| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2014-04-08 | add lock | Calvin Morrison | |
| 2014-04-08 | update arg info | Calvin Morrison | |
| 2014-04-07 | tabular output | Calvin Morrison | |
| 2014-04-07 | working output full genome.py | Calvin Morrison | |
| 2014-04-07 | fix stream counting so it doesn't count over | Calvin Morrison | |
| 2014-04-07 | initial commit of output_full_genome.py | Calvin Morrison | |
| 2014-04-07 | add genome length | Calvin Morrison | |
| 2014-04-07 | +x average_binding | Calvin Morrison | |
| 2014-04-07 | fix reverse counts and output genome length | Calvin Morrison | |
| 2014-04-02 | add exit codes | Calvin Morrison | |
| 2014-04-01 | remove a debug line | Calvin Morrison | |
| 2014-04-01 | add feature to read from previously scored all-scores file, clean up code as ↵ | Calvin Morrison | |
| well | |||
| 2014-04-01 | check exit status and more error checking in check_feasilbe | Calvin Morrison | |
| 2014-03-31 | fix bug in using combination file. this closes #18 | Calvin Morrison | |
| 2014-03-31 | add UI for scorign func, update doc and varaibles | Calvin Morrison | |
| 2014-03-31 | add scorign to header and paramters and such | Calvin Morrison | |
| 2014-03-31 | add custom scoring | Calvin Morrison | |
| 2014-03-31 | proper sizes with custom mers | Calvin Morrison | |
| 2014-03-31 | This closes bug #19. adds variables into the scoring header for later reference | Calvin Morrison | |
| 2014-03-31 | Add feature to have a top-scores file. closes issue #21 | Calvin Morrison | |
| 2014-03-27 | Scoring all mer combinations from a file with a -m | Calvin Morrison | |
| 2014-03-27 | improve output, add number of primers in first colum. this closes #12 | Calvin Morrison | |
| 2014-03-27 | move stuff around | Calvin Morrison | |
| 2014-03-27 | Add scoring for specific combinations. | Calvin Morrison | |
| - add scoring for specific combos - update readme - add CLI args for score_mers.py - update score_wrapper - use more generic print functions in score_mers | |||
| 2014-03-26 | majorly rewrite and revamp the script to support runnign parts at a time | Calvin Morrison | |
| 2014-03-26 | add primer_weight to our score function | Calvin Morrison | |
| 2014-03-26 | use float | Calvin Morrison | |
| 2014-03-25 | Score mer statistics. This closes #6 | Calvin Morrison | |
| 2014-03-25 | update selectivity equation, and update readme | 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 | 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 | |
| 2014-03-23 | 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 | |
| 2014-03-13 | 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 | |||
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index : SelectiveWholeGenomeAmplification.git | |
| Parameterized sweeps of FASTA files to help locate useful primers. Work done for Penn bio research guys |
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