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Circtools2: Meta-data module #4

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Circtools2: Meta-data module #4

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Commits on Nov 8, 2023

  1. Added CIRIquant command line arguments

    shubhada-kulkarni committed Nov 8, 2023
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Commits on Nov 9, 2023

  1. Added CIRiquant integration part in detect module

    shubhada-kulkarni committed Nov 9, 2023
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  2. Added cleanup string argument in detect module

    shubhada-kulkarni committed Nov 9, 2023
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  3. Changed the function to take arguments from detect class

    shubhada-kulkarni committed Nov 9, 2023
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  4. Added metatool part with command line checks and logging file printing

    shubhada-kulkarni committed Nov 9, 2023
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Commits on Nov 14, 2023

  1. Fixed the duplicate -C option in detect module. Now replaced with -S

    shubhada-kulkarni committed Nov 14, 2023
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  2. Added nargs for list_ciriquant argument to remove parse arguments rea… 

    …ding error
    shubhada-kulkarni committed Nov 14, 2023
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  3. Argument parser error fixed

    shubhada-kulkarni committed Nov 14, 2023
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  4. Remove bad line causing error

    shubhada-kulkarni committed Nov 14, 2023
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Commits on Nov 16, 2023

  1. Commit after making sure the testing worked successfully

    shubhada-kulkarni committed Nov 16, 2023
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  2. Fixed column names writing in merged output files in combining script

    shubhada-kulkarni committed Nov 16, 2023
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  3. Commented the comment deleted by mistake

    shubhada-kulkarni committed Nov 16, 2023
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Commits on Nov 22, 2023

  1. Fixing typo in primer design link

    @tjakobi
    tjakobi committed Nov 22, 2023
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  2. Updating documentation links to new URL

    @tjakobi
    tjakobi committed Nov 22, 2023
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  3. Updating RTD config

    @tjakobi
    tjakobi committed Nov 22, 2023
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  4. Updating RTF config

    @tjakobi
    tjakobi committed Nov 22, 2023
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  5. Adding parser dependency for RTD

    @tjakobi
    tjakobi committed Nov 22, 2023
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  6. Changes to config file for new requirements format

    @tjakobi
    tjakobi committed Nov 22, 2023
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  7. Another fix

    @tjakobi
    tjakobi committed Nov 22, 2023
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  8. Wrong indents

    @tjakobi
    tjakobi committed Nov 22, 2023
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  9. Updating links

    @tjakobi
    tjakobi committed Nov 22, 2023
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Commits on Nov 28, 2023

  1. Making sure every run outputs same file using sorting of dictionary keys

    shubhada-kulkarni committed Nov 28, 2023
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  2. Update Detect.rst 

    Added CIRIquant links for installation
    @shubhada-kulkarni
    shubhada-kulkarni authored Nov 28, 2023
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  3. Added CIRIquant code snippet to Detect.rst

    @shubhada-kulkarni
    shubhada-kulkarni authored Nov 28, 2023
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  4. Code block CIRIquant space fixed Detect.rst

    @shubhada-kulkarni
    shubhada-kulkarni authored Nov 28, 2023
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  5. Script to run SLURM jobs for CIRIquant alignment

    shubhada-kulkarni committed Nov 28, 2023
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Commits on Dec 6, 2023

  1. Added padlock probe module part

    shubhada-kulkarni committed Dec 6, 2023
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  2. Merge branch 'master' of https://github.com/shubhada-kulkarni/circtools

    shubhada-kulkarni committed Dec 6, 2023
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Commits on Dec 7, 2023

  1. Added scanning window part

    shubhada-kulkarni committed Dec 7, 2023
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Commits on Dec 8, 2023

  1. Added the primer3 check part

    shubhada-kulkarni committed Dec 8, 2023
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  2. Padlock directory with padlock.py script

    shubhada-kulkarni committed Dec 8, 2023
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Commits on Dec 10, 2023

