-------------------
* 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 <mycalesisgmail.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 <mycalesisgmail.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 <mycalesisgmail.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 <mycalesisgmail.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 <mycalesisgmail.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 <mycalesisgmail.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 <mycalesisgmail.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 <mycalesisgmail.com>
adding developers to front page
2013-09-20 Carlos Peña <mycalesisgmail.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 <mycalesisgmail.com>
polishing test for BLAST
2013-09-18 Carlos Peña <mycalesisgmail.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 <mycalesisgmail.com>
version 0.3.5
2013-09-14 Carlos Peña <mycalesisgmail.com>
preparing separtion by index function to be used in parallel
2013-09-13 Carlos Peña <mycalesisgmail.com>
using parallel python for dividing reads into bins according to genes
fixing typo in documentation
2013-09-12 Carlos Peña <mycalesisgmail.com>
unittest for test_blastn
continue unittest BLAST module
more unittest for BLAST module
2013-09-08 Carlos Peña <mycalesisgmail.com>
adding script to run all unit tests
2013-09-04 Carlos Peña <mycalesisgmail.com>
package cleaning
file cleaning
removing unneeded files
2013-08-31 Carlos Peña <mycalesisgmail.com>
unittest for BLAST in part
OrthoDB unittest end
start writing unittests
removing unneded DB module
2013-08-05 Carlos.Peña <mycalesisgmail.com>
adding Python version 2.7
2013-07-17 mezarino <vm_solismyahoo.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 <mycalesisgmail.com>
removing unneded files
2013-07-05 Carlos.Peña <mycalesisgmail.com>
adding some info for module NGS
2013-07-05 Carlos Pena <mycalesisgmail.com>
end assembly scripts
2013-06-28 Carlos Pena <mycalesisgmail.com>
making sure we use FASTA instead of FAS
2013-06-26 mezarino <vm_solismyahoo.es>
Update BLAST.py
2013-06-25 Carlos Pena <mycalesisgmail.com>
continue from NGS.parse_blats_results
2013-06-24 Carlos Pena <mycalesisgmail.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 <mycalesisgmail.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 <mycalesisgmail.com>
adding assembly function
index bins prefixed by "index_"
2013-06-19 Carlos.Peña <mycalesisgmail.com>
levenshtein distance = 0
output messages
BLAST.blastn output message
NGS.prepare_data output to data/modified
2013-06-16 Carlos.Peña <mycalesisgmail.com>
barcode length as variable
2013-06-14 Carlos.Peña <mycalesisgmail.com>
doc files
doc files
2013-06-14 Carlos Pena <mycalesisgmail.com>
adding info for separation by index
batch of gene files into indexes
2013-06-13 Carlos Pena <mycalesisgmail.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 <mycalesisgmail.com>
split ionfile
2013-06-12 Carlos Pena <mycalesisgmail.com>
fixing typo
script for NGS analysis
splitting BLAST output and ionrun data
preparing fasta file
2013-06-12 mezarino <vm_solismyahoo.es>
Update MUSCLE.py
bluntSplicer function: MSA-objects splicer was incorporated.
2013-06-11 Carlos.Peña <mycalesisgmail.com>
NGS analysis
some text in NGS analysis
2013-06-11 Carlos Pena <mycalesisgmail.com>
start guide for iontorrent data analysis
2013-06-11 mezarino <vm_solismyahoo.es>
Update BLAST.py
2013-06-10 Carlos.Peña <mycalesisgmail.com>
small fix, echo
2013-06-10 Carlos Pena <mycalesisgmail.com>
start IonTorrent NGS analysis
fix do primers
2013-06-10 Carlos.Peña <mycalesisgmail.com>
fixing silkgenome blast
2013-06-10 Carlos Pena <mycalesisgmail.com>
sequences with taxon header between brackets
primer design
alingment warmimg
2013-06-09 Carlos Pena <mycalesisgmail.com>
doing alignment
do_gene_search.py do Heliconius
2013-06-09 Carlos.Peña <mycalesisgmail.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 <mycalesisgmail.com>
fixing importin upper case modules
2013-05-15 Carlos.Peña <mycalesisgmail.com>
adding dependencies
2013-04-24 Carlos.Peña <mycalesisgmail.com>
end primers section
