| 27354a3 | Leighton Pritchard | 07 September 2016, 17:08:34 UTC | demote multiple records from error to warning, fix stop codons | 07 September 2016, 17:08:34 UTC |
| 4460fb8 | Leighton Pritchard | 18 April 2016, 16:58:11 UTC | Added warning notice to calculate_ani.py script | 18 April 2016, 16:58:11 UTC |
| 2799cb6 | widdowquinn | 04 November 2015, 15:35:40 UTC | genbank_get_genomes_by_taxon.py: First time in complete working state | 04 November 2015, 15:35:40 UTC |
| a93b432 | widdowquinn | 04 November 2015, 14:35:50 UTC | genbank_get_genomes_by_taxon.py: Gets as far as identifying contig UIDs for each assembly | 04 November 2015, 14:35:50 UTC |
| 0ca71cf | widdowquinn | 04 November 2015, 12:13:48 UTC | Merge branch 'master' of https://github.com/widdowquinn/scripts | 04 November 2015, 12:13:48 UTC |
| e8e2d35 | widdowquinn | 04 November 2015, 12:12:36 UTC | Added .gitignores | 04 November 2015, 12:12:36 UTC |
| 893a3ef | widdowquinn | 04 November 2015, 12:10:43 UTC | genbank_get_genomes_by_taxon.py: Added output directory check Code broken in this state | 04 November 2015, 12:10:43 UTC |
| c9a4a14 | widdowquinn | 04 November 2015, 11:10:14 UTC | genbank_get_genomes_by_taxon.py: Added script framework | 04 November 2015, 11:10:14 UTC |
| f579549 | widdowquinn | 09 January 2015, 18:13:07 UTC | Updated .gitignore | 09 January 2015, 18:13:07 UTC |
| 86f5d41 | widdowquinn | 25 October 2014, 13:09:22 UTC | Updated license text in code headers | 25 October 2014, 13:09:22 UTC |
| 305bc08 | widdowquinn | 25 October 2014, 12:49:01 UTC | Added -s --short option to stitch_six_frame_stops.py | 25 October 2014, 12:49:01 UTC |
| 4639313 | widdowquinn | 25 October 2014, 12:48:09 UTC | Changed from GPLv3 to MIT license | 25 October 2014, 12:48:09 UTC |
| 9de611c | widdowquinn | 02 October 2014, 13:03:25 UTC | Total time now also reported in HHMM. | 02 October 2014, 13:03:25 UTC |
| 5f21d2f | widdowquinn | 02 October 2014, 09:02:09 UTC | justify_me no longer reports subsections, and now reports standard HHMM times The new standard HHMM times are in addition to the decimal time reporting. This change was made for convenience when filling in new JHI timesheets. | 02 October 2014, 09:02:09 UTC |
| 56613d8 | widdowquinn | 12 August 2014, 08:48:46 UTC | Fixed separator string. There was an extra 'T' in the separator string that meant a Met was not being created in the appropriate place on one of the reverse strands. This is now fixed. | 12 August 2014, 08:48:46 UTC |
| 7555623 | widdowquinn | 18 June 2014, 19:48:19 UTC | Minor change to text output, and unification of topic names | 18 June 2014, 19:48:19 UTC |
| 2b968bb | widdowquinn | 22 March 2014, 09:59:02 UTC | Added excel_to_tab.scpt script, and updated README.md | 22 March 2014, 09:59:02 UTC |
| 7ddc0ff | widdowquinn | 16 March 2014, 13:01:29 UTC | rename_to_hash no longer clobbers. Added usage to README.md | 16 March 2014, 13:01:29 UTC |
| 5e2ce36 | widdowquinn | 16 March 2014, 12:46:20 UTC | rename_to_hash now catches empty inputs | 16 March 2014, 12:46:20 UTC |
| 7779b99 | widdowquinn | 16 March 2014, 12:37:50 UTC | Added rename_to_hash script | 16 March 2014, 12:37:50 UTC |
| 904bb42 | widdowquinn | 02 March 2014, 16:42:01 UTC | Updated README.md to reflect stitching script | 02 March 2014, 16:42:01 UTC |
