History¶
0.4.x (201x-xx-xx)¶
- Do some PEP8 fixes.
- Refactor orthodb module.
- Port code and tests to py33.
0.3.13 (2014-12-23)¶
- Move documentation to readthedocs.
- Do some PEP8 fixes.
- Replace library pp for multiprocessing.
0.3.12 (2013-11-14)¶
- Using Orthodb_ids for genes
- In order to get only those genes with no paralogs. We want only single-copy genes.
- Updated UnitTest for OrthoDB and BLAST
- 2013-11-12 Carlos Peña <mycalesis@gmail.com>
v0.3.11
Parallel running of function filter_reads of module NGS didn’t work because the depending function prune was not submitted to the parallel jobs. Fixed by importing the function inside filter_reads.
- 2013-11-11 Carlos Peña <mycalesis@gmail.com>
v0.3.10
Updated internal function filter_reads of module NGS. It is more efficient and much quicker now.
Added UnitTest for filter_reads function It is an internal function in the module NGS that extracts the FASTQ reads according to a BLAST table output and stores them into gene bins.
- 2013-11-07 Carlos Peña <mycalesis@gmail.com>
v0.3.9
Adding assembly_velvet.sh files These are used when doing assembly of contigs. If they are not in current folder they get downloaded from github.
- 2013-10-18 Carlos Peña <mycalesis@gmail.com>
v0.3.8
Primer design, only process .fas[ta]* ending files The funcion MUSCLE.designPrimers searches in a folder for files to design primers for. It accepted any file. Now it accept only files ending with the extension .fasta or .fas (case insensitive).
- 2013-10-04 Carlos Peña <mycalesis@gmail.com>
v0.3.7
BLAST database making Avoid redoing the BLAST database when user wants to use dustmaker as this is slow. If no dustmaker required, redo the database as it is quick to do.
- 2013-10-03 Carlos Peña <mycalesis@gmail.com>
- BLAST: splitting input FASTA files If the FASTA file doesn’t need to be splitted, then don’t remove the original file!
- 2013-10-03 Carlos Peña <mycalesis@gmail.com>
- Before BLAST, don’t split fasta file all the time Module BLAST, function blastn was spliting all input FASTA files so accelerate a BLAST. I happened even though the input FASTA consisted of few FASTA sequences. It now checks that it happens when the input file has more than 399 sequences.
- 2013-09-24 Carlos Peña <mycalesis@gmail.com>
- adding developers to front page
- 2013-09-20 Carlos Peña <mycalesis@gmail.com>
- end for now testing travis upgrading distribute adding distribute adding blast fixing run_test and removing it from readme adding build status using Travis CI adding script for tests adding dependencies adding dependencies adding language to travis start using travis ci fixing right extension for Bombyx_exons
- 2013-09-19 Carlos Peña <mycalesis@gmail.com>
- polishing test for BLAST
- 2013-09-18 Carlos Peña <mycalesis@gmail.com>
- adding more genes for tests, even adding more genes for testing and fixing doc adding two more genes for testing adding test_getLargestExon and fixing typo in docs
- 2013-09-16 Carlos Peña <mycalesis@gmail.com>
- version 0.3.5
- 2013-09-14 Carlos Peña <mycalesis@gmail.com>
- preparing separtion by index function to be used in parallel
- 2013-09-13 Carlos Peña <mycalesis@gmail.com>
- using parallel python for dividing reads into bins according to genes fixing typo in documentation
- 2013-09-12 Carlos Peña <mycalesis@gmail.com>
- unittest for test_blastn continue unittest BLAST module more unittest for BLAST module
- 2013-09-08 Carlos Peña <mycalesis@gmail.com>
- adding script to run all unit tests
- 2013-09-04 Carlos Peña <mycalesis@gmail.com>
- package cleaning file cleaning removing unneeded files
- 2013-08-31 Carlos Peña <mycalesis@gmail.com>
- unittest for BLAST in part OrthoDB unittest end start writing unittests removing unneded DB module
- 2013-08-05 Carlos.Peña <mycalesis@gmail.com>
- adding Python version 2.7
- 2013-07-17 mezarino <vm_solism@yahoo.es>
- Set ‘mask=True’ as the default for our blastn function; and eliminated ‘-parse_seqids’ option from the command. We made mask=True as the default for blastn, so that low-complexity regions are discarded previous the blast. On the other hand, we eliminated ‘-parse_seqids’ option to make the function suitable for local databases, whose sequences have ID formats different to those defined by NCBI.
