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mattb112885
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clusterDbAnalysis
ITEP - Integrated Toolkit for Exploration of microbial Pan-genomes
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Neighborhood-based clustering
#33
mattb112885
opened
11 years ago
1
convertGenbankToTable should not depend on GI Ids being available
#32
mattb112885
closed
11 years ago
2
Downloading from NCBI should default to completed genomes if both complete and incomplete are available (but doesn't)
#31
mattb112885
opened
11 years ago
1
pubseed interface has broken
#30
mattb112885
closed
11 years ago
1
Very short genes are excluded from clustering results
#29
mattb112885
closed
11 years ago
1
Switch to argparse and use argcomplete to deal with options with fixed list of possibilities
#28
mattb112885
opened
11 years ago
0
James r hcommits
#27
JamesRH
closed
11 years ago
1
James r hcommits
#26
JamesRH
closed
11 years ago
2
JamesRH commits - small updates, genbank d/l and two treeing scripts
#25
JamesRH
closed
11 years ago
1
Functions limited to only singular inputs should have command-line options
#24
mattb112885
opened
11 years ago
0
db_getClusterGeneInformation.py uses wrong columns
#23
JamesRH
closed
11 years ago
6
permission on /data/Cluster_Files/completeCoreAnalysis.sh
#22
JamesRH
closed
11 years ago
3
Need option to add filtering (SEG or DUST) to automatically-generated BLAST databases
#21
mattb112885
opened
11 years ago
2
Use metadata to identify location of organism and groups files
#20
mattb112885
closed
11 years ago
1
come up with better mapping from org groups to runid names
#19
JamesRH
closed
11 years ago
4
getPresenceAbsence functions should be combined
#18
JamesRH
closed
11 years ago
2
modularizing commonly used functions
#17
JamesRH
opened
11 years ago
2
removeOrganisms and removeOrganisms_SAFE need cleanup
#16
mattb112885
closed
11 years ago
1
Request: Obtain sequences of HSPs from the blast results
#15
mattb112885
closed
11 years ago
0
Automatic adding of gene aliases
#14
mattb112885
closed
11 years ago
1
duplicate contigs in contig table
#13
mattb112885
closed
11 years ago
0
Bad column names in blastres_selfbit
#12
mattb112885
closed
11 years ago
1
db_listDbFiles.py features for easier grepping
#11
JamesRH
closed
11 years ago
2
Automatic adding of organism name and ID from NCBI or pubseed parsing functions
#10
mattb112885
closed
11 years ago
2
getClusterFastas.py fails if output folder does not exist
#9
mattb112885
closed
11 years ago
1
TBLASTN output needs percent overlap of query as a metric
#8
mattb112885
closed
11 years ago
1
Add nucleotide option to getClusterFastas.py
#7
mattb112885
closed
11 years ago
1
Issue with duplicate clusterIDs in getClusterFastas.py
#6
mattb112885
closed
11 years ago
1
Hook up the db to a real ortholog finder
#5
mattb112885
closed
11 years ago
3
Feature request: Find missing organisms in a cluster
#4
mattb112885
opened
11 years ago
0
BLASTN all vs all
#3
mattb112885
closed
11 years ago
2
Output formats for tables need documentation within the function
#2
mattb112885
opened
11 years ago
1
Different number of columns from db_getGeneInformation.py and db_getClusterGeneInformation.py
#1
mattb112885
closed
11 years ago
1
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