Ecosyste.ms: Issues

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GitHub / andrewsanchez/NCBITK issues and pull requests

#88 - Bump numpy from 1.12.0 to 1.22.0

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

#87 - Bump numpy from 1.12.0 to 1.21.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#86 - Develop

Pull Request - State: closed - Opened by andrewsanchez over 7 years ago

#85 - Develop

Pull Request - State: closed - Opened by andrewsanchez almost 8 years ago

#84 - Process hangs indefinitely after MASH finishes

Issue - State: closed - Opened by andrewsanchez almost 8 years ago - 1 comment

#83 - Redirect stdout from MASH

Issue - State: closed - Opened by andrewsanchez almost 8 years ago

#82 - print some logging info to stderr

Issue - State: open - Opened by andrewsanchez almost 8 years ago

#81 - Update curate.clean_up

Issue - State: closed - Opened by andrewsanchez almost 8 years ago

#79 - Investigate ftplib.error_temp

Issue - State: closed - Opened by andrewsanchez about 8 years ago

#78 - make sbatch scripts for remove_old_genomes and rename

Issue - State: closed - Opened by andrewsanchez about 8 years ago

#77 - make gen_sbatch_script handle arrays as well

Issue - State: closed - Opened by andrewsanchez about 8 years ago

#76 - Get your shit together and write unit tests!!!!

Issue - State: closed - Opened by andrewsanchez about 8 years ago

#75 - Create log files with pandas

Issue - State: closed - Opened by andrewsanchez about 8 years ago
Labels: priority

#72 - Use sbatch instead of salloc

Issue - State: closed - Opened by andrewsanchez about 8 years ago

#71 - Python script to run as cron job

Issue - State: closed - Opened by andrewsanchez about 8 years ago

#70 - Make each job in the array submit 3 requests

Issue - State: closed - Opened by andrewsanchez about 8 years ago

#69 - function for grabbing single genome

Issue - State: closed - Opened by andrewsanchez about 8 years ago

#68 - Create genbank_stats using pandas instead

Issue - State: closed - Opened by andrewsanchez about 8 years ago

#67 - work all commands into single NCBITK.py

Issue - State: closed - Opened by andrewsanchez about 8 years ago

#66 - try submitting array automatically

Issue - State: closed - Opened by andrewsanchez about 8 years ago

#65 - Hand URLError

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#64 - latest_assembly_versions or assembly_summary.txt?

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#63 - Recreate genbank dir structure

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#62 - What to do with matching genomes?

Issue - State: closed - Opened by andrewsanchez over 8 years ago - 1 comment

#61 - mash dist command not taking advantage of sketch files

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#60 - Don't loop through both renamed and local mirror

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#59 - Create a function to link out genomes based on given passed.csv

Issue - State: closed - Opened by andrewsanchez over 8 years ago - 1 comment

#57 - Create several dirty versions of B. anthracis

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#56 - Check for empty FASTA's

Issue - State: open - Opened by andrewsanchez over 8 years ago

#55 - Improve summary.txt output

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#54 - Improve summary.txt output

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#53 - Remove rows from failed.csv where all colums = "passed"

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#52 - Change output for failed

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#51 - Filtering based on contigs

Issue - State: closed - Opened by andrewsanchez over 8 years ago - 1 comment

#50 - Create a summary file

Issue - State: closed - Opened by andrewsanchez over 8 years ago - 1 comment

#49 - Add temporary functions to check for potential errors

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#48 - Why are some genomes ending up with multiple avlues in failed.txt

Issue - State: closed - Opened by andrewsanchez over 8 years ago - 1 comment

#47 - Why are genomes with < 10 contigs being filtered out?

Issue - State: closed - Opened by andrewsanchez over 8 years ago - 1 comment

#46 - Explore setting thresholds for acceptable MASH distances

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#45 - Use mean instead of median absolute distance on MASH matrix

Issue - State: closed - Opened by andrewsanchez over 8 years ago - 1 comment

#44 - Hide compressed genbank mirror

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#43 - Curate a collection of genomes, both mixed and "clean"

Issue - State: closed - Opened by andrewsanchez over 8 years ago - 1 comment

#42 - Order columns in order of filtering process

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#41 - Don't filter out contigs if they are < contigs.median()

Issue - State: closed - Opened by andrewsanchez over 8 years ago
Labels: question

