joshuagryphon/plastid issues and pull requests

#57 - Building wheel is failing in local install

Issue - State: open - Opened by BeastyBlacksmith about 1 year ago - 1 comment

#56 - Bump scipy from 1.5.4 to 1.10.0

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#55 - numpy 1.24.1 and plastid 0.6.1 appear to have an issue due to dropping of support for numpy.int by numpy.

Issue - State: open - Opened by cjhull almost 2 years ago - 6 comments

#54 - Bump numpy from 1.19.5 to 1.22.0 in /docs

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#53 - Bump numpy from 1.19.5 to 1.22.0

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#52 - installation problems

Issue - State: open - Opened by LidiaML over 2 years ago - 2 comments

#51 - Bump numpy from 1.19.5 to 1.21.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments
Labels: dependencies

#50 - Bump numpy from 1.19.5 to 1.21.0 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#49 - Problem install plastid 'no attribute 'PileupColumn'

Issue - State: closed - Opened by Markestine over 2 years ago - 2 comments
Labels: conda issue

#48 - the p site offset problem

Issue - State: closed - Opened by z626093820 almost 3 years ago - 1 comment
Labels: help wanted

#47 - the bam file choose

Issue - State: closed - Opened by z626093820 almost 3 years ago - 1 comment
Labels: help wanted

#46 - Roitools module error when running psite: "ValueError: too many values to unpack (expected 2)"

Issue - State: open - Opened by marcasriv almost 4 years ago

#45 - Incompatible with BioPython 1.78+

Issue - State: closed - Opened by lparsons about 4 years ago - 2 comments

#44 - Error when converting GFF3 to GTF2

Issue - State: open - Opened by ale07alvarez about 4 years ago - 3 comments
Labels: conda issue

#43 - logging dependency should be remove from setup.py when installing with Python3

Issue - State: closed - Opened by EricDeveaud over 4 years ago - 1 comment

#42 - ModuleNotFoundError: No module named 'plastid.genomics.roitools'

Issue - State: closed - Opened by pkerpedjiev over 4 years ago - 5 comments
Labels: bug, resolved

#41 - Undefined symbol caused by compilation error only under Python 2.7.17 (3.x, 2.7.15 are ok)

Issue - State: closed - Opened by joshuagryphon over 4 years ago - 3 comments
Labels: wontfix

#40 - ‘phase_by_size’ command-line script problem with Numpy(1.18.1)

Issue - State: closed - Opened by rbmk1000 over 4 years ago - 1 comment

#39 - RuntimeWarning

Issue - State: open - Opened by YueZhang2019 over 4 years ago - 1 comment

#38 - Question on --gff_transcript_types and --mask_gff_transcript_types

Issue - State: closed - Opened by Zhuxitong almost 5 years ago - 1 comment
Labels: question

#37 - Plotting a metagene plot for two different samples at the same time

Issue - State: closed - Opened by kaltinel almost 5 years ago - 1 comment
Labels: question

#36 - Support CRAM files

Issue - State: closed - Opened by joshuagryphon almost 5 years ago - 1 comment

#35 - Remove deprecated features

Issue - State: open - Opened by joshuagryphon almost 5 years ago

#34 - Support Python 3.8

Issue - State: closed - Opened by joshuagryphon almost 5 years ago - 1 comment
Labels: resolved

#33 - Generated .bed file has "0" score in the 3rd line - When generating .bedgraph out of this .bed, no coverage of Ribo-seq data.

Issue - State: closed - Opened by AlexFryd about 5 years ago - 2 comments
Labels: help wanted

#32 - Add zlib library when building bigbed

Pull Request - State: closed - Opened by lparsons over 5 years ago - 4 comments

#31 - Compatilibity update for Py3.7: fix generator implementation

Issue - State: closed - Opened by joshuagryphon over 5 years ago - 1 comment
Labels: enhancement / feature request

#30 - Simplify get_short_name regex

Pull Request - State: closed - Opened by lparsons over 5 years ago - 5 comments

#29 - Conda packages hang

Issue - State: closed - Opened by lparsons over 5 years ago - 8 comments
Labels: help wanted

#28 - No module name `plastid`

Issue - State: closed - Opened by kerfar over 5 years ago - 5 comments
Labels: help wanted

#27 - could not open alignment file - psite offset

Issue - State: closed - Opened by AnaHowellsFerreira almost 6 years ago - 3 comments

#26 - KeyError: 'zero_point' when running metagene count

Issue - State: closed - Opened by JPMARKS about 6 years ago - 8 comments

#25 - Add Bioconda to installation instructions

Pull Request - State: closed - Opened by lparsons over 6 years ago - 1 comment

#24 - Request new version release - 0.4.9

Issue - State: closed - Opened by lparsons over 6 years ago - 19 comments
Labels: resolved

#23 - Supported opposite-strand protocols (for metagene)

Issue - State: open - Opened by sarahhcarl over 6 years ago - 5 comments
Labels: enhancement / feature request

#22 - Requesting help on how to exclude codons from rfp density measurement..