- 2013-07-06 Carlos.Peña <mycalesis@gmail.com>
- removing unneded files
- 2013-07-05 Carlos.Peña <mycalesis@gmail.com>
- adding some info for module NGS
- 2013-07-05 Carlos Pena <mycalesis@gmail.com>
- end assembly scripts
- 2013-06-28 Carlos Pena <mycalesis@gmail.com>
- making sure we use FASTA instead of FAS
- 2013-06-26 mezarino <vm_solism@yahoo.es>
- Update BLAST.py
- 2013-06-25 Carlos Pena <mycalesis@gmail.com>
- continue from NGS.parse_blats_results
- 2013-06-24 Carlos Pena <mycalesis@gmail.com>
- show how to do bluntSplicing of FASTA sequences adding blast to requirements instructions for MUSCLE under windows pointing online documentation adding beautiful soup to dependency list
- 2013-06-21 Carlos.Peña <mycalesis@gmail.com>
- Preparing inofile.fastq: removing indexes before BLASTn Filtering of FASTQ reads, accepting those that align more than 40 bp to expected genes
- 2013-06-20 Carlos Pena <mycalesis@gmail.com>
- adding assembly function index bins prefixed by “index_“
- 2013-06-19 Carlos.Peña <mycalesis@gmail.com>
- levenshtein distance = 0 output messages BLAST.blastn output message NGS.prepare_data output to data/modified
- 2013-06-16 Carlos.Peña <mycalesis@gmail.com>
- barcode length as variable
- 2013-06-14 Carlos.Peña <mycalesis@gmail.com>
- doc files doc files
- 2013-06-14 Carlos Pena <mycalesis@gmail.com>
- adding info for separation by index batch of gene files into indexes
- 2013-06-13 Carlos Pena <mycalesis@gmail.com>
- start separation by index saving gene files into output folder filtering reads according to gene match changing folder to folder_path adding folder argument fo bluntSplicer fixes
- 2013-06-12 Carlos.Peña <mycalesis@gmail.com>
- split ionfile
- 2013-06-12 Carlos Pena <mycalesis@gmail.com>
- fixing typo script for NGS analysis splitting BLAST output and ionrun data preparing fasta file
- 2013-06-12 mezarino <vm_solism@yahoo.es>
- Update MUSCLE.py bluntSplicer function: MSA-objects splicer was incorporated.
- 2013-06-11 Carlos.Peña <mycalesis@gmail.com>
- NGS analysis some text in NGS analysis
- 2013-06-11 Carlos Pena <mycalesis@gmail.com>
- start guide for iontorrent data analysis
- 2013-06-11 mezarino <vm_solism@yahoo.es>
- Update BLAST.py
- 2013-06-10 Carlos.Peña <mycalesis@gmail.com>
- small fix, @echo
- 2013-06-10 Carlos Pena <mycalesis@gmail.com>
- start IonTorrent NGS analysis fix do primers
- 2013-06-10 Carlos.Peña <mycalesis@gmail.com>
- fixing silkgenome blast
- 2013-06-10 Carlos Pena <mycalesis@gmail.com>
- sequences with taxon header between brackets primer design alingment warmimg
- 2013-06-09 Carlos Pena <mycalesis@gmail.com>
- doing alignment do_gene_search.py do Heliconius
- 2013-06-09 Carlos.Peña <mycalesis@gmail.com>
- do_gene_search.py Doing BLASTn fixing downloading silkgenome adding Makefile for reproducible analysis removing README.txt file fastx-toolkit as reference adding instructions to install dependencies
- 2013-06-06 Carlos Pena <mycalesis@gmail.com>
- fixing importin upper case modules
- 2013-05-15 Carlos.Peña <mycalesis@gmail.com>
- adding dependencies
- 2013-04-24 Carlos.Peña <mycalesis@gmail.com>
- end primers section
- 2013-04-22 Carlos Pena <mycalesis@gmail.com>
- printing primer desing restuls to file
- 2013-04-20 Carlos.Peña <mycalesis@gmail.com>
- removing old scripts
- 2013-04-19 Carlos.Peña <mycalesis@gmail.com>
- changing headers design primers in MUSCLE module
- 2013-04-19 Carlos Pena <mycalesis@gmail.com>
- designing primers
- 2013-04-19 Carlos.Peña <mycalesis@gmail.com>
- primer design adding MUSCLE to dependencies fixing MUSCLE documentation: exon alignment
- 2013-04-18 mezarino <vm_solism@yahoo.es>
- Update MUSCLE.py Update MUSCLE.py The code has been change accordingly to recognize the ID format of the input sequences. Update BLAST.py Now the IDs of the stored sequences have the NCBI’s format.
- 2013-04-18 Carlos.Peña <mycalesis@gmail.com>
- adding sp_name adding sp_name for parsing BLAST table fixing documentation fixing documentation
- 2013-04-17 mezarino <vm_solism@yahoo.es>
- Update OrthoDB.py The statement “print gene ...” from single_copy_genes function was removed because it’s irrelevant to print that information. Update BLAST.py The sp_name parameter was add to the function blastParser.
