformNtFasta = args$transcriptome,
367 showProgress = TRUE 398 showProgress = TRUE
368 ) 399 )
369 } 400 }
370
371 401
372 geneCountMatrix <- extractGeneExpression( 402 geneCountMatrix <- extractGeneExpression(
373 SwitchList, 403 SwitchList,
374 extractCounts = TRUE, 404 extractCounts = TRUE,
375 addGeneNames = FALSE, 405 addGeneNames = FALSE,
482 onlySigIsoforms = args$onlySigIsoforms, 512 onlySigIsoforms = args$onlySigIsoforms,
483 keepIsoformInAllConditions = args$keepIsoformInAllConditions2, 513 keepIsoformInAllConditions = args$keepIsoformInAllConditions2,
484 showProgress = TRUE, 514 showProgress = TRUE,
485 ) 515 )
486 516
487 SwitchList <- analyzeNovelIsoformORF( 517 if (!is.null(args$stringtieAnnotation)) {
488 SwitchList, 518 SwitchList <- analyzeNovelIsoformORF(
489 analysisAllIsoformsWithoutORF = TRUE, 519 SwitchList,
490 minORFlength = args$minORFlength, 520 analysisAllIsoformsWithoutORF = TRUE,
491 orfMethod = args$orfMethod, 521 minORFlength = args$minORFlength,
492 PTCDistance = args$PTCDistance, 522 orfMethod = args$orfMethod,
493 startCodons = "ATG", 523 PTCDistance = args$PTCDistance,
494 stopCodons = c("TAA", "TAG", "TGA"), 524 startCodons = "ATG",
495 showProgress = TRUE, 525 stopCodons = c("TAA", "TAG", "TGA"),
496 ) 526 showProgress = TRUE,
527 )
528 }
497 529
498 ### Extract Sequences 530 ### Extract Sequences
499 SwitchList <- extractSequence( 531 SwitchList <- extractSequence(
500 SwitchList, 532 SwitchList,
501 onlySwitchingGenes = args$onlySwitchingGenes, 533 onlySwitchingGenes = args$onlySwitchingGenes,