  1. Primer3 changes

    shubhada-kulkarni committed Dec 10, 2023
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Commits on Dec 11, 2023

  1. Added -GL input gene list file option to padlock probe module

    shubhada-kulkarni committed Dec 11, 2023
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  2. Input gene list file option added

    shubhada-kulkarni committed Dec 11, 2023
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  3. Removed dependency on R primer wrapper script

    shubhada-kulkarni committed Dec 11, 2023
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  4. Changes in BLAST step, running successfully

    shubhada-kulkarni committed Dec 11, 2023
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  5. Added function to calculate GC content

    shubhada-kulkarni committed Dec 11, 2023
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  6. Formatter R script for padlock probe designing

    shubhada-kulkarni committed Dec 11, 2023
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  7. Added the formatter part to write html outputs

    shubhada-kulkarni committed Dec 11, 2023
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  8. Probe outputs to CSV

    shubhada-kulkarni committed Dec 11, 2023
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  9. Added 5G check in probe

    shubhada-kulkarni committed Dec 11, 2023
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  10. Change html header

    shubhada-kulkarni committed Dec 11, 2023
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Commits on Dec 12, 2023

  1. Removed non-used command line parameters

    shubhada-kulkarni committed Dec 12, 2023
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  2. Removed non-used command line parameters from padlock module

    shubhada-kulkarni committed Dec 12, 2023
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Commits on Dec 14, 2023

  1. Added flag for circular or linear RNA in padlock module

    shubhada-kulkarni committed Dec 14, 2023
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  2. Linear RNA flag added from circtools.py

    shubhada-kulkarni committed Dec 14, 2023
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Commits on Dec 15, 2023

  1. Added missing gene names in the original function read_annotation_file

    shubhada-kulkarni committed Dec 15, 2023
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  2. Fixed the error in annotation_function for special entries

    shubhada-kulkarni committed Dec 15, 2023
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  3. Added exon extraction part for linear RNAs

    shubhada-kulkarni committed Dec 15, 2023
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  4. Added linear RNA scanning window part

    shubhada-kulkarni committed Dec 15, 2023
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  5. Code cleaning and adding linear temp exon file output

    shubhada-kulkarni committed Dec 15, 2023
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  6. Added full probe melting temperature criteria + code cleaning

    shubhada-kulkarni committed Dec 15, 2023
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  7. Cleaning up comments

    shubhada-kulkarni committed Dec 15, 2023
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Commits on Dec 18, 2023

  1. Added BLAST offtarget search for linear probes

    shubhada-kulkarni committed Dec 18, 2023
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  2. Fixed all tmp files for linear RNA probes

    shubhada-kulkarni committed Dec 18, 2023
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Commits on Dec 19, 2023

  1. Added HTML output for linear probes

    shubhada-kulkarni committed Dec 19, 2023
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Commits on Dec 20, 2023

  1. Adding slurm scripts for circtools

    @tjakobi
    tjakobi committed Dec 20, 2023
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  2. Adding CI test data to repository

    @tjakobi
    tjakobi committed Dec 20, 2023
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  3. Fixed multi genes output error for linear RNA probes

    shubhada-kulkarni committed Dec 20, 2023
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  4. Added BLAST step with command-line

    shubhada-kulkarni committed Dec 20, 2023
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Commits on Jan 8, 2024

  1. Printing some additional columns for linear output to be consistent w… 

    …ith the HTML formatter script
    shubhada-kulkarni committed Jan 8, 2024
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  2. Adding full length melting temperature into output columns

    shubhada-kulkarni committed Jan 8, 2024
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  3. Changed ligation junction to strings from numbers

    shubhada-kulkarni committed Jan 8, 2024
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  4. Merge branch 'jakobilab:master' into master

    @shubhada-kulkarni
    shubhada-kulkarni authored Jan 8, 2024
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Commits on Jan 10, 2024

