1. RGMQL
  2. Commit 85cd7ab0596d03ba65a9194e10008afaa04bca22
Browse code

fix on take function

Simone authored on 21/02/2018 18:07:18
Showing 6 changed files
R/gmql_init.R
History View file @ 85cd7ab
... ... 
@@ -12,7 +12,7 @@
12 12 
 #' \item{GTF: tab-delimited text standard format based on the General
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 #' Feature Format}
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 #' \item{COLLECT: used for storing output in memory (only in the case of local
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-#' processing, i.e., remote_processing = FALSE,)}
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+#' processing, i.e., remote_processing = FALSE)}
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 #' }
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 #' @param remote_processing logical value specifying the processing mode.
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 #' True for processing on cluster (remote), false for local processing.
R/gmql_materialize.R
History View file @ 85cd7ab
... ... 
@@ -264,9 +264,12 @@ gmql_take <- function(input_data, rows)
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                                     start.field = "start",
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                                     end.field = "end")
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         })
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+
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     gRange_list <- GRangesList(sampleList)
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+    len = length(gRange_list)
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+    names(gRange_list) <- paste0("S_",seq_len(len))
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     meta_list <- .metadata_from_frame_to_list(meta)
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-
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+    names(meta_list) <- paste0("S_",seq_len(len))
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     S4Vectors::metadata(gRange_list) <- meta_list
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     return(gRange_list)
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 }
inst/example/files/S_1.gtf
History View file @ 85cd7ab
... ... 
@@ -1,574 +1,574 @@
1 1 
 ##gff-version 2
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 ##source-version rtracklayer 1.36.6
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-##date 2018-02-03
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3 
+##date 2018-02-20
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456 
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470 
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475 
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476 
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481 
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483 
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484 
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485 
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486 
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488 
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492 
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498 
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503 
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504 
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505 
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506 
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508 
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509 
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510 
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511 
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512 
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514 
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515 
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516 
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518 
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522 
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524 
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528 
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531 
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551 
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552 
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555 
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556 
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557 
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558 
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559 
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560 
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562 
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565 
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567 
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568 
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569 
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570 
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571 
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572 
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573 
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574 
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inst/example/files/granges.schema
History View file @ 85cd7ab
... ... 
@@ -1,5 +1,5 @@
1 1 
 <?xml version="1.0" encoding="UTF-8"?>
2 
-<gmqlSchemaCollection xmlns="http://genomic.elet.polimi.it/entities" name="DatasetName_SCHEMAS">
2 
+<gmqlSchemaCollection xmlns="http://genomic.elet.polimi.it/entities" name="DatasetName_SCHEMAS" type="gtf" coordinate_system="1-based">
3 3 
   <gmqlSchema>
4 4 
     <field type="STRING">seqname</field>
5 5 
     <field type="STRING">source</field>
man/init_gmql.Rd
History View file @ 85cd7ab
... ... 
@@ -15,7 +15,7 @@ files. It can be TAB, GTF or COLLECT:
15 15 
 \item{GTF: tab-delimited text standard format based on the General
16 16 
 Feature Format}
17 17 
 \item{COLLECT: used for storing output in memory (only in the case of local
18 
-processing, i.e., remote_processing = FALSE,)}
18 
+processing, i.e., remote_processing = FALSE)}
19 19 
 }}
20 20
21 21 
 \item{remote_processing}{logical value specifying the processing mode.
vignettes/multi_metadata.png
History View file @ 85cd7ab
22 22 
Binary files a/vignettes/multi_metadata.png and b/vignettes/multi_metadata.png differ