Ecosyste.ms: Issues

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GitHub / guma44/GEOparse issues and pull requests

#85 - Fix failing tests: Add compatibility with pandas 2

Pull Request - State: open - Opened by olp-cs 4 months ago

#83 - Fix issue when GEO metadata contains commas

Pull Request - State: closed - Opened by alexbarrera 7 months ago - 1 comment

#82 - UnboundLocalError when GSE non-existent

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

#81 - download all supplementary file instead of only one

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

#80 - download fails because of content-length mismatch when content-encoding=gzip

Issue - State: open - Opened by vttrifonov almost 3 years ago - 1 comment

#79 - Summary GSM metadata table

Issue - State: open - Opened by RemyLau about 3 years ago

#78 - Skip conversion to fastq if existing

Issue - State: open - Opened by hschult about 3 years ago

#77 - Declare total_size outside of try block so it can't be undeclared.

Pull Request - State: closed - Opened by kurtwheeler about 3 years ago

#74 - Phenotype data does not use pandas dtype inference

Issue - State: open - Opened by hardingnj about 3 years ago - 1 comment

#73 - Fixes typo in documentation

Pull Request - State: closed - Opened by MichaelLampe over 3 years ago - 1 comment

#72 - GEOparse not downloading a supplementary file for a GSE

Issue - State: open - Opened by grisaitis over 3 years ago

#71 - fix typo with print function in usage

Pull Request - State: closed - Opened by grisaitis over 3 years ago - 5 comments

#70 - DtypeWarning: Columns (7) have mixed types.

Issue - State: open - Opened by CholoTook over 3 years ago - 4 comments

#69 - Am I doin it rong?

Issue - State: open - Opened by CholoTook over 3 years ago - 1 comment

#68 - using merge_and_average with annotation

Issue - State: closed - Opened by tyasird almost 4 years ago - 1 comment

#67 - is there any way to re-write downloaded files?

Issue - State: closed - Opened by tyasird almost 4 years ago - 1 comment

#66 - is there any way to get GSM sample names without full download?

Issue - State: closed - Opened by tyasird almost 4 years ago - 5 comments

#65 - UnboundLocalError while trying the example from documentation

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

#64 - BUGFIX: shutil.move can lead to "operation not permitted" error

Pull Request - State: closed - Opened by mvonpapen about 4 years ago - 1 comment

#63 - Allow the file encoding to be specified in smart_open()

Issue - State: closed - Opened by ghost over 4 years ago - 3 comments
Labels: enhancement

#62 - cannot download and parse GEO files

Issue - State: open - Opened by Mengflz over 4 years ago - 11 comments

#61 - Can you read XML files with this tool?

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

#60 - Check if GSE entry is public

Issue - State: closed - Opened by adirot about 5 years ago - 2 comments

#59 - Debugging everything

Issue - State: closed - Opened by liugaocn over 5 years ago - 3 comments

#58 - Warning if fastq-dump is not installed or on $PATH

Issue - State: open - Opened by JohnWSteill over 5 years ago - 1 comment

#57 - gsm2fastq: allow for dynamic allocation of threads

Pull Request - State: closed - Opened by Maarten-vd-Sande over 5 years ago

#56 - Develop

Pull Request - State: closed - Opened by guma44 over 5 years ago - 1 comment

#55 - Parallel fastq

Pull Request - State: closed - Opened by simonvh over 5 years ago - 1 comment

#54 - Add partial arg to parse_GPL and get_GEO. #53

Pull Request - State: closed - Opened by ttyskg almost 6 years ago - 3 comments

#53 - Partially parsing of large GPL file

Issue - State: closed - Opened by ttyskg almost 6 years ago - 2 comments
Labels: enhancement

#52 - Replace ix to loc

Pull Request - State: closed - Opened by ttyskg almost 6 years ago - 1 comment

#51 - Missing File Error when GEO is Down

Issue - State: open - Opened by Miserlou almost 6 years ago - 1 comment
Labels: bug, enhancement

#50 - ValueError when trying to reproduce tutorials

Issue - State: closed - Opened by CiaranWelsh about 6 years ago - 1 comment

#49 - Add Timeout to urlopen Calls

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

#48 - Cut a New Release?