  1. Primer to Probe text changes

    shubhada-kulkarni committed Jan 10, 2024
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  2. Merge branch 'master' of https://github.com/shubhada-kulkarni/circtools

    shubhada-kulkarni committed Jan 10, 2024
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  3. Added coordinates for linear HTML output

    shubhada-kulkarni committed Jan 10, 2024
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  4. Primer3 calling converted into a function

    shubhada-kulkarni committed Jan 10, 2024
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  5. Added rna_type flag conditions

    shubhada-kulkarni committed Jan 10, 2024
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Commits on Jan 15, 2024

  1. Removed dependency on -d option for runs with linear RNAs only

    shubhada-kulkarni committed Jan 15, 2024
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Commits on Jan 18, 2024

  1. Changed BLAST command to make consistent with command before

    shubhada-kulkarni committed Jan 18, 2024
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  2. Changed color steps for numbers to make coloring uniform

    shubhada-kulkarni committed Jan 18, 2024
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Commits on Jan 19, 2024

  1. Changed BLAST to original python command

    shubhada-kulkarni committed Jan 19, 2024
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Commits on Jan 24, 2024

  1. Changed melting temperature colors to red-yellow-green

    shubhada-kulkarni committed Jan 24, 2024
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  2. Changed BLAST back to local command

    shubhada-kulkarni committed Jan 24, 2024
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  3. Fixed typo ligation

    shubhada-kulkarni committed Jan 24, 2024
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  4. Changed outputfile names and CSV headers

    shubhada-kulkarni committed Jan 24, 2024
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Commits on Jan 25, 2024

  1. Changed steps to 8 and color palette to RdYlBu for colorblind-friendl… 

    …y colors
    shubhada-kulkarni committed Jan 25, 2024
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  2. Changed construct_color_column to take custom min and max values for … 

    …Tm and GC content
    shubhada-kulkarni committed Jan 25, 2024
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  3. Fixed linear coordinates gap in sequence + bed file for linear probes… 

    … generations
    shubhada-kulkarni committed Jan 25, 2024
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  4. Rounding of melting temperatures and GC content

    shubhada-kulkarni committed Jan 25, 2024
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  5. Changed GC and Tm to integers

    shubhada-kulkarni committed Jan 25, 2024
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  6. Changed palette to 11 colors + changed default GC to 35% + fixed bug … 

    …in TM_right column
    shubhada-kulkarni committed Jan 25, 2024
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  7. Changed palette back to 8 steps and GC percent to 40

    shubhada-kulkarni committed Jan 25, 2024
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Commits on Jan 26, 2024

  1. Changed default exp name for padlock module

    shubhada-kulkarni committed Jan 26, 2024
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  2. Removed hover info from probe designsss

    shubhada-kulkarni committed Jan 26, 2024
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  3. Fixed the bug in Right_ column after previous change

    shubhada-kulkarni committed Jan 26, 2024
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  4. Added colour legends to HTML report

    shubhada-kulkarni committed Jan 26, 2024
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Commits on Jan 29, 2024

  1. Added visualisation for circular probes

    shubhada-kulkarni committed Jan 29, 2024
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Commits on Jan 30, 2024

  1. Re-added the hover-over for graphical representation

    shubhada-kulkarni committed Jan 30, 2024
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  2. Re-added the hover-over for graphical representation

    shubhada-kulkarni committed Jan 30, 2024
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  3. Modified svg filename for each circle

    shubhada-kulkarni committed Jan 30, 2024
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  4. Merge branch 'master' of https://github.com/shubhada-kulkarni/circtools

    shubhada-kulkarni committed Jan 30, 2024
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  5. Fixed the bug in the HTML output (was only printing one line)

    shubhada-kulkarni committed Jan 30, 2024
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  6. Fixed the font of RBD sequences from black to white

    shubhada-kulkarni committed Jan 30, 2024
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  7. Fixed the error after previous commit

    shubhada-kulkarni committed Jan 30, 2024
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Commits on Jan 31, 2024

