-------------------
- Added test_sam_verifier. [TheOneHyer]
Added test_sam_verifier and confirmed working
- Updated sam_verifier. [TheOneHyer]
Brough sam_verifier up to par with other verifiers,
untested.
- Improved CLI of gff3_verifier. [TheOneHyer]
gff3_verifier has better CLI as per other verifiers.
- Added test_gff3_verifier. [TheOneHyer]
Added test_gff3_verifier and confirmed working.
Changes to gff3_verifier based on test_gff3_verifier
- Improved test_b6_verifier. [TheOneHyer]
test_b6_verifier now tests multi-entry
case.
- Updated gff3_verifier. [TheOneHyer]
gff3_verifier updated to use errors.
Reduced code in b6_verifier.
- Added test_fastq_verifier. [TheOneHyer]
Added test_fastq_verifier and confirmed working.
- Improved fastq_verifier. [TheOneHyer]
fsatq_verifier brought up to standards with other
verifiers: not tested.
- Can select bytes for binary_verifier. [TheOneHyer]
binary_guesser now takes a bytes argument
which determines the number of bytes to use
to guess if a file is binary or not.
- Added test_binary_guesser. [TheOneHyer]
Added test_binary_guesser and confirmed working.
Fixed errors with binary_verifier as discovered by
test_binary_guesser.
- Streamlined b6_verifier. [TheOneHyer]
Significantly reduced the lines of code in
b6_verifiers and updated test_b6_verifier to
match. Updated __init__ of verifiers package
to fix error with order of imports.
- Updated binary_guesser. [TheOneHyer]
Updated binary_guesser to use FormatError, untested.
- Improved test_fasta_verifier. [TheOneHyer]
test_fasta_verifier improved to better
test just fasta_verifier
- Added test_b6_verifier. [TheOneHyer]
Added test_b6_verifier.py. Found better way
to unit test errors using classes directly.
- Updated b6_verifier. [TheOneHyer]
b6_verifier is now up to par with new standards but
is not tested. Updated fasta_verifier to work
better with piping.
- Added test_fasta_verifier. [TheOneHyer]
Added test_fasta_verifier and confirmed it worked.
- Added test_entry_verifier. [TheOneHyer]
Added test_entry_verifier and confirmed it works.
- Rolled Verifier Status to Alpha. [TheOneHyer]
Verifier status changed to alpha to reflect
their current developement state.
- Modified Verifiers Layout. [TheOneHyer]
Verifiers now use custom errors instead of
simply returning true or false in order to
give more fine tune data on what why a format
failed. verify_entries and fasta tested
successfully.
- Added test_subject_sequence_retriever. [TheOneHyer]
Added test_subject_sequence_retriever.py. Rolled
project version forward as all blast_tools are
now "complete."
- Added test_query_sequence_retriever.py. [TheOneHyer]
Added test_query_sequence_retriever.py and fixed bugs in
query_sequence_retriever.py
- Added test_b6_evalue_filter.py. [TheOneHyer]
Added test_b6_evalue_filter.py, made float fields of
iters return float and have hidden variable store original
formatting for the write() function. iter tests changed
to test these new conditions.
- Removed Redundant Code From blast_tools. [TheOneHyer]
retrieve_[query,subject]_sequences.py now call
filter_b6_evalue instead of copying code.
- Added *args and **kwargs to blast_tools scripts. [TheOneHyer]
*args and **kwargs allows b6_iter options to change
without needing to change code on blast_tools scripts.
- Added test_blast_to_cigar. [TheOneHyer]
Added test_blast_to_cigar.py. Both this test and
blast_to_cigar "complete."
- Added Example to subject_sequence_retriever. [TheOneHyer]
Forgot example last commit, rectifying.
- Made retrieve_subject_sequences.py Docs "Googley" [TheOneHyer]
Made retrieve_subject_sequences.py documentation
"Googley." Minro internal code improvements. Untested.
- Made retrieve_query_sequences.py Docs Googley. [TheOneHyer]
Made retrieve_query_sequences.py documentation
"Googley." Minor internal code improvements. Untested.