2013-04-22 Carlos Pena <mycalesisgmail.com>
printing primer desing restuls to file
2013-04-20 Carlos.Peña <mycalesisgmail.com>
removing old scripts
2013-04-19 Carlos.Peña <mycalesisgmail.com>
changing headers
design primers in MUSCLE module
2013-04-19 Carlos Pena <mycalesisgmail.com>
designing primers
2013-04-19 Carlos.Peña <mycalesisgmail.com>
primer design
adding MUSCLE to dependencies
fixing MUSCLE
documentation: exon alignment
2013-04-18 mezarino <vm_solismyahoo.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 <mycalesisgmail.com>
adding sp_name
adding sp_name for parsing BLAST table
fixing documentation
fixing documentation
2013-04-17 mezarino <vm_solismyahoo.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 <mycalesisgmail.com>
editing documentation
saving alignments into folder
2013-04-17 Carlos Pena <mycalesisgmail.com>
adding muscle.py
updating quick guide
merge
2013-04-13 Carlos.Peña <mycalesisgmail.com>
documentation: Exon alignment
2013-04-12 Carlos.Peña <mycalesisgmail.com>
Heliconius
Heliconius
working with Danaus
working with Danaus
2013-04-11 Carlos.Peña <mycalesisgmail.com>
blasting Danaus
blasting Danaus
dont print divisor
dont print divisor
editing module
editing module
2013-04-10 Carlos Pena <mycalesisgmail.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 <mycalesisgmail.com>
adding install pp to README
adding install pp to README
2013-04-09 Carlos Pena <mycalesisgmail.com>
adding progress bar to blastn
adding progress bar to blastn
2013-04-09 Carlos.Peña <mycalesisgmail.com>
do parallel blast, part
do parallel blast, part
2013-04-08 Carlos Pena <mycalesisgmail.com>
fixing argument in blastn function
fixing argument in blastn function
2013-04-06 Carlos.Peña <mycalesisgmail.com>
using WTF public license
using WTF public license
2013-04-05 Carlos.Peña <mycalesisgmail.com>
expanded BLAST module
expanded BLAST module
2013-04-05 Carlos Pena <mycalesisgmail.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 <mycalesisgmail.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 <mycalesisgmail.com>
making db
making db
2013-03-12 Carlos Pena <mycalesisgmail.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 <mycalesisgmail.com>
TODO blast
TODO blast
gitignore
gitignore
2013-03-08 Carlos Pena <mycalesisgmail.com>
some work on BLAST
some work on BLAST
2013-03-05 Carlos.Peña <mycalesisgmail.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 <mycalesisgmail.com>
including documentation in HTML files
including documentation in HTML files
2013-03-04 Carlos Pena <mycalesisgmail.com>
OrthoDB and documentation
OrthoDB and documentation
start documentation
start documentation
2013-03-04 Carlos.Peña <mycalesisgmail.com>
fixes
fixes
setup fixes
setup fixes
2013-01-28 Carlos.Peña <mycalesisgmail.com>
modified: README.md
modified: README.md
2012-12-05 Carlos Pena <mycalesisgmail.com>
author mezarino
author mezarino
ready script
ready script
2012-12-05 Carlos.Peña <mycalesisgmail.com>
finished script
finished script
2012-12-04 Carlos.Peña <mycalesisgmail.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 <mycalesisgmail.com>
readme in reST
readme in reST
2012-11-28 Carlos.Peña <mycalesisgmail.com>
adding OrthoDB6 gene table
adding OrthoDB6 gene table
adding OrthoDB6 gene table
adding OrthoDB6 gene table
2012-11-28 Carlos Pena <mycalesisgmail.com>
update README
update README
2012-11-28 Carlos.Peña <mycalesisgmail.com>
finish renaming repository
finish renaming repository
BLAST.py
BLAST.py
2012-11-27 Carlos.Peña <mycalesisgmail.com>
Merge remote-tracking branch 'mezarino/master'
update Blast script
Merge remote-tracking branch 'mezarino/master'
update Blast script
2012-11-27 mezarino <vm_solismyahoo.es>
Update pyphylogenomics/BLAST.py
Update pyphylogenomics/BLAST.py
2012-11-27 Carlos.Peña <mycalesisgmail.com>
more scripts
more scripts
adding scripts
adding scripts
2012-11-25 Carlos.Peña <mycalesisgmail.com>
test README
test README
rename
rename
setup.py
setup.py
rename
rename
renaming repository
renaming repository
2012-09-23 Carlos.Peña <mycalesisgmail.com>
more scripts
more scripts
2012-05-14 Carlos.Peña <mycalesisgmail.com>
README markdown
README markdown