Ecosyste.ms: Issues

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GitHub / jorvis/biocode issues and pull requests

#83 - Issue with convert prodigal output to standard GFF3

Issue - State: open - Opened by jjuradoc about 1 month ago - 4 comments

#82 - Python upgrade/conversion?

Issue - State: closed - Opened by RPINerd about 1 year ago - 1 comment

#81 - change python-igraph to igraph

Pull Request - State: closed - Opened by szhorvat over 1 year ago - 1 comment

#80 - Update fasta_size_report script to python3.10

Pull Request - State: closed - Opened by RPINerd almost 2 years ago - 2 comments

#79 - Keep introns

Pull Request - State: open - Opened by christopher-holt almost 2 years ago - 4 comments

#78 - change the lines

Pull Request - State: closed - Opened by Mona-2022 about 2 years ago

#77 - rename fasta headers with regex

Pull Request - State: open - Opened by CSynodinos over 2 years ago - 2 comments

#76 - [convert_genbank_to_gff3.py] No Locus_tag present in my genbank file

Issue - State: closed - Opened by j-bacal over 2 years ago - 2 comments
Labels: bug

#75 - fasta/fasta_simple_stats.py fails on any file with only one sequence

Issue - State: closed - Opened by jorvis about 3 years ago
Labels: bug

#74 - product info not printout in tbl

Issue - State: open - Opened by shuhailaMSR over 3 years ago - 2 comments
Labels: bug

#73 - biocode error

Issue - State: closed - Opened by shuhailaMSR over 3 years ago - 16 comments

#72 - Formatting Issue?

Issue - State: open - Opened by remiketchum over 3 years ago - 2 comments
Labels: bug

#71 - remove the obsolete TODO comment

Pull Request - State: closed - Opened by beyondacm almost 4 years ago - 1 comment

#70 - Incorrect parent features from convert_tRNAScanSE_to_gff3.pl

Issue - State: open - Opened by 14zac2 almost 4 years ago - 2 comments

#69 - Update convert_tRNAScanSE_to_gff3.pl

Pull Request - State: closed - Opened by pgonzale60 almost 4 years ago

#68 - Update convert_tRNAScanSE_to_gff3.pl

Pull Request - State: closed - Opened by pgonzale60 almost 4 years ago - 3 comments

#67 - convert_gff_to_ncbi_tbl.py

Issue - State: closed - Opened by stanislasmorand almost 4 years ago - 3 comments

#66 - convert_gff3_to_ncbi_tbl.py

Issue - State: closed - Opened by stanislasmorand almost 4 years ago - 2 comments

#65 - Conda based install

Issue - State: open - Opened by nhartwic about 5 years ago - 2 comments
Labels: enhancement

#64 - convert_augustus_to_gff3.py error

Issue - State: closed - Opened by JingXia730 about 5 years ago - 6 comments
Labels: bug

#63 - Insert EC numbers into chado database issue

Issue - State: closed - Opened by nsuvarnaiari over 5 years ago - 5 comments

#62 - AttributeError: 'Gene' object has no attribute 'add_CDS'

Issue - State: closed - Opened by PlantDr430 over 5 years ago - 4 comments

#61 - AttributeError: type object 'str' has no attribute 'maketrans'

Issue - State: closed - Opened by PengXieAMJ over 5 years ago - 2 comments

#60 - [convert_genbank_to_gff3.py] key_error: locus_tag

Issue - State: open - Opened by Piplopp over 5 years ago - 5 comments
Labels: bug

#59 - Create gff3_to_bed_II

Pull Request - State: open - Opened by pirekupcode over 5 years ago - 1 comment

#58 - Biocode.gff module error

Issue - State: closed - Opened by PlantDr430 almost 6 years ago - 2 comments

#57 - Attribute error for update_selected_column9_values.py

Issue - State: closed - Opened by gjaqu054 over 6 years ago - 1 comment

#56 - Exclude mRNA features in bacterial TBL exports

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

#55 - Syntax error on gff.py

Issue - State: closed - Opened by PlantDr430 over 6 years ago - 4 comments

#54 - convert_gff3_to_ncbi_tbl

Issue - State: open - Opened by bernt-matthias almost 7 years ago - 5 comments

#53 - NameError: name 'utils' is not defined

Issue - State: closed - Opened by arsilan324 almost 7 years ago - 13 comments

#52 - correct_gff_feature_order.pl doesn't work

Issue - State: closed - Opened by arsilan324 almost 7 years ago - 5 comments

#51 - Augustus conversion failing

Issue - State: open - Opened by jorvis almost 7 years ago - 5 comments

#50 - Resolve competing functions to serialize GFF3

Issue - State: closed - Opened by jorvis almost 7 years ago - 1 comment

#49 - pip2 install biocode error

Issue - State: closed - Opened by kayDaramola almost 7 years ago - 10 comments

#48 - Added parsing for predicted introns and anticodon

Pull Request - State: closed - Opened by JWDebler about 7 years ago - 2 comments

#47 - Bug fix duplicated genes when converting Genbank into GFF.