- Made retrieve_query_sequence.py Docs Googley. [TheOneHyer]
- Made filter_b6_evalue.py Documentation Googley. [TheOneHyer]
filter_b6_evalue.py documentation is now "Googley."
Fixed various errors in filter_b6_evalue.py script.
- Made blast_to_cigar.py Documentation Googley. [TheOneHyer]
blast_to_cigar.py documentation is now "Googley."
Added a raised exception to blast_to_cigar.py if
sequences aren't same length.
- Updated README.md. [TheOneHyer]
README.md updated to reflect project state
- Made sam_iter documentation Googley. [TheOneHyer]
sam_iter documentation is now "Googley."
Minor additions to documentations of other iterators.
Upped version number of iterators, tests, and project.
All iterators are now "complete."
- Made gff3_iter documentation Googley. [TheOneHyer]
gff3_iter documentation is "Googley."
Improved test_gff3_iter with more robust examples.
- Made b6_iter Documentation Googley. [TheOneHyer]
b6_iter is now "Googley" and b6_iter is "complete."
- Rolled Project Version to 0.7.14a1. [TheOneHyer]
Given the number of changes recently, it is fitting to
roll the project forward in the alpha for another large
version increase.
- Made fastq_iter Documentation Googley. [TheOneHyer]
fastq_iter documentation is now "Googley."
Updated fastq_iter to better test fsatq_entries.
fastq_iter "completed."
- Made fasta_iter Documentation Googley. [TheOneHyer]
fasta_iter documentation updated to be "Googley."
Rolled major version of fasta_iter to 3.0.0 as it is
"complete."
- Properly rolled Developement Status back to Alpha. [TheOneHyer]
Lower developement status in light of cahnges
- Added test_sam_iter, improved iterators. [TheOneHyer]
Added test_sam_iter. Modified iterators to use less code.
gff3_iter now properly skips FASTA files in GFF3 files.
Updated iterators to return inegers as appropriate.
- Fixed errors if gff3_iter, added test_gff3_iter. [TheOneHyer]
gff3_iter was returning an empty dictionary value when
a semicolon is at the end of the attributes line and attributes
were not ordered and thus returned in the same format they were
read. Both issues fixed. Added test_gff3_iter.
Comments added to certain scripts to prevent PyCharm from
throwing false-positive warning about iterators.
- Added test_gff3_iter and updated GFF3_iter. [TheOneHyer]
Updated gff3_iter to have ints where appropriate.
Added incomplete test_gff3_iter
- Fixed b6_iter and added unit test. [TheOneHyer]
Added test_b6_iter. Changed b6_iter values to ints
and floats as appropriate. write() still writes as string.
- Fixed Error in fastq_iter, added test_fastq_iter. [TheOneHyer]
fastq_iter had a major error, was fixed. test_fastq_iter added.
test_fasta_iter has new function to test header line ability.
- Updated Iterators and Added First Unit Test. [TheOneHyer]
Created tests directory, fasta_iter unit test, and
updated iterators to take any iterator.
- Updated gitignore and ChangeLog. [TheOneHyer]
Last commit didn't include changes to gitignore or
ChangeLog, rectifying
- Removed .pypirc. [TheOneHyer]
.pypirc was being inappropriately tracked, has been removed.
- Giant Changes. [TheOneHyer]
This commit sadly breaks normal rules of small commits
and will be the lsat of it's kind. This commit implements
huge changes and thus this commit message is giant.
* Added GitChangeLog package and created first ChangeLog.rst
* Updated Docuemntation
* Updated READEME
* Changed Copyright to GPLv3
* Added proper copyright infor to each file
* Greatly improved speed and flexibility of iterators
* Added FASTQ iterator
* Changed all isntances of 'm8' to 'b6' as appropriate
* Iterators tested for functionality
* verifiers updated for iterator changes, NOT TESTED
* blast_tools updated for iterator changes, NOT TESTED
* function documentation made 'Sphinxy'
* Created directory for future Sphinx documentation
* Added more package level imports
- Updated README.md. [TheOneHyer]
README.md updated to match recent changes.