- 2013-04-17 Carlos.Peña <mycalesis@gmail.com>
- editing documentation saving alignments into folder
- 2013-04-17 Carlos Pena <mycalesis@gmail.com>
- adding muscle.py updating quick guide merge
- 2013-04-13 Carlos.Peña <mycalesis@gmail.com>
- documentation: Exon alignment
- 2013-04-12 Carlos.Peña <mycalesis@gmail.com>
- Heliconius Heliconius working with Danaus working with Danaus
- 2013-04-11 Carlos.Peña <mycalesis@gmail.com>
- blasting Danaus blasting Danaus dont print divisor dont print divisor editing module editing module
- 2013-04-10 Carlos Pena <mycalesis@gmail.com>
- adding instuctions and distrubuted script adding instuctions and distrubuted script using distribute using distribute fixing code blocks fixing code blocks
- 2013-04-10 Carlos.Peña <mycalesis@gmail.com>
- adding install pp to README adding install pp to README
- 2013-04-09 Carlos Pena <mycalesis@gmail.com>
- adding progress bar to blastn adding progress bar to blastn
- 2013-04-09 Carlos.Peña <mycalesis@gmail.com>
- do parallel blast, part do parallel blast, part
- 2013-04-08 Carlos Pena <mycalesis@gmail.com>
- fixing argument in blastn function fixing argument in blastn function
- 2013-04-06 Carlos.Peña <mycalesis@gmail.com>
- using WTF public license using WTF public license
- 2013-04-05 Carlos.Peña <mycalesis@gmail.com>
- expanded BLAST module expanded BLAST module
- 2013-04-05 Carlos Pena <mycalesis@gmail.com>
- Merge branch ‘BlastExonParser’ output a list of candidate genes Merge branch ‘BlastExonParser’ output a list of candidate genes including blast table parse functions in BLAST module including blast table parse functions in BLAST module including blast table parse functions in BLAST module including blast table parse functions in BLAST module including blast table parse functions in BLAST module including blast table parse functions in BLAST module
- 2013-04-04 Carlos.Peña <mycalesis@gmail.com>
- removing blank pages from documentation pdf removing blank pages from documentation pdf adding print messages adding print messages ignoring csv gz zip files ignoring csv gz zip files edited script edited script
- 2013-03-23 Carlos.Peña <mycalesis@gmail.com>
- making db making db
- 2013-03-12 Carlos Pena <mycalesis@gmail.com>
- doc doc guide - blast part guide - blast part blast script blast script blast script by Mezarino blast script by Mezarino
- 2013-03-10 Carlos.Peña <mycalesis@gmail.com>
- TODO blast TODO blast gitignore gitignore
- 2013-03-08 Carlos Pena <mycalesis@gmail.com>
- some work on BLAST some work on BLAST
- 2013-03-05 Carlos.Peña <mycalesis@gmail.com>
- get_cds intro adding get_cds intro adding get_cds intro function get_cds function get_cds getting cds file getting cds file removing build filess removing build filess 0.2.0 0.2.0
- 2013-03-04 Carlos.Peña <mycalesis@gmail.com>
- including documentation in HTML files including documentation in HTML files
- 2013-03-04 Carlos Pena <mycalesis@gmail.com>
- OrthoDB and documentation OrthoDB and documentation start documentation start documentation
- 2013-03-04 Carlos.Peña <mycalesis@gmail.com>
- fixes fixes setup fixes setup fixes
- 2013-01-28 Carlos.Peña <mycalesis@gmail.com>
- modified: README.md modified: README.md
- 2012-12-05 Carlos Pena <mycalesis@gmail.com>
- author mezarino author mezarino ready script ready script
- 2012-12-05 Carlos.Peña <mycalesis@gmail.com>
- finished script finished script
- 2012-12-04 Carlos.Peña <mycalesis@gmail.com>
- arg species_name arg species_name added pars arguments added pars arguments work in progress work in progress initial script initial script
- 2012-11-29 Carlos.Peña <mycalesis@gmail.com>
- readme in reST readme in reST
- 2012-11-28 Carlos.Peña <mycalesis@gmail.com>
- adding OrthoDB6 gene table adding OrthoDB6 gene table adding OrthoDB6 gene table adding OrthoDB6 gene table
- 2012-11-28 Carlos Pena <mycalesis@gmail.com>
- update README update README
- 2012-11-28 Carlos.Peña <mycalesis@gmail.com>
- finish renaming repository finish renaming repository BLAST.py BLAST.py
- 2012-11-27 Carlos.Peña <mycalesis@gmail.com>
- Merge remote-tracking branch ‘mezarino/master’ update Blast script Merge remote-tracking branch ‘mezarino/master’ update Blast script
- 2012-11-27 mezarino <vm_solism@yahoo.es>
- Update pyphylogenomics/BLAST.py Update pyphylogenomics/BLAST.py
- 2012-11-27 Carlos.Peña <mycalesis@gmail.com>
- more scripts more scripts adding scripts adding scripts
- 2012-11-25 Carlos.Peña <mycalesis@gmail.com>
test README test README rename rename
setup.py setup.pyrename rename renaming repository renaming repository
- 2012-09-23 Carlos.Peña <mycalesis@gmail.com>
- more scripts more scripts
- 2012-05-14 Carlos.Peña <mycalesis@gmail.com>
- README markdown README markdown
v0.1.0, 2012-04-08 – Initial release