#39 - Investigate Panda's SettingWithCopyWarning

Issue - State: closed - Opened by andrewsanchez over 8 years ago - 1 comment

#38 - Separate contigs filtering into its own function

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#37 - Organize failed log better

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#36 - Add information for contigs to failed log

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#35 - Resolve TypeError

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#34 - Filter based on if not ATCG instead of N's

Issue - State: closed - Opened by andrewsanchez over 8 years ago
Labels: quality filtering

#33 - Use x * median absolute difference instead of percentiles

Issue - State: closed - Opened by andrewsanchez over 8 years ago - 1 comment
Labels: quality filtering

#32 - Write failed FASTA's to filter_log.txt

Issue - State: closed - Opened by andrewsanchez over 8 years ago
Labels: quality filtering

#31 - Filtering based on contigs

Issue - State: closed - Opened by andrewsanchez over 8 years ago - 1 comment

#30 - Determine whether or not STD is useful

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#29 - Any case in which large MASH scores are acceptable?

Issue - State: open - Opened by andrewsanchez over 8 years ago - 3 comments
Labels: question, quality filtering

#28 - Don't do QC on dirs with < 5 FASTA's

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#27 - Use more values at the extremes

Issue - State: closed - Opened by andrewsanchez over 8 years ago
Labels: quality filtering

#26 - Make necessary changes to run with slurm array

Issue - State: closed - Opened by andrewsanchez over 8 years ago
Labels: priority, quality filtering

#25 - Create log file for quality_filters.py

Issue - State: closed - Opened by andrewsanchez over 8 years ago
Labels: priority, quality filtering

#24 - Smarter filtering of contigs

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#23 - Stop filtering when left with < 5 FASTA's

Issue - State: closed - Opened by andrewsanchez over 8 years ago
Labels: priority, quality filtering

#22 - Don't run on QC on directories with too few FASTA's

Issue - State: closed - Opened by andrewsanchez over 8 years ago
Labels: quality filtering

#21 - Handle Panda's ValueError, just in case of MASH error

Issue - State: closed - Opened by andrewsanchez over 8 years ago - 3 comments
Labels: priority, quality filtering

#20 - Update stats DataFrame rather than overwriting

Issue - State: open - Opened by andrewsanchez over 8 years ago
Labels: priority

#19 - Options for running different filtering options

Issue - State: closed - Opened by andrewsanchez over 8 years ago
Labels: priority, quality filtering

#18 - Add options to specify which species to run QF's on

Issue - State: open - Opened by andrewsanchez over 8 years ago
Labels: priority, quality filtering

#17 - retest -from_file and -from_list

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#16 - Test more efficient ways to recreate directory structure

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#15 - Test other tools for getting all bacteria

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#14 - Run mash and quality filters as part of NCBITK?

Issue - State: closed - Opened by andrewsanchez over 8 years ago
Labels: question

#13 - handle FileNotFoundError

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#12 - Double check failed fastas

Issue - State: closed - Opened by andrewsanchez over 8 years ago
Labels: priority

#11 - Append entries to sketch file if new FASTA's are added

Issue - State: closed - Opened by andrewsanchez over 8 years ago

#10 - link files into "passed" directory instead of writing names to disk

Issue - State: closed - Opened by andrewsanchez over 8 years ago
Labels: priority

#9 - Find first line of assembly_summary.txt

Issue - State: closed - Opened by andrewsanchez almost 9 years ago - 1 comment

#8 - Add evaluation functions to NCBITK

Issue - State: closed - Opened by andrewsanchez almost 9 years ago

#7 - Bring renaming function into NCBITK

Issue - State: closed - Opened by andrewsanchez almost 9 years ago

#6 - Handle spelling errors

Issue - State: open - Opened by andrewsanchez almost 9 years ago

#5 - duplicate strain names

Issue - State: closed - Opened by jasonsahl almost 9 years ago - 6 comments

#4 - Automatically download assembly_summary.txt

Issue - State: closed - Opened by andrewsanchez almost 9 years ago

#3 - Add documentation

Issue - State: closed - Opened by andrewsanchez almost 9 years ago

#2 - Revert "Update rsync_ncbi.py"

Pull Request - State: closed - Opened by andrewsanchez almost 9 years ago

#1 - Update rsync_ncbi.py

Pull Request - State: closed - Opened by jasonsahl almost 9 years ago