------------------
- Fixing merge issues. [Alex Jay Hyer]
- Fixing merging issues. [Alex Jay Hyer]
- Merge branch 'master' of https://github.com/Brazelton-Lab/bio_utils.
[Alex Jay Hyer]
Conflicts:
bio_utils/mothur_tools/modify_tax_summary.py
setup.py
- Update setup.py. [Alex Hyer]
Incremented version number
- Update modify_tax_summary.py. [Alex Hyer]
Changed FileChecker to IOChecker
- Update setup.py. [Alex Hyer]
Incremented version number
- Update modify_tax_summary.py. [Alex Hyer]
Fixed bug in file checking
- Bug fix to modify_tax_summary.py. [Alex Jay Hyer]
- Added group_from_filenames under Mothur_tools. [Alex Jay Hyer]
group_from_filenames creates MOTHUR formatted group
files from FASTA fiel anmes. Thsi is much easier to do then
allowign MOTHUR to create the group file itself.
- ANother minor bug fix. [Alex Jay Hyer]
- Minor bug fix. [Alex Jay Hyer]
- Added convert_count_to_shared.py. [Alex Jay Hyer]
convert_count_to_shared added to mothur_tools. This script
effectively bypasses OTU generation in MOTHUR whiel allowing
downstream analysis.
- Fixed error output in modify_tax_summary and updated README. [Alex Jay
Hyer]
- Finalized file_check and modify_tax_summary. [Alex Jay Hyer]
Documentation in README.md will follow soon. file_check now contains
the class IOChecker which performs all file checking actions.
modify_tax_summary has a slightly different user interface and is
fully functional.
- Made changes to modify_tax_summary input. [Alex Jay Hyer]
- Fixed bug in modify_tax_summary. [Alex Jay Hyer]
- Added modify_tax_summary to console scripts. [Alex Jay Hyer]
- Added file_tools and mothur_tools. [Alex Jay Hyer]
All files now up to PEP standards. file_Tools created to house generic
file related tools. It currently contains a permission checking system
for reading and writing files. mothur_tools added to hold tools related
to assisst in processing files for and from Mothur. Currently contains
a taxonomy summary editing script.
- Blast_tools now also executable. [Alex Jay Hyer]
- Modified scripts so that console_scripts works. [Alex Jay Hyer]
- Testing creation of console scripts. [Alex Jay Hyer]
- Fixed FASTA iter. [Alex Jay Hyer]
- Fixed FASTA iter. [Alex Jay Hyer]
- Fixed FASTA iter. [Alex Jay Hyer]
- Fixed FASTA iter. [Alex Jay Hyer]
- Added FASTA iter. [Alex Jay Hyer]
- Fixed FASTA stop from alst commit. [Alex Jay Hyer]
- Fixed gff3_iter to stop reading before FASTA entries. [Alex Jay Hyer]
- Gff3_iter can now further parse attributes. [Alex Jay Hyer]
- Gff3_iter can now further parse attributes. [Alex Jay Hyer]
- Fixed import errors. [Alex Jay Hyer]
- Edited README. [TheOneHyer]
README now looks better
- Fixed Bug. [TheOneHyer]
Fixed bug from last update
- Update setup.py. [TheOneHyer]
setup.py now properly shows where packages are
- Don't Worry. [TheOneHyer]
Don't Worry
- Minor changes. [TheOneHyer]
Some minor changes, mostly with PEP formatting but more still needs to
be done
- Added retrieve_query_sequences.py. [TheOneHyer]
added retrieve_query_sequences.py to retrieve the query sequences of
BLAST hits from an M8 (BLAST+ output format 6) file. updated
retrieve_subject_sequences.py to remove bug where repeats were erased.
- Added blast_tools and documentation. [TheOneHyer]
added blast_tools which consists of scripts to assist with interpreting
and using BLAST data. Added documentation to stand-alone scripts. All
scripts tested and fully functional
- README Update. [TheOneHyer]
README updated to actually be a README
- Verifiers work as stand-alone scripts. [TheOneHyer]
All the file verifiers now work as stand alone programs in addition to
their previous function as an importable module. Each verifier simply
takes a single argument which is the file to verify and prints whether
or no the file is valid.
- Initial Commit. [TheOneHyer]
A package of Python Modules containing generally useful bioinformatic
scripts
- Initial commit. [Alex Hyer]