| cec932f | widdowquinn | 02 March 2014, 16:35:55 UTC | Added licence/copyright and pep8 changes to stitch_six_frame_stops.py | 02 March 2014, 16:35:55 UTC |
| 3a27a57 | widdowquinn | 02 March 2014, 15:53:42 UTC | Merge branch 'master' of https://github.com/widdowquinn/scripts | 02 March 2014, 15:53:42 UTC |
| fc2cf9e | widdowquinn | 02 March 2014, 15:51:11 UTC | First addition of sequence stitching script | 02 March 2014, 15:51:11 UTC |
| 991b728 | widdowquinn | 01 March 2014, 19:06:12 UTC | Modified ANIb method better to match JSpecies The previously implemented BLASTN+ method did not correspond very well with the legacy BLASTN method used in JSpecies (http://www.imedea.uib.es/jspecies/). Two main changes were made. 1) The BLASTN command now uses -task blastn, to modify wordlength and other parameters to better match legacy BLASTN. This also required changes to gapopen and gapextend parameters (i.e. their removal) 2) As the max_target_seqs and num_alignments parameters cannot restrict tabular output to a single match, this is now managed in the script. ANIb output is now a much better match for JSpecies, but some differences remain. These appear to have been minor in testing. | 01 March 2014, 19:06:12 UTC |
| 5df0c24 | widdowquinn | 28 February 2014, 18:11:46 UTC | Fixed incorrect method name in output. Tidied FASTA file reading. | 28 February 2014, 18:11:46 UTC |
| 94b35d8 | widdowquinn | 23 February 2014, 10:59:28 UTC | Noted the one-line awk equivalent to nucmer_to_crunch.py | 23 February 2014, 10:59:28 UTC |
| f462254 | widdowquinn | 22 February 2014, 16:51:43 UTC | Fixed issue with two colons in a title | 22 February 2014, 16:51:43 UTC |
| 95dab38 | widdowquinn | 22 February 2014, 16:31:18 UTC | Merge branch 'master' of https://github.com/widdowquinn/scripts | 22 February 2014, 16:31:18 UTC |
| a848128 | widdowquinn | 22 February 2014, 16:30:28 UTC | Added nucmer_to_crunch.py script, with test data and corresponding README text. | 22 February 2014, 16:30:28 UTC |
| 3b11bc4 | Leighton Pritchard | 10 February 2014, 20:21:49 UTC | Changed title of README.md | 10 February 2014, 20:21:49 UTC |
| 61e106a | Leighton Pritchard | 10 February 2014, 20:12:38 UTC | Created README.md | 10 February 2014, 20:12:38 UTC |
| b99f03a | widdowquinn | 09 February 2014, 17:27:04 UTC | Added GPLv3 license file | 09 February 2014, 17:27:04 UTC |
| 53a967a | widdowquinn | 09 February 2014, 14:14:00 UTC | justify_me.py now calculates and reports basic summary | 09 February 2014, 14:14:00 UTC |
| 752fd66 | widdowquinn | 09 February 2014, 13:06:51 UTC | mp4_to_mp3 now handles filenames with spaces | 09 February 2014, 13:06:51 UTC |
| f7c1b32 | widdowquinn | 08 February 2014, 10:21:41 UTC | Merge branch 'master' of https://github.com/widdowquinn/scripts | 08 February 2014, 10:21:41 UTC |
| 0746ff1 | widdowquinn | 08 February 2014, 10:20:59 UTC | Added justify_me.py script | 08 February 2014, 10:20:59 UTC |
| 7f2d2f8 | widdowquinn | 07 February 2014, 11:38:07 UTC | Changed default output formats, and added 'tab' as output format | 07 February 2014, 11:38:07 UTC |
| 3123302 | widdowquinn | 06 February 2014, 16:23:24 UTC | Minor typo fixed | 06 February 2014, 16:23:24 UTC |
