| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2014-03-25 | update selectivity equation, and update readme | Calvin Morrison | |
| 2014-03-25 | revert makefile | Calvin Morrison | |
| 2014-03-25 | add average binding filter | Calvin Morrison | |
| 2014-03-25 | don't populate, use the bg conts from selectivity | Calvin Morrison | |
| 2014-03-25 | update header | Calvin Morrison | |
| 2014-03-25 | fix len | Calvin Morrison | |
| 2014-03-25 | working upscore_wrapper.sh | Calvin Morrison | |
| Score wrapper essentially does a few things 1) backgrounds score_mers.py 2) creates an intercept for any Ctrl+C 3) waits for score_mers.py to finish 4) if there's an intercept, send a SEGV to the process and try and exit it works, it might be dirty, you might see some output... but still at least you can exit now | |||
| 2014-03-25 | formatting changes, pylint up in this b**** | Calvin Morrison | |
| 2014-03-25 | remove stray ; | Calvin Morrison | |
| 2014-03-25 | add score wrapper and SelectiveGenomeUI to make install | Calvin Morrison | |
| 2014-03-25 | start to add debug variable to score_mers | Calvin Morrison | |
| 2014-03-25 | Update scoring function. | Calvin Morrison | |
| Before we were incorrectly scoring our background. Using the new equation: score = (nb_primers * fg_mean_dist * fg_variance_dist) / (bg_ratio) where bg_ratio is bg_genome_length / count_of_bg_mers This will be faster, and will simplify our code (no whcky appends or anything. It can be even faster if we want to by not even storing the background points, just their hits. Should be relatively easy to do that. | |||
| 2014-03-24 | add non-functioning score wrapper | Calvin Morrison | |
| 2014-03-24 | Major Updates: | Calvin Morrison | |
| SelectiveGenomeAmplication: remove need (again) for any temporary fasta file, instead do all parsing in house with strstreamone and python correctly get reverse compliment. a combination of tac and rev, not just tac add non_melitng and filtered_binding variables to bash for clarity and to reduce clutter score_mers: This should speed up our loading and memory and probably each job since there's less memory overhead. revamp mer points - remove class, save as arrays instead - only allocate mers we need, - don't bother getting counts - reduce command line arguments - use original fasta files now, so it's easier for a user to use (as per issue #5 - remove weird pop_fg/bg functions - add one to total incase of zero div. | |||
| 2014-03-24 | use biopython's temperature calculator... slow as dirt | Calvin Morrison | |
| 2014-03-24 | fix strstream to work with mers list | Calvin Morrison | |
| 2014-03-24 | add below and fix tabs | Calvin Morrison | |
| 2014-03-23 | add mer list reading to strstream | Calvin Morrison | |
| 2014-03-21 | add end of sequences in as points in our array | Calvin Morrison | |
| 2014-03-21 | fix warning | Calvin Morrison | |
| 2014-03-21 | add sequence length command | Calvin Morrison | |
| 2014-03-19 | add output also to scores file | Calvin Morrison | |
| 2014-03-18 | update scoring equation | Calvin Morrison | |
| 2014-03-17 | fix issue with readme | Calvin Morrison | |
| 2014-03-13 | whistpace and 1 | Calvin Morrison | |
| 2014-03-13 | Refactoring, features, rage! | Calvin Morrison | |
| - rename apply filters to filter_mers - return True instead of False - Use this function in score mers - Add total scored check - use np.diff() instead of manually doing it for fg. - fix long line comments - check if len bg_pts <= 1 | |||
| 2014-03-13 | add coutning points for reverses | Calvin Morrison | |
| 2014-03-13 | add comments, add workflow explaination, move pop_{fg,bg} fns | Calvin Morrison | |
| 2014-03-13 | refactor binding layout, add comments | Calvin Morrison | |
| 2014-03-13 | add message and don't >> | Calvin Morrison | |
| 2014-03-06 | use kmer_continuous_count instead of kmer_total_count, remove tmp file, ↵ | Calvin Morrison | |
| update parameters for select_mers.py | |||
| 2014-03-05 | fix background as foreground | Calvin Morrison | |
| 2014-03-05 | should work: | Calvin Morrison | |
| 2014-03-05 | more verbose score output | Calvin Morrison | |
| 2014-03-05 | fix type | Calvin Morrison | |
| 2014-03-03 | update defaults and align variable names with global env variables | Calvin Morrison | |
| 2014-03-03 | update readnme | Calvin Morrison | |
| 2014-03-03 | update readnme | Calvin Morrison | |
| 2014-03-03 | add load_heterodimer_dic function | Calvin Morrison | |
| 2014-03-03 | check heterodimer dic first because it's likely to be the #1 cause of issues | Calvin Morrison | |
| 2014-03-03 | add check to see if results are even possible, and use gzip out | Calvin Morrison | |
| 2014-03-03 | update arguemnts, make {fg,bg}_genome_length global | Calvin Morrison | |
| 2014-03-03 | update parameters file | Calvin Morrison | |
| 2014-02-17 | output filters into output directory not temp to enable multiple runs at once | Calvin Morrison | |
| 2014-02-05 | use a ifilter outside | Calvin Morrison | |
| 2014-02-04 | seperate out scoring stuff into our iterator as a filter | Calvin Morrison | |
| 2014-02-04 | add check functions to filter without calling the jobs | Calvin Morrison | |
| 2014-02-04 | max_consecutive speed up | Calvin Morrison | |
| 2014-02-04 | update save locations | Calvin Morrison | |
| 2014-01-30 | update score mers with hererodimers | Calvin Morrison | |
 |
index : SelectiveWholeGenomeAmplification.git | |
| Parameterized sweeps of FASTA files to help locate useful primers. Work done for Penn bio research guys |
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