Ecosyste.ms: Issues

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GitHub / mscook/SeqFindR issues and pull requests

#60 - Bump wheel from 0.24.0 to 0.38.1

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#59 - Bump numpy from 1.8.1 to 1.22.0

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#58 - Bump numpy from 1.8.1 to 1.21.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments
Labels: dependencies

#57 - Switched broken pypip.in badges to shields.io

Pull Request - State: open - Opened by movermeyer almost 7 years ago

#56 - Prints out line that is not formatted correctly.

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

#55 - Correction of cutoff scoring function

Pull Request - State: closed - Opened by nbenzakour almost 10 years ago - 3 comments

#54 - Figure plotting function now has the matrix fully in svg format

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

#53 - (possibly redundant), remind user when db size >= pixels

Issue - State: open - Opened by mscook almost 10 years ago

#52 - Split out list of categories colors

Issue - State: open - Opened by mscook almost 10 years ago

#51 - Local packages not always installed in ~/.local/

Issue - State: open - Opened by BioMinnie almost 10 years ago

#50 - SeqFindr-web compatibility and support for other fasta formats.

Pull Request - State: open - Opened by jling90 almost 10 years ago - 1 comment

#49 - Added support for alternative fasta file formatted inputs.

Pull Request - State: closed - Opened by jling90 about 10 years ago - 2 comments

#48 - Clustering by column should work when providing an index.

Issue - State: open - Opened by mscook about 10 years ago

#47 - Give the user options to set the the clustering algorithm

Issue - State: open - Opened by mscook about 10 years ago

#46 - Write out matrix with labels

Issue - State: open - Opened by mscook about 10 years ago

#45 - Read in results/matrix without needing to re-run!

Issue - State: open - Opened by mscook about 10 years ago - 1 comment

#43 - Handle cases where matrix is very simple (& cannot be clustered)

Issue - State: open - Opened by mscook about 10 years ago - 1 comment

#42 - Warn user if all values in the matrix are equal

Issue - State: closed - Opened by mscook about 10 years ago

#41 - Checking for a singular matrix (i.e no hits/all hits)

Issue - State: closed - Opened by mscook about 10 years ago - 1 comment

#40 - underscores in input filesnames/directories

Issue - State: open - Opened by mscook about 10 years ago

#39 - Combine HSP to make pseudo-hit

Issue - State: open - Opened by mscook about 10 years ago

#38 - Hit shading by identity/score

Issue - State: open - Opened by mscook about 10 years ago

#37 - Get Jun's "simple database header" code into master

Issue - State: open - Opened by mscook about 10 years ago

#36 - Option to translate & cdhit for "closely related" genes

Issue - State: open - Opened by mscook about 10 years ago

#35 - Option remove "empty" columns

Issue - State: closed - Opened by mscook about 10 years ago

#34 - Provide a single executable (pyinstaller)

Issue - State: open - Opened by mscook over 10 years ago

#33 - Invert coloring

Issue - State: closed - Opened by mscook over 10 years ago

#32 - We have y axis label offset by 1 in current release!

Issue - State: closed - Opened by mscook over 10 years ago - 1 comment
Labels: bug

#30 - Add an option to build DB with sequences that have a non-standard format header

Issue - State: closed - Opened by nbenzakour over 10 years ago - 1 comment

#29 - Stashed some changes - not sure why...

Issue - State: open - Opened by mscook over 10 years ago

#28 - database validator

Issue - State: open - Opened by mscook almost 11 years ago - 1 comment
Labels: enhancement

#27 - Clustering of the x-axis if the index is provided.

Issue - State: closed - Opened by bawee almost 11 years ago - 4 comments
Labels: enhancement

#26 - Save data, regen data & compress matrix

Pull Request - State: closed - Opened by hamzakhanvit almost 11 years ago

#25 - Significant API changes to SeqFindR

Pull Request - State: closed - Opened by hamzakhanvit almost 11 years ago - 1 comment

#24 - Issue with categories

Issue - State: closed - Opened by mscook almost 11 years ago - 1 comment
Labels: bug

#23 - Added all authors

Pull Request - State: closed - Opened by hamzakhanvit almost 11 years ago

#22 - Output stats of blast hits

Issue - State: closed - Opened by bawee almost 11 years ago - 2 comments

#21 - Enforce latest version of pip

Issue - State: closed - Opened by mscook about 11 years ago - 1 comment

#20 - Distribute in a docker container

Issue - State: closed - Opened by mscook about 11 years ago - 1 comment

#19 - Add shields

Issue - State: closed - Opened by mscook about 11 years ago
Labels: enhancement

#18 - Cannot split a category

Issue - State: closed - Opened by happykhan about 11 years ago - 2 comments
Labels: bug

#17 - Travis-CI build system

Issue - State: closed - Opened by mscook about 11 years ago - 2 comments

#16 - Fixed plot_matrix, svg works now.

Pull Request - State: closed - Opened by happykhan about 11 years ago - 1 comment

#15 - Offset x & y axes

Issue - State: closed - Opened by mscook about 11 years ago - 1 comment
Labels: bug

#14 - matplotlib install on pip requires freetype

Issue - State: closed - Opened by happykhan about 11 years ago - 2 comments
Labels: enhancement

#13 - Unique gene requirement names should just be a warning.

Issue - State: closed - Opened by bawee over 11 years ago - 2 comments

#12 - Updated installer & added svg

Pull Request - State: closed - Opened by happykhan over 11 years ago - 1 comment

#11 - OSx install issues

Issue - State: closed - Opened by mscook over 11 years ago - 3 comments
Labels: bug, enhancement

#10 - Colours in category colours seems to set an upper limit

Issue - State: closed - Opened by happykhan over 11 years ago

#9 - Scott may prefer task options with blastn

Issue - State: open - Opened by happykhan over 11 years ago
Labels: question

#8 - User might want control of e-value

Issue - State: closed - Opened by happykhan over 11 years ago - 1 comment

#7 - Genbank support

Issue - State: closed - Opened by happykhan over 11 years ago - 1 comment

#6 - Better exception handling if query directory is empty or do_run fails

Issue - State: open - Opened by happykhan over 11 years ago - 1 comment
Labels: enhancement

#5 - Merged with latest seqfindr

Pull Request - State: closed - Opened by happykhan over 11 years ago

#4 - Shading = level of similarity

Issue - State: closed - Opened by bawee over 11 years ago - 2 comments

#3 - Protein searches

Issue - State: closed - Opened by bawee over 11 years ago - 7 comments

#2 - Investigate the effects of using hsp.identities/float(record.query_length) >= tol vs max_identity >= tol

Issue - State: open - Opened by mscook over 11 years ago - 2 comments
Labels: question

#1 - Work on Argparse

Issue - State: closed - Opened by mscook over 11 years ago - 1 comment
Labels: enhancement