Issue - State: closed - Opened by jusu-E404 over 6 years ago - 2 comments
Labels: question, resolved

#21 - the system cannot find the file specified. Please help!

Issue - State: closed - Opened by akkshita96 almost 7 years ago

#20 - fatal error: 'stdio.h' file not found

Issue - State: closed - Opened by bzeraee about 7 years ago - 1 comment

#19 - Using 'centered' for read mapping - why and when?

Issue - State: closed - Opened by bdweave about 7 years ago - 1 comment

#18 - ‘phase_by_size’ command-line script problem with newer Numpy(1.13.1)

Issue - State: closed - Opened by zyllifeworld about 7 years ago - 4 comments
Labels: resolved

#17 - `crossmap` output file contains very short reads?

Issue - State: closed - Opened by AlicePsyche over 7 years ago - 2 comments
Labels: question

#16 - Stratified Variable Five Prime Map Factory Error when passed .txt file

Issue - State: closed - Opened by bdweave over 7 years ago - 2 comments
Labels: resolved

#15 - pysam ImportError

Issue - State: closed - Opened by JeanMiCarter over 7 years ago - 1 comment
Labels: duplicate

#14 - bug in PSLreader: end coordinates of protein->DNA query results are mis-parsed

Issue - State: open - Opened by joshuagryphon over 7 years ago - 1 comment

#13 - Plastid 0.4.7 completing installation but not importable on OSX

Issue - State: closed - Opened by joshuagryphon over 7 years ago - 2 comments
Labels: bug

#12 - Corrected 2 lines in docs

Pull Request - State: closed - Opened by jlncrnt over 7 years ago - 1 comment

#11 - Plastid now available through bioconda

Issue - State: closed - Opened by lparsons over 7 years ago - 9 comments
Labels: enhancement / feature request, resolved

#10 - single gene for phase_by_size

Issue - State: closed - Opened by chouhj over 7 years ago - 1 comment
Labels: enhancement / feature request

#9 - make_wiggle output format & get_count_vectors zero counts

Issue - State: closed - Opened by bontus over 7 years ago - 10 comments

#8 - Incompatibility with Pysam 0.10.0: Cythonize error while compiling map_factories.pyx

Issue - State: closed - Opened by Cobrec11 over 7 years ago - 10 comments
Labels: resolved

#7 - Crossmap fails on hg38 unplaced and unlocalized scaffolds

Issue - State: closed - Opened by grantdjones almost 8 years ago - 6 comments
Labels: help wanted, resolved

#6 - Cython not running during `python setup.py build` : missing c_common.c file when building version 0.4.6

Issue - State: closed - Opened by blaiseli almost 8 years ago - 10 comments
Labels: help wanted

#5 - Procedure for P-site estimation using stop codon peaks

Issue - State: closed - Opened by purplerainf almost 8 years ago - 3 comments
Labels: resolved

#4 - Conda / Cython incompatibility: GCC finding different version of Pysam from that in Conda environment (formerly: possible pysam 0.9.1 compatibility issue)

Issue - State: closed - Opened by calvinjan about 8 years ago - 2 comments
Labels: wontfix, conda issue

#3 - Feature request: create / simulate UTRs in `metagene generate` when annotations do not include them. (formerly: Unable to generate proper cds_start ROIs using `metagene generate`)

Issue - State: open - Opened by lparsons over 8 years ago - 8 comments
Labels: enhancement / feature request

#2 - Conda / Cython incompatibility: GCC finding different versions of numpy; Cython also not called by pip (formerly: Can't install)

Issue - State: closed - Opened by jfreimer over 8 years ago - 10 comments
Labels: wontfix, conda issue

#1 - todo: finish migration of SegmentChain & Transcript to Cython

Issue - State: closed - Opened by joshuagryphon about 9 years ago - 2 comments
Labels: resolved

GitHub / joshuagryphon/plastid issues and pull requests