Pull Request - State: closed - Opened by ArnaudBelcour about 7 years ago - 1 comment

#46 - Bug fix polypeptide.locations typechecking

Pull Request - State: closed - Opened by ktmeaton about 7 years ago - 2 comments

#45 - convert_gff3_to_gbk.py template error

Issue - State: closed - Opened by BenjaminSchwessinger over 7 years ago - 4 comments

#44 - write_fasta_from_gff.py error

Issue - State: closed - Opened by ncpalmateer almost 8 years ago - 5 comments

#43 - Can't import things with write_fasta_from_gff.py

Issue - State: closed - Opened by ktretina almost 8 years ago - 6 comments

#42 - Add py2 compatability to fastq subsample script

Pull Request - State: closed - Opened by kastman almost 8 years ago

#41 - convert_gff3_to_ncbi_tbl.py error generated

Issue - State: closed - Opened by wyim-pgl almost 8 years ago - 2 comments

#40 - Python 2 Compatability?

Issue - State: closed - Opened by kastman over 8 years ago - 1 comment

#39 - Add fasta/subsample_fasta.py and sandbox/jcrabtree.

Pull Request - State: closed - Opened by jonathancrabtree over 8 years ago

#38 - Minor fasta script naming issue

Issue - State: closed - Opened by jonathancrabtree over 8 years ago - 1 comment

#37 - problem with compare_gene_structures.py

Issue - State: closed - Opened by lfaino over 8 years ago - 2 comments

#36 - Script needed for assembly evaluation

Issue - State: open - Opened by jorvis almost 9 years ago - 1 comment
Labels: enhancement

#35 - To extract longest isoform from trinity assembly

Issue - State: closed - Opened by bioinfonext over 9 years ago - 3 comments

#34 - Fixes for parsing of GFF3 ##FASTA section. Closes #32.

Pull Request - State: closed - Opened by jonathancrabtree over 9 years ago - 1 comment

#33 - convert_metagenemark_gff_to_gff3.py produces invalid GFF3

Issue - State: closed - Opened by jonathancrabtree over 9 years ago - 1 comment

#31 - Add descriptions to ArgumentParser definitions

Pull Request - State: closed - Opened by mfitzp over 9 years ago - 2 comments

#30 - biocodeutils.py add error output mRNA ID

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

#29 - correct_gff_feature_order.pl misplacing ##FASTA

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

#28 - write_fasta_from_gff.pl

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

#27 - bioannotation.py - check for properly-formed EC numbers

Issue - State: closed - Opened by jorvis over 10 years ago - 2 comments

#25 - Check and/or correct coordinate column order in biocodegff.py

Issue - State: closed - Opened by jonathancrabtree over 10 years ago - 2 comments

#24 - convert_gff3_to_gbk.py, add full support for non-protein-coding genes

Issue - State: closed - Opened by jonathancrabtree over 10 years ago - 8 comments
Labels: bug

#23 - Add --locus_id_prefix to convert_gff3_to_gbk.py

Pull Request - State: closed - Opened by jonathancrabtree over 10 years ago

#21 - Improved option handling

Pull Request - State: closed - Opened by jonathancrabtree over 10 years ago

#20 - Add --lineage, --include_sequence, and --output_dir to convert_gff3_to_gbk.py

Pull Request - State: closed - Opened by jonathancrabtree over 10 years ago - 3 comments

#19 - report_gc_content_by_feature_type.pl definition of telomere

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

#17 - GFF3 validator

Issue - State: open - Opened by ktretina over 10 years ago - 1 comment
Labels: enhancement

#16 - report_gff3_statistics.py, 'Gene' object has no attribute 'length'

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

#15 - convert_gff3_to_gbk.py with no embedded FASTA

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

#14 - Model UTRs explicitly

Issue - State: open - Opened by jorvis over 10 years ago - 2 comments
Labels: enhancement

#13 - Annotation parsing file output options

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

#12 - The biothings module needs to support multiple parentage

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

#10 - gff/write_fasta_from_gff.pl mistranslates some Augustus -> GFF3 output

Issue - State: open - Opened by jorvis almost 11 years ago
Labels: bug

#9 - report_gff3_statistics.py unsupported operand type(s) error

Issue - State: open - Opened by mchibucos almost 11 years ago
Labels: bug

#8 - Needed: Speed-optimized FASTQ to FASTA script

Issue - State: closed - Opened by jorvis almost 11 years ago - 1 comment
Labels: enhancement

#7 - Needed: Speed-optimized FASTA statistics script

Issue - State: open - Opened by jorvis almost 11 years ago
Labels: enhancement

#6 - Needed: Speed-optimized FASTQ statistics script

Issue - State: open - Opened by jorvis almost 11 years ago - 1 comment
Labels: enhancement

#5 - Structural comparison script deletes all bed files

Issue - State: closed - Opened by jorvis almost 11 years ago - 3 comments
Labels: bug

#4 - Corrected link to the khmer implementation of diginorm

Pull Request - State: closed - Opened by mr-c about 11 years ago

#3 - Modified structural comparison script

Pull Request - State: closed - Opened by priti88 about 11 years ago

#2 - Added documentation

Pull Request - State: closed - Opened by priti88 about 11 years ago

#1 - added author information

Pull Request - State: closed - Opened by priti88 about 11 years ago