  1. Fixed linear FSJ CSV printing issue

    shubhada-kulkarni committed Jan 31, 2024
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  2. Temporarily turned off the melting temperature filtering criteria

    shubhada-kulkarni committed Jan 31, 2024
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Commits on Feb 1, 2024

  1. Remove the havana annotation filter issue

    shubhada-kulkarni committed Feb 1, 2024
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  2. Fixed the background color issue when no hover over for sequence

    shubhada-kulkarni committed Feb 1, 2024
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Commits on Feb 5, 2024

  1. Added the graphical representation part for circular RNAs

    shubhada-kulkarni committed Feb 5, 2024
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  2. Revert "Added the graphical representation part for circular RNAs" 

    This reverts commit 1805c67.
    shubhada-kulkarni committed Feb 5, 2024
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  3. Revert "Added the graphical representation part for circular RNAs" 

    This reverts commit 1805c67.
    shubhada-kulkarni committed Feb 5, 2024
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Commits on Feb 6, 2024

  1. Fixed 1bp gap issue in start coordinates for circles

    shubhada-kulkarni committed Feb 6, 2024
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Commits on Feb 7, 2024

  1. Fixed the merging exon bug for linear part

    shubhada-kulkarni committed Feb 7, 2024
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Commits on Feb 8, 2024

  1. Added BED12 file writing for linear RNAs

    shubhada-kulkarni committed Feb 8, 2024
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Commits on Feb 9, 2024

  1. Added first and last exon dictionary for circles (for BED12)

    shubhada-kulkarni committed Feb 9, 2024
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  2. Added 50bp fasta files for Xenium

    shubhada-kulkarni committed Feb 9, 2024
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Commits on Feb 12, 2024

  1. Added BED file for circles

    shubhada-kulkarni committed Feb 12, 2024
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Commits on Feb 13, 2024

  1. Added graphical representation function for circular RNAs

    shubhada-kulkarni committed Feb 13, 2024
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Commits on Feb 14, 2024

  1. Added visualisation for linear probes

    shubhada-kulkarni committed Feb 14, 2024
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  2. Fixed the linear probe visualisation to one track

    shubhada-kulkarni committed Feb 14, 2024
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Commits on Feb 15, 2024

  1. Fixed circles bed12 start position

    shubhada-kulkarni committed Feb 15, 2024
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  2. Corrected the FSJ probe graphical representation

    shubhada-kulkarni committed Feb 15, 2024
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Commits on Feb 16, 2024

  1. Added -no-svg flag for graphical representation

    shubhada-kulkarni committed Feb 16, 2024
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  2. Default no_svg flag changed

    shubhada-kulkarni committed Feb 16, 2024
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  3. Added conditional formatting for probe representation based on no_svg… 

    … flag
    shubhada-kulkarni committed Feb 16, 2024
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  4. Added conditional SVG files generated based on no_svg flag

    shubhada-kulkarni committed Feb 16, 2024
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Commits on Feb 20, 2024

  1. Target fasta sequences for all FSJs

    shubhada-kulkarni committed Feb 20, 2024
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Commits on Mar 11, 2024

  1. Added target fasta writing with conditions

    shubhada-kulkarni committed Mar 11, 2024
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Commits on Mar 13, 2024

  1. Corrected reverse complementing for genes on - strand

    shubhada-kulkarni committed Mar 13, 2024
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  2. Fixed the RBD3 and RBD5 for circles on reverse strand

    shubhada-kulkarni committed Mar 13, 2024
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Commits on Mar 18, 2024

  1. Changed BLASTing individual probes to combined oligo BLAST

    shubhada-kulkarni committed Mar 18, 2024
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Commits on Mar 21, 2024

  1. Added hairpin, homo-heterodimer checks

    shubhada-kulkarni committed Mar 21, 2024
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Commits on Mar 28, 2024

