eclarke/swga issues and pull requests

#56 - setuptools pip failed with error code 1

Issue - State: open - Opened by alxespinosa almost 2 years ago

#55 - Error: Path '.fasta' does not exist

Issue - State: closed - Opened by Alexharrott over 2 years ago

#54 - TypeError: filename expected str, os.PathLike or fsspec.OpenFile, got: u'/data/cm/soapswga/gemomes/cpar_genome.fasta'

Issue - State: open - Opened by chemy-cm over 2 years ago - 9 comments

#53 - Using a custom list of primers for finding or scoring specific sets

Issue - State: open - Opened by felbaido over 2 years ago

#52 - Could not reproduce example

Issue - State: open - Opened by Rohit-Satyam almost 3 years ago - 3 comments

#51 - Support for Python 3

Issue - State: open - Opened by eloizahd almost 4 years ago

#50 - SWGA init error from peewee

Issue - State: open - Opened by mts11-art over 4 years ago

#49 - Problem with swga count

Issue - State: open - Opened by Rcoppee over 4 years ago - 2 comments

#48 - Problem with swga count

Issue - State: open - Opened by PaQwecy about 5 years ago - 4 comments

#47 - swga version for python 3?

Issue - State: closed - Opened by PaQwecy about 5 years ago - 1 comment

#46 - remove omp private directive

Pull Request - State: closed - Opened by corburn over 6 years ago - 3 comments

#45 - Primers without gini and temp

Issue - State: open - Opened by jan36 over 6 years ago

#44 - Finding Custom List of Primers Not Working

Issue - State: open - Opened by MatthewHiggins2017 over 6 years ago

#43 - GC content

Issue - State: closed - Opened by kaushia almost 7 years ago - 1 comment

#42 - Dimer issue and melt temp query

Issue - State: open - Opened by saclarkPHE almost 7 years ago - 3 comments

#41 - SWGA error related to dependencies

Issue - State: closed - Opened by eclarke almost 7 years ago - 2 comments

#40 - Parameters for similar genomes

Issue - State: open - Opened by Niyo2fine over 7 years ago - 3 comments

#39 - Sets with overlapping primers

Issue - State: open - Opened by ClarkLabUCB almost 8 years ago - 3 comments

#38 - Unknown error swga

Issue - State: open - Opened by ClarkLabUCB almost 8 years ago - 10 comments

#37 - Problem with swga filter

Issue - State: closed - Opened by jonbparr over 8 years ago - 7 comments

#36 - Identifying gaps

Issue - State: open - Opened by sesh-sas almost 9 years ago
Labels: enhancement

#35 - Masking repetitive regions

Issue - State: open - Opened by sesh-sas almost 9 years ago - 3 comments
Labels: enhancement

#34 - Installation issue

Issue - State: open - Opened by Will338 about 9 years ago - 9 comments

#33 - removing large numbers of sets takes too long

Issue - State: open - Opened by eclarke about 9 years ago

#32 - pip install uses incorrect binaries

Issue - State: closed - Opened by eclarke about 9 years ago

#31 - Problem scoring old sets

Issue - State: closed - Opened by sesh-sas about 9 years ago - 2 comments

#30 - Backwards compatible, Python error with new version of swga and old version files

Issue - State: closed - Opened by stsmall over 9 years ago - 6 comments

#29 - swga count fails if no exclude file is present

Issue - State: closed - Opened by sesh-sas over 9 years ago - 1 comment

#28 - Need a better error message for trying to score a set whose primers are not in the database or are not active

Issue - State: closed - Opened by sesh-sas over 9 years ago - 1 comment

#27 - Sliding window step size doesn't work

Issue - State: closed - Opened by sesh-sas over 9 years ago - 1 comment

#26 - Changed bg_ratio to bg_dist_mean

Pull Request - State: closed - Opened by sesh-sas over 9 years ago

#25 - Set IDs should be included in the output of `swga export sets`

Issue - State: closed - Opened by sesh-sas over 9 years ago - 1 comment

#24 - Primer locations not stored as integers

Issue - State: closed - Opened by sesh-sas over 9 years ago - 5 comments

#23 - Gini plot

Issue - State: open - Opened by sesh-sas over 9 years ago
Labels: enhancement

#22 - bedgraph output sliding window

Issue - State: closed - Opened by sesh-sas over 9 years ago - 3 comments

#21 - Change parameters named bg_ratio

Issue - State: closed - Opened by sesh-sas almost 10 years ago - 2 comments
Labels: enhancement

#20 - Missing table error when using `swga count --input ...`

Issue - State: closed - Opened by sesh-sas almost 10 years ago - 1 comment

#19 - exclude fp error in `swga count` when no exclusionary file is specified

Issue - State: closed - Opened by sesh-sas almost 10 years ago
Labels: invalid

#18 - Duplicate key error while parsing background genome fasta file

Issue - State: closed - Opened by alex-berry almost 10 years ago - 17 comments

#17 - DSK merges kmers and reverse complements

Issue - State: closed - Opened by sesh-sas almost 10 years ago - 1 comment

#16 - Binding average rate to binding frequency filter changes

Pull Request - State: closed - Opened by sesh-sas almost 10 years ago - 2 comments

#15 - Filter output confusing

Issue - State: closed - Opened by sesh-sas almost 10 years ago - 1 comment

#14 - Change fg_min_avg_rate and bg_max_avg_rate

Issue - State: closed - Opened by sesh-sas almost 10 years ago - 1 comment
Labels: enhancement

#13 - init should prompt for "fasta files from which to exclude primers (e.g. mitochondria)"

Issue - State: closed - Opened by seifst almost 10 years ago - 3 comments

#12 - update installations - should be in virtual environment rather than just steps 3-5

Issue - State: closed - Opened by seifst almost 10 years ago - 1 comment

#11 - swga filter output

Issue - State: closed - Opened by sesh-sas almost 10 years ago - 1 comment
Labels: enhancement

#10 - bedgraph sliding window should count absolute number of binding sites

Issue - State: closed - Opened by sesh-sas almost 10 years ago - 4 comments

#9 - memory usage for kmers > 14 too high

Issue - State: closed - Opened by eclarke almost 10 years ago

#8 - case insensitive

Issue - State: closed - Opened by sesh-sas about 10 years ago - 1 comment
Labels: enhancement

#7 - test_correct_write error

Issue - State: closed - Opened by sesh-sas over 10 years ago - 1 comment
Labels: wontfix

#6 - Filter primers that bind a given genome or from a list

Issue - State: closed - Opened by sesh-sas over 10 years ago - 2 comments
Labels: enhancement

GitHub / eclarke/swga issues and pull requests