| c30a783 | widdowquinn | 06 February 2014, 16:14:06 UTC | Renamed readme.md -> README.md | 06 February 2014, 16:14:06 UTC |
| a70067c | widdowquinn | 06 February 2014, 16:13:04 UTC | Added run_MLST.py readme to readme.md | 06 February 2014, 16:13:04 UTC |
| b2cffb1 | widdowquinn | 06 February 2014, 16:12:15 UTC | Added run_MLST test data | 06 February 2014, 16:12:15 UTC |
| e363e7a | widdowquinn | 06 February 2014, 16:11:47 UTC | Added newline to STDOUT table, for display neatness. | 06 February 2014, 16:11:47 UTC |
| b31c4c6 | widdowquinn | 06 February 2014, 15:50:01 UTC | PEP8 corrections to run_MLST.py | 06 February 2014, 15:50:01 UTC |
| 2103a28 | widdowquinn | 06 February 2014, 15:44:57 UTC | run_MLST.py now assigns sequence types on an input dataset | 06 February 2014, 15:44:57 UTC |
| 329e088 | widdowquinn | 05 February 2014, 17:49:01 UTC | Added usage information to lead comments | 05 February 2014, 17:49:01 UTC |
| d302fc2 | widdowquinn | 04 February 2014, 21:32:33 UTC | run_MLST.py script now gives allele profiles | 04 February 2014, 21:32:33 UTC |
| 47f155b | widdowquinn | 04 February 2014, 18:59:39 UTC | run_MLST.py now working up to and including BLAST | 04 February 2014, 18:59:39 UTC |
| 1ce5f0b | widdowquinn | 04 February 2014, 17:51:04 UTC | Merge branch 'master' of https://github.com/widdowquinn/scripts | 04 February 2014, 17:51:04 UTC |
| 60248a8 | widdowquinn | 04 February 2014, 16:30:11 UTC | First addition of run_MLST.py Script not yet in working state. | 04 February 2014, 16:30:11 UTC |
| 40348fb | widdowquinn | 04 February 2014, 11:54:54 UTC | PEP8 corrections to tabular_to_wikitable.py | 04 February 2014, 11:54:54 UTC |
| 229b1e0 | widdowquinn | 04 February 2014, 11:51:38 UTC | Removed .gitignore from repo | 04 February 2014, 11:51:38 UTC |
| 826735a | widdowquinn | 04 February 2014, 11:27:23 UTC | Added --skip option, and modified USAGE text. | 04 February 2014, 11:27:23 UTC |
| cf2f16a | widdowquinn | 01 February 2014, 13:07:40 UTC | PEP8 corrections to run_tmhmm.py | 01 February 2014, 13:07:40 UTC |
| 3c55050 | widdowquinn | 01 February 2014, 13:04:42 UTC | PEP8 corrections to run_signal.py | 01 February 2014, 13:04:42 UTC |
| a73e797 | widdowquinn | 01 February 2014, 13:01:38 UTC | PEP8 corrections and usage information to restrict_long_contigs.py | 01 February 2014, 13:01:38 UTC |
| 719ffe5 | widdowquinn | 01 February 2014, 12:56:36 UTC | PEP8 fixes to get_NCBI_cds_from_protein.py | 01 February 2014, 12:56:36 UTC |
| e73082b | widdowquinn | 01 February 2014, 12:29:28 UTC | PEP8 corrections to draw_gd_all_core.py | 01 February 2014, 12:29:28 UTC |
| e5756f9 | widdowquinn | 31 January 2014, 19:11:28 UTC | PEP8 changes to calculate_ani.py | 31 January 2014, 19:11:28 UTC |
| ad44456 | widdowquinn | 31 January 2014, 18:36:27 UTC | First addition of tabular_to_wikitable.py script | 31 January 2014, 18:36:27 UTC |
| b3e6517 | widdowquinn | 31 January 2014, 16:23:49 UTC | Merge branch 'master' of https://github.com/widdowquinn/scripts | 31 January 2014, 16:23:49 UTC |
| 560aa3d | widdowquinn | 31 January 2014, 16:22:34 UTC | Removed stray .gitignore | 31 January 2014, 16:22:34 UTC |
| f08f0df | widdowquinn | 31 January 2014, 16:22:06 UTC | Removed stray .gitignore | 31 January 2014, 16:22:06 UTC |