  1. Added conservation module

    shubhada-kulkarni committed Mar 28, 2024
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  2. Added conservation module

    shubhada-kulkarni committed Mar 28, 2024
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  3. Added conservation module

    shubhada-kulkarni committed Mar 28, 2024
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  4. Added conservation module

    shubhada-kulkarni committed Mar 28, 2024
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  5. Merge branch 'master' of https://github.com/shubhada-kulkarni/circtools

    shubhada-kulkarni committed Mar 28, 2024
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  6. Conservation module framework

    shubhada-kulkarni committed Mar 28, 2024
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Commits on Apr 26, 2024

  1. Added import of FetchData class

    shubhada-kulkarni committed Apr 26, 2024
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  2. Script to fetch and parse ortholog information using REST API

    shubhada-kulkarni committed Apr 26, 2024
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Commits on May 3, 2024

  1. Change function arguments to call from main wrapper script

    shubhada-kulkarni committed May 3, 2024
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  2. Added fetch ortho call + first-last exon info for circle

    shubhada-kulkarni committed May 3, 2024
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  3. Parsing REST JSON output

    shubhada-kulkarni committed May 3, 2024
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  4. Calling parse ortho funciton

    shubhada-kulkarni committed May 3, 2024
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  5. Revert "Calling parse ortho funciton" 

    This reverts commit 149d2da.
    shubhada-kulkarni committed May 3, 2024
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  6. Class to fetch gene sequence from REST API

    shubhada-kulkarni committed May 3, 2024
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Commits on May 21, 2024

  1. Class for liftover funtions

    shubhada-kulkarni committed May 21, 2024
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  2. Fixed the function description

    shubhada-kulkarni committed May 21, 2024
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Commits on May 22, 2024

  1. test commit

    shubhada-kulkarni committed May 22, 2024
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  2. test commit 2

    shubhada-kulkarni committed May 22, 2024
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  3. Modifications in function calling

    shubhada-kulkarni committed May 22, 2024
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  4. Removed unwanted function + added more tmp file in arguments

    shubhada-kulkarni committed May 22, 2024
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  5. Liftover command working

    shubhada-kulkarni committed May 22, 2024
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  6. Calling liftover class

    shubhada-kulkarni committed May 22, 2024
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  7. Corrected the liftover function calling

    shubhada-kulkarni committed May 22, 2024
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  8. liftover command run + added parsing function

    shubhada-kulkarni committed May 22, 2024
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Commits on Jun 3, 2024

  1. Encapsulated the liftover binary call

    shubhada-kulkarni committed Jun 3, 2024
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  2. Added hg19 and mm10 flags to conservation part

    shubhada-kulkarni committed Jun 3, 2024
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  3. Added hg19 and mm10 flags and code to call liftover for these

    shubhada-kulkarni committed Jun 3, 2024
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  4. Added hg19 and mm10 check + conversion code

    shubhada-kulkarni committed Jun 3, 2024
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Commits on Jun 4, 2024

  1. Added part to call liftover on first and last exon

    shubhada-kulkarni committed Jun 4, 2024
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  2. Added function to fetch exon info from ensmbl

    shubhada-kulkarni committed Jun 4, 2024
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Commits on Jun 6, 2024

  1. Ortho dict info into liftover function

    shubhada-kulkarni committed Jun 6, 2024
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  2. Ortho dict + added function to parse GFF info from REST API

    shubhada-kulkarni committed Jun 6, 2024
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Commits on Jun 7, 2024

  1. Removed unwanted scripts

    shubhada-kulkarni committed Jun 7, 2024
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  2. Converted sequence fetching from gene to region

    shubhada-kulkarni committed Jun 7, 2024
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  3. Replaced

    shubhada-kulkarni committed Jun 7, 2024
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  4. Added target organism argument

    shubhada-kulkarni committed Jun 7, 2024
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  5. Added overlapping exon identification

    shubhada-kulkarni committed Jun 7, 2024
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  6. Added target species argument + fetch exon sequence function call

    shubhada-kulkarni committed Jun 7, 2024
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Commits on Jun 10, 2024

