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  1. IGB
  2. IGBF-1147

better bedgraph formatting

        Details

        • Type: Bug
        • Status: In Progress (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          -IGB live does produce the duplicated lines. (see * below)
          -The lines are not (strictly) ordered. (See **)

          Chr1 8227506 8227522 2.0
          Chr1 8227506 8227522 2.0 *
          Chr1 8227534 8227542 5.0
          Chr1 8227534 8227542 5.0
          Chr1 8227542 8227553 6.0
          Chr1 8227534 8227542 5.0
          Chr1 20998229 20998235 5.0
          Chr1 20998235 20998333 0.0
          Chr1 8227506 8227522 2.0 **

          For some downstream use cases, non-overlap and being sorted are required, or at least desired.

            Attachments

              Issue Links

              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-2197 Investigate: Graph files grayed out

              • Minor - Minor loss of function, or other problem where easy workaround is present.
              • To-Do

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1090 Implement saving of all chromosomes when exporting as bedgraph

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                ieclabau Ivory Blakley (Inactive) created issue -
                ieclabau Ivory Blakley (Inactive) made changes -
                Field Original Value New Value
                Link This issue relates to IGBF-1090 [ IGBF-1090 ]
                ieclabau Ivory Blakley (Inactive) made changes -
                Description
                -IGB live does produce the duplicated lines. (see * below)
                -The lines are not (strictly) ordered. (See **)

                Chr1 8227506 8227522 2.0
                Chr1 8227506 8227522 2.0 *
                Chr1 8227534 8227542 5.0
                Chr1 8227534 8227542 5.0
                Chr1 8227542 8227553 6.0
                Chr1 8227534 8227542 5.0
                Chr1 20998229 20998235 5.0
                Chr1 20998235 20998333 0.0
                Chr1 8227506 8227522 2.0 **

                For some downstream use cases, non-overlap and being sorted are required, or at least desired.
                ieclabau Ivory Blakley (Inactive) made changes -
                Rank Ranked higher
                sneha Sneha Ramesh Watharkar (Inactive) made changes -
                Assignee Ann Loraine [ aloraine ] Jennifer Daly [ jdaly ]
                sneha Sneha Ramesh Watharkar (Inactive) made changes -
                Status Open [ 1 ] In Progress [ 3 ]
                sneha Sneha Ramesh Watharkar (Inactive) made changes -
                Sprint Spring 2017 [ 47 ]
                sneha Sneha Ramesh Watharkar (Inactive) made changes -
                Rank Ranked lower
                sneha Sneha Ramesh Watharkar (Inactive) made changes -
                Comment [ I made this script to find duplicates so I don't have to look through the file:

                #! /usr/bin/env python

                from __future__ import print_function
                log = open("output.txt", "w")

                def find_duplicates(file):
                with open(file) as f:
                seen = set()
                for line in f:
                line_lower = line.lower()
                if line_lower in seen:
                print(line, file = log)
                else:
                seen.add(line_lower)


                find_duplicates("test1.bedgraph")

                I tested it by creating a duplicate on purpose, it works.
                I tested 4 files from master branch, and 4 files from IGB live, none of them produced duplicates.

                @Ivory, is this issue a result of IGB saving multiple tiers, the issue we just fixed by re-writing exportfileaction? I know you said you were able to reproduce it in IGB live, can you test it again? ]
                sneha Sneha Ramesh Watharkar (Inactive) made changes -
                Attachment find_duplicates.py [ 14033 ]
                ann.loraine Ann Loraine made changes -
                Assignee Jennifer Daly [ jdaly ]
                ann.loraine Ann Loraine made changes -
                Sprint Early Fall 2017 [ 47 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 17788 ] Fall 2019 Workflow Update [ 19065 ]
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 19065 ] Revised Fall 2019 Workflow Update [ 21183 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2197 [ IGBF-2197 ]

                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    ieclabau Ivory Blakley (Inactive)
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                    Dates

                    • Created:
                      Updated: