HullUni-bioinformatics/ReproPhylo issues and pull requests

#62 - How to keep only one sequence per species (after the remonal of the outliers)?

Issue - State: open - Opened by yannisdim over 6 years ago

#61 - mafft version cannot be parsed in V7.221

Issue - State: closed - Opened by szitenberg almost 9 years ago - 1 comment
Labels: bug

#60 - get_qualifiers_dictionary fetches from wrong record

Issue - State: closed - Opened by szitenberg almost 9 years ago - 3 comments
Labels: bug

#59 - Auto-generate short methods section?

Issue - State: open - Opened by kcranston over 9 years ago - 1 comment

#58 - When pickle_pj, confirm pickle name == repo description

Issue - State: open - Opened by szitenberg over 9 years ago

#57 - exclude brakes on first execution and then runs OK in tthe second

Issue - State: closed - Opened by szitenberg almost 10 years ago - 1 comment
Labels: bug

#56 - Things to fix before publication

Issue - State: open - Opened by szitenberg almost 10 years ago

#55 - exonerate_ryo_to_gb

Issue - State: open - Opened by szitenberg almost 10 years ago

#54 - Allow opting-out droping seq poor loci in alignment

Issue - State: open - Opened by szitenberg almost 10 years ago

#53 - Git and Pickle integration in ReproPhylo

Issue - State: closed - Opened by szitenberg almost 10 years ago

#52 - Fix PAUP charset reader

Issue - State: closed - Opened by szitenberg almost 10 years ago - 1 comment

#51 - N for missing data in prot concat

Issue - State: closed - Opened by szitenberg about 10 years ago - 1 comment
Labels: bug

#50 - Report scalability

Issue - State: open - Opened by szitenberg about 10 years ago

#49 - make 'iterate non source features'

Issue - State: open - Opened by szitenberg about 10 years ago - 1 comment

#48 - sort pj.fta and fa to return independent objets

Issue - State: closed - Opened by szitenberg about 10 years ago

#47 - Project allows reading Locus instead of a list

Issue - State: closed - Opened by szitenberg about 10 years ago
Labels: bug

#46 - add raxmlHPC f S alignment column statistic?

Issue - State: open - Opened by szitenberg about 10 years ago

#45 - possible biopython sequence statistics to add

Issue - State: open - Opened by szitenberg about 10 years ago

#44 - get list_loci_in_genbank to also accept embl files

Issue - State: open - Opened by szitenberg about 10 years ago

#43 - consider to_dict or index for pj.records. IMPORTANT

Issue - State: open - Opened by szitenberg about 10 years ago - 1 comment
Labels: bug

#42 - In pj.align, change the Conf objects list to a positional argument.

Issue - State: open - Opened by szitenberg about 10 years ago

#41 - order node support legend correctly

Issue - State: closed - Opened by szitenberg about 10 years ago
Labels: bug

#40 - allow to modify the sequence header in project.write_by_locus()

Issue - State: open - Opened by szitenberg about 10 years ago

#39 - allow to fit a sequence length filter to each locus separately

Issue - State: closed - Opened by szitenberg about 10 years ago - 1 comment

#38 - In read_alignement, remove all gap sequences

Issue - State: closed - Opened by szitenberg about 10 years ago

#37 - project.tree_summaries, project.trimming_summaries

Issue - State: open - Opened by szitenberg about 10 years ago

#36 - Make sure gaps are removed when alignment read as devovo, also warn

Issue - State: closed - Opened by szitenberg about 10 years ago - 1 comment

#35 - Some needed checks for concatenations

Issue - State: open - Opened by szitenberg about 10 years ago

#34 - Change "concat_must_all_of" to "otus_must_have_all_of"

Issue - State: closed - Opened by szitenberg about 10 years ago - 1 comment

#33 - box plots - move them left

Issue - State: closed - Opened by szitenberg about 10 years ago

#32 - methods for looking at (into) outputs

Issue - State: closed - Opened by szitenberg about 10 years ago
Labels: enhancement