  1. Added try-exception for REST API requests

    shubhada-kulkarni committed Jun 10, 2024
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  2. Remaining API request count added

    shubhada-kulkarni committed Jun 10, 2024
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Commits on Jun 14, 2024

  1. Class function for sequence alignment

    shubhada-kulkarni committed Jun 14, 2024
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  2. Removed choices from target species (was causing errors)

    shubhada-kulkarni committed Jun 14, 2024
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  3. Added rat ID to dictionary + fixed the chain file name error

    shubhada-kulkarni committed Jun 14, 2024
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  4. Rearranged distance function + changed Align IO type to clustal

    shubhada-kulkarni committed Jun 14, 2024
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  5. Added multi-target species loop + fixed the target species ID input t… 

    …o functions
    shubhada-kulkarni committed Jun 14, 2024
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Commits on Jun 18, 2024

  1. Added liftover case with no overlap with exon

    shubhada-kulkarni committed Jun 18, 2024
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Commits on Jun 19, 2024

  1. Fixed bug for target species available choices if condition

    shubhada-kulkarni committed Jun 19, 2024
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Commits on Jun 21, 2024

  1. Added __main_condition for independent running

    shubhada-kulkarni committed Jun 21, 2024
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  2. Corrected first/BSJ temp liftover file names

    shubhada-kulkarni committed Jun 21, 2024
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Commits on Jun 27, 2024

  1. Removed hard-coded species + added __main__ condition

    shubhada-kulkarni committed Jun 27, 2024
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  2. Added BED output file

    shubhada-kulkarni committed Jun 27, 2024
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Commits on Jul 3, 2024

  1. Removed y-axis labels and ticks

    shubhada-kulkarni committed Jul 3, 2024
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  2. Added genome versions to the plot

    shubhada-kulkarni committed Jul 3, 2024
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  3. Code cleanup

    shubhada-kulkarni committed Jul 3, 2024
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  4. Changed fasta header to contain circle coordinates for each species

    shubhada-kulkarni committed Jul 3, 2024
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  5. Added circle coordinate information function to the plot

    shubhada-kulkarni committed Jul 3, 2024
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Commits on Jul 4, 2024

  1. Added function to perform pairwise alignments for all combinations wi… 

    …th source species
    shubhada-kulkarni committed Jul 4, 2024
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  2. Pairwise alignment flag option added

    shubhada-kulkarni committed Jul 4, 2024
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  3. Pairwise alignment if condition added

    shubhada-kulkarni committed Jul 4, 2024
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Commits on Jul 12, 2024

  1. Removed plot borders for phylogenetic plot

    shubhada-kulkarni committed Jul 12, 2024
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  2. Normalised the pairwise alignment score

    shubhada-kulkarni committed Jul 12, 2024
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  3. Check and skip for unlifted coordinates

    shubhada-kulkarni committed Jul 12, 2024
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  4. Added single-exon circle conditions

    shubhada-kulkarni committed Jul 12, 2024
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  5. Added plot title

    shubhada-kulkarni committed Jul 12, 2024
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  6. Fixed coordinates and sequences for circles on negative strand

    shubhada-kulkarni committed Jul 12, 2024
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  7. Ortho gene found check + remove species if not

    shubhada-kulkarni committed Jul 12, 2024
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Commits on Jul 19, 2024

  1. Increased font of labes

    shubhada-kulkarni committed Jul 19, 2024
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  2. Pairwise alignment plot title

    shubhada-kulkarni committed Jul 19, 2024
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  3. Increased label fonts

    shubhada-kulkarni committed Jul 19, 2024
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  4. Changed circle name for titles + increase phylo plot tick font

    shubhada-kulkarni committed Jul 19, 2024
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