| 9a357a4 | widdowquinn | 30 January 2014, 11:50:30 UTC | Merge branch 'master' of https://github.com/widdowquinn/scripts | 30 January 2014, 11:50:30 UTC |
| 7e96ebd | widdowquinn | 30 January 2014, 11:49:56 UTC | Added output image for draw_gd_all_core.py script | 30 January 2014, 11:49:56 UTC |
| 956273d | Leighton Pritchard | 29 January 2014, 23:37:12 UTC | Updated readme.md for iadhore.py URL | 29 January 2014, 23:37:12 UTC |
| 2a8c61c | widdowquinn | 28 January 2014, 21:34:09 UTC | Added more usage information for restrict_long_contigs.py | 28 January 2014, 21:34:09 UTC |
| 8069ab1 | widdowquinn | 28 January 2014, 21:30:04 UTC | Added example graphical output to calculate_ani.py script readme. | 28 January 2014, 21:30:04 UTC |
| 4b757e3 | widdowquinn | 28 January 2014, 21:26:14 UTC | Added example data graphical output for calculate_ani.py script. | 28 January 2014, 21:26:14 UTC |
| c173646 | widdowquinn | 28 January 2014, 21:21:38 UTC | Added four Caulobacter chromosomes as test data for the calculate_ani.py script. | 28 January 2014, 21:21:38 UTC |
| 7de98af | widdowquinn | 28 January 2014, 21:11:58 UTC | Changed mode of calculate_ani.py, draw_gd_all_core.py, get_NCBI_cds_from_protein.py to allow execution. | 28 January 2014, 21:11:58 UTC |
| 41fa271 | Leighton Pritchard | 28 January 2014, 21:08:05 UTC | Added one-line summary to draw_gd_all_core.py readme. | 28 January 2014, 21:08:05 UTC |
| 3d9b510 | Leighton Pritchard | 28 January 2014, 21:05:47 UTC | Added readme for draw_gd_all_core.py to readme.md. Note that the draw_gd_all_core.py script cannot yet be run as provided, as the data and the module iadhore.py are both absent. | 28 January 2014, 21:05:47 UTC |
| 6bec4db | widdowquinn | 28 January 2014, 08:49:20 UTC | Added restrict_long_contigs.py README to readme.md | 28 January 2014, 08:49:20 UTC |
| fca7a60 | Leighton Pritchard | 27 January 2014, 22:39:10 UTC | Updated .gitignore, and added get_NCBI_cds_from_protein docs to readme.md. | 27 January 2014, 22:39:10 UTC |
| 69743d2 | widdowquinn | 27 January 2014, 18:51:57 UTC | Fixed internal anchors | 27 January 2014, 18:51:57 UTC |
| 831723f | widdowquinn | 27 January 2014, 18:50:05 UTC | Added README for run_tmhmm.py, and corrected internal links. | 27 January 2014, 18:50:05 UTC |
| 92cb027 | widdowquinn | 27 January 2014, 18:46:59 UTC | Added run_signalp.py to readme.md. | 27 January 2014, 18:46:59 UTC |
| 16492b0 | widdowquinn | 27 January 2014, 18:33:41 UTC | Tried out GFM line breaks in README.md | 27 January 2014, 18:33:41 UTC |
| f7b87bf | widdowquinn | 27 January 2014, 18:31:27 UTC | Merge branch 'master' of https://github.com/widdowquinn/scripts | 27 January 2014, 18:31:27 UTC |
| cada352 | Leighton Pritchard | 27 January 2014, 18:28:33 UTC | Added readme.md with details for calculate_ani.py. | 27 January 2014, 18:28:33 UTC |
| 0002cd5 | Leighton Pritchard | 15 January 2014, 18:33:25 UTC | Added command-line option to use NUCmer's --maxmatch option. This can help if input sequences are distantly related. | 15 January 2014, 18:33:25 UTC |
| 4f7a12d | Leighton Pritchard | 15 January 2014, 18:25:08 UTC | Fixed several occurrences where the CUM_RETVALS global was not declared in a function. | 15 January 2014, 18:25:08 UTC |