#31 - alpha test issues

Issue - State: closed - Opened by szitenberg over 10 years ago
Labels: bug

#30 - Genbank records without a sequence break the genbank parser

Issue - State: open - Opened by szitenberg over 10 years ago
Labels: bug

#29 - in the RF matrix, change colors to absolute not relative

Issue - State: closed - Opened by szitenberg over 10 years ago

#28 - Bug: Protein fatsa not working

Issue - State: closed - Opened by szitenberg over 10 years ago - 1 comment
Labels: bug

#27 - user metadata file

Issue - State: closed - Opened by szitenberg over 10 years ago - 1 comment

#26 - include ad on to make the heatmap nicer in ete

Issue - State: closed - Opened by szitenberg over 10 years ago
Labels: enhancement

#25 - fix -t in raxmlHPC serial

Issue - State: closed - Opened by szitenberg over 10 years ago - 1 comment

#24 - program default usage should fit docker image

Issue - State: closed - Opened by szitenberg over 10 years ago - 1 comment
Labels: enhancement

#23 - Make pdf version of the report

Issue - State: open - Opened by szitenberg over 10 years ago
Labels: enhancement

#22 - Report fixes

Issue - State: closed - Opened by szitenberg over 10 years ago - 1 comment
Labels: enhancement

#21 - TreSpex

Issue - State: open - Opened by szitenberg over 10 years ago

#20 - Sort species report alphabetically

Issue - State: closed - Opened by szitenberg over 10 years ago - 1 comment

#19 - fix dealing with undetermined sequences

Issue - State: closed - Opened by szitenberg over 10 years ago - 1 comment
Labels: enhancement

#18 - Sequence statistic plots stretch too much with many loci

Issue - State: closed - Opened by szitenberg over 10 years ago - 1 comment
Labels: bug

#17 - When the values in the OTU meta have spaces, raxml brakes

Issue - State: closed - Opened by szitenberg over 10 years ago - 2 comments
Labels: bug

#16 - Fix making partfile for raxml

Issue - State: closed - Opened by szitenberg over 10 years ago - 1 comment
Labels: bug

#15 - predict if raxml will break for any of the alignments

Issue - State: closed - Opened by szitenberg over 10 years ago - 1 comment
Labels: enhancement

#14 - default node support annotaions

Issue - State: open - Opened by szitenberg over 10 years ago
Labels: enhancement

#13 - Add thread to the MafftCommandLine calss

Issue - State: open - Opened by szitenberg over 10 years ago
Labels: enhancement

#12 - make sure locus names in list_loci_in_genbank never have spaces

Issue - State: closed - Opened by szitenberg over 10 years ago - 1 comment
Labels: bug

#11 - When filter_by_length, notify about depleted loci and kick them out

Issue - State: open - Opened by szitenberg over 10 years ago
Labels: bug

#10 - To Do: Fix the version line for mafft

Issue - State: closed - Opened by szitenberg over 10 years ago

#9 - To Do: Add a list of trimmed position numbers to trim results

Issue - State: open - Opened by szitenberg over 10 years ago
Labels: enhancement

#8 - To Do: Fix the readability of methods in a report of an unpickled `Project`.

Issue - State: closed - Opened by szitenberg over 10 years ago

#7 - To Do: Hard code genebank synonyms

Issue - State: closed - Opened by szitenberg over 10 years ago - 1 comment
Labels: enhancement

#6 - ToDo: Rename RpGIt as rpgit

Issue - State: closed - Opened by szitenberg over 10 years ago

#5 - ToDo: make RpGit configurable

Issue - State: open - Opened by szitenberg over 10 years ago
Labels: enhancement

#4 - To Do: Change Database to Project

Issue - State: closed - Opened by szitenberg over 10 years ago - 1 comment
Labels: question

#3 - To Do: PbConf

Issue - State: closed - Opened by szitenberg over 10 years ago - 1 comment
Labels: enhancement

#2 - To Do: Add tree scale option to anotate

Issue - State: closed - Opened by szitenberg over 10 years ago
Labels: enhancement

#1 - To Do: Integrate gb_to_loci and synonymize_loci

Issue - State: closed - Opened by szitenberg over 10 years ago
Labels: enhancement

GitHub / HullUni-bioinformatics/ReproPhylo issues and pull requests