Issue - State: closed - Opened by Miserlou over 6 years ago - 3 comments

#47 - GEOparse.logger.set_verbosity doesn't work

Issue - State: closed - Opened by Miserlou over 6 years ago - 2 comments
Labels: bug

#46 - wgetter/urlget have no timeouts

Issue - State: closed - Opened by Miserlou over 6 years ago - 1 comment
Labels: bug, enhancement

#45 - use `pandas.read_csv` rather than `DataFrame.from_csv`

Issue - State: closed - Opened by Miserlou over 6 years ago - 2 comments
Labels: enhancement

#44 - Library citation for scientific paper

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

#43 - Parallel download

Pull Request - State: closed - Opened by agalitsyna over 6 years ago - 5 comments

#42 - showing all SRRs for a particular GSM

Issue - State: open - Opened by golobor over 6 years ago - 1 comment
Labels: possible enhancement

#41 - Remove downloaded archive // Cleanup

Issue - State: open - Opened by Miserlou over 6 years ago - 1 comment
Labels: enhancement

#40 - Download MINiML

Issue - State: open - Opened by Miserlou over 6 years ago - 1 comment
Labels: enhancement

#39 - parallel fastq_dump support

Issue - State: closed - Opened by antonkulaga almost 7 years ago - 1 comment
Labels: enhancement

#38 - Broken download when supplementary_files is empty or contains invalid URLs

Issue - State: closed - Opened by antonkulaga almost 7 years ago - 7 comments
Labels: bug

#37 - SRR type now known

Issue - State: open - Opened by antonkulaga almost 7 years ago - 1 comment

#36 - Some samples don't have table data!

Issue - State: open - Opened by halioui almost 7 years ago - 6 comments
Labels: bug

#35 - NCBI GEO FTP has changed their URL structures AGAIN

Issue - State: closed - Opened by halioui almost 7 years ago - 2 comments

#34 - Parse data table

Issue - State: closed - Opened by halioui almost 7 years ago - 1 comment
Labels: bug

#33 - Fixed the FTP link.

Pull Request - State: closed - Opened by simonvh almost 7 years ago - 1 comment

#32 - fix #31

Pull Request - State: closed - Opened by eric6356 about 7 years ago

#31 - wrong name in parse_GSE

Issue - State: closed - Opened by eric6356 about 7 years ago - 2 comments
Labels: bug

#30 - BUG: cannot " GEOparse.get_GEO(filepath= path)" On windows

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

#29 - silent mode not working.

Issue - State: closed - Opened by ppanteliadis over 7 years ago - 4 comments
Labels: bug

#28 - Possibility to download all GEO data locally.

Issue - State: open - Opened by bgriffen over 7 years ago - 1 comment
Labels: enhancement

#27 - check for converted sra-s

Issue - State: open - Opened by antonkulaga over 7 years ago - 1 comment
Labels: enhancement

#26 - fastq-dump parameters are not optimal

Issue - State: closed - Opened by antonkulaga over 7 years ago - 3 comments
Labels: enhancement

#25 - email is optional

Issue - State: closed - Opened by antonkulaga over 7 years ago - 3 comments

#24 - more meaningful error in gsm.download_supplementary_files

Issue - State: closed - Opened by antonkulaga over 7 years ago - 9 comments

#23 - In parse_GDS_columns(), unknown subset_types discarded

Issue - State: closed - Opened by n1mus over 7 years ago - 1 comment
Labels: bug

#22 - returning pathes by download supplementary files

Issue - State: closed - Opened by antonkulaga over 7 years ago - 1 comment
Labels: enhancement

#21 - biopython requirement

Issue - State: closed - Opened by antonkulaga over 7 years ago - 2 comments

#20 - no columns at GSE

Issue - State: closed - Opened by antonkulaga over 7 years ago - 3 comments

#19 - get_GEO(... silent=True) is NOT silent

Issue - State: closed - Opened by dtenenba over 7 years ago - 8 comments
Labels: bug

#18 - Httpsfix and how logic

Pull Request - State: closed - Opened by miguelroboso over 7 years ago

#17 - fixed typo

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

#16 - Error with GSE52666

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

#14 - Reporting issues with loading the following 2 datasets

Issue - State: closed - Opened by KwatMDPhD over 7 years ago - 5 comments

#13 - Rename README.rst to README.md

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

#12 - Update setup.py

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

#11 - Enhance documentation with pre-requisite python module (pandas)

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

#10 - Make compatible tutorial for Python3

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

#9 - Bugfix: some titles contain ; characters, should be replaced with _

Pull Request - State: closed - Opened by simonvh almost 8 years ago - 3 comments

#8 - Python 3 Compatibility

Pull Request - State: closed - Opened by tychobismeijer about 8 years ago - 6 comments

#7 - How can I get gsm-gpl relation in multi-gpls gse.

Issue - State: closed - Opened by yong27 about 8 years ago - 2 comments

#6 - Automatically generate pheno data

Issue - State: closed - Opened by guma44 about 8 years ago - 1 comment
Labels: enhancement

#5 - Illegal filenames and no filtering of user input from GEO to create the filenames

Issue - State: closed - Opened by theselim over 8 years ago - 3 comments
Labels: bug

#4 - python 2.7 only?

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

#3 - V0.1.7

Pull Request - State: closed - Opened by guma44 over 8 years ago

#2 - Better support for HTS accessions

Pull Request - State: closed - Opened by simonvh over 8 years ago - 3 comments

#1 - stderr.write missing

Issue - State: closed - Opened by yxngl over 8 years ago - 1 comment
Labels: bug