Comments (1)
nvm got it!!
bionode-ncbi search sra SRR490990
returns a big ole json that I can parse:
{u'createdate': u'2013/08/12',
u'expxml': {u'Bioproject': u'SRP011546',
u'Experiment': {u'acc': u'SRX144369',
u'name': u'GSM922175: 8-cell embryo#3 -Cell#6; Homo sapiens; RNA-Seq',
u'status': u'public',
u'ver': u'1'},
u'Instrument': {u'ILLUMINA': u'Illumina HiSeq 2000'},
u'Library_descriptor': {u'LIBRARY_LAYOUT': {u'SINGLE': u''},
u'LIBRARY_NAME': u'GSM922175: 8-cell embryo#3 -Cell#6',
u'LIBRARY_SELECTION': u'cDNA',
u'LIBRARY_SOURCE': u'TRANSCRIPTOMIC',
u'LIBRARY_STRATEGY': u'RNA-Seq'},
u'Organism': {u'ScientificName': u'Homo sapiens', u'taxid': u'9606'},
u'Sample': {u'acc': u'SRS310960', u'name': u''},
u'Study': {u'acc': u'SRP011546',
u'name': u'Tracing pluripotency of human early embryos and embryonic stem cells by single cell RNA-seq'},
u'Submitter': {u'acc': u'SRA050912',
u'center_name': u'GEO',
u'contact_name': u'Gene Expression Omnibus (GEO), NCBI, NLM, NIH, htt',
u'lab_name': u''},
u'Summary': {u'Platform': {u'_': u'ILLUMINA',
u'instrument_model': u'Illumina HiSeq 2000'},
u'Statistics': {u'cluster_name': u'public',
u'load_done': u'true',
u'total_bases': u'4750085700',
u'total_runs': u'1',
u'total_size': u'3178301878',
u'total_spots': u'47500857'},
u'Title': u'GSM922175: 8-cell embryo#3 -Cell#6; Homo sapiens; RNA-Seq'}},
u'extlinks': u' ',
u'runs': {u'Run': [{u'acc': u'SRR490990',
u'cluster_name': u'public',
u'is_public': u'true',
u'load_done': u'true',
u'static_data_available': u'true',
u'total_bases': u'4750085700',
u'total_spots': u'47500857'}]},
u'uid': u'174404',
u'updatedate': u'2013/09/23'}
thanks!!
from bionode-ncbi.
Related Issues (20)
- Implement efetch API
- Download the GFF file of the Cycas taitungensis mitochondrion HOT 9
- Uncaught, unspecified "error" event HOT 1
- Tests are broken because of NCBI side metadata changes (again) HOT 2
- rna_from_genomic instead of genomic.fna
- geo is not searchable HOT 5
- download in the examples printing too much info HOT 3
- We need a smaller assembly from NCBI for testing HOT 3
- Git rid of git-lfs
- Error handling when NCBI connection is lost HOT 4
- User-friendly CLI
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- Output some warning to terminal when there is no output
- Add Blast API HOT 2
- Use progress bar on download HOT 5
- Downloading one run download the whole Bioproject
- TypeError: Cannot create property 'Run' on string ' ' HOT 1
- Dependencies error: Prototype Pollution (lodash dependencies)
- Unexpected error when running 'bionode' HOT 4
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from bionode-ncbi.