| a9527a4 | Leighton Pritchard | 15 January 2014, 18:18:16 UTC | Modified calculate_ani.py script to: 1 - monitor the number of number of nonzero external return values in the multiprocessing step 2 - catch a divide by zero error on receiving 'empty' NUCmer output 3 - suggest the cause of the divide by zero problem on the basis of whether the NUCmer multiprocessing steps threw errors or not | 15 January 2014, 18:18:16 UTC |
| 51190db | Leighton Pritchard | 15 January 2014, 18:15:07 UTC | Updated bioinformatics script .gitignore | 15 January 2014, 18:15:07 UTC |
| c0c32fd | Leighton Pritchard | 15 January 2014, 18:14:23 UTC | Updated media script .gitignore | 15 January 2014, 18:14:23 UTC |
| 40a41b1 | Leighton Pritchard | 15 January 2014, 18:12:13 UTC | Merge branch 'master' of https://github.com/widdowquinn/scripts | 15 January 2014, 18:12:13 UTC |
| c839f78 | Leighton Pritchard | 15 January 2014, 18:11:46 UTC | Added mp4 to mp3 conversion script. | 15 January 2014, 18:11:46 UTC |
| d7d67f4 | Leighton Pritchard | 12 December 2013, 15:56:10 UTC | Added script to render large GenomeDiagram image, as example code for Twitter conversation (https://twitter.com/widdowquinn/status/411160563742294016). It is still lacking data, and the iadhore.py module which would be necessary to complete the figure, but it could act as a guide. | 12 December 2013, 15:56:10 UTC |
| 8273b29 | Leighton Pritchard | 20 November 2013, 11:52:34 UTC | First inclusion of SNP-finding script in repository. This script uses MUMmer (nucmer and snow-snps) to find all SNPs in uniquely-aligning regions, pairwise, between FASTA files in a supplied directory. | 20 November 2013, 11:52:34 UTC |
| 463e508 | Leighton Pritchard | 20 November 2013, 11:51:52 UTC | Modified logging behaviour. Specifying a logfile now writes to the file in parallel, rather than replacing sys.stderr outright. | 20 November 2013, 11:51:52 UTC |
| 4d9781f | Leighton Pritchard | 12 November 2013, 15:59:25 UTC | Added new licensing and copyright information to four scripts. | 12 November 2013, 15:59:25 UTC |
| cf32861 | Leighton Pritchard | 12 November 2013, 15:50:19 UTC | Revised copyright statement, and added GPL3 license. | 12 November 2013, 15:50:19 UTC |
| eef86be | Leighton Pritchard | 12 November 2013, 15:48:17 UTC | Modified the R command string to change bounds on the colour scale. | 12 November 2013, 15:48:17 UTC |
| 69d5ea5 | Leighton Pritchard | 10 November 2013, 10:42:18 UTC | Added emacs temp files to .gitignore | 10 November 2013, 10:42:18 UTC |
| f0d9603 | Leighton Pritchard | 10 November 2013, 10:39:31 UTC | Added header output to logfile | 10 November 2013, 10:39:31 UTC |
| 839af35 | Leighton Pritchard | 09 November 2013, 18:52:20 UTC | Added .gitignore file, and added graphics output format option to calculate_ani.py | 09 November 2013, 18:52:20 UTC |
| 2693940 | Leighton Pritchard | 09 November 2013, 17:44:48 UTC | Added ability to write log to a file with -l option. | 09 November 2013, 17:44:48 UTC |
| d63054b | Leighton Pritchard | 09 November 2013, 17:31:09 UTC | Fixed R code to account for when no comparisons give more than 90% identity/correlation. | 09 November 2013, 17:31:09 UTC |
| fd92bea | Leighton Pritchard | 09 November 2013, 16:54:06 UTC | Corrected fragsize -> options.fragsize as cmd-line options are globals. | 09 November 2013, 16:54:06 UTC |
