metadata#
metadata outputs a metatable for a SRA study accession (SRP).
Usage and options#
$ pysrab metadata -h
Usage: pysradb metadata [OPTIONS] SRP_ID
Fetch metadata for SRA project (SRPnnnn)
Options:
--saveto TEXT Save metadata dataframe to file
--detailed Display detailed metadata table
-h, --help Show this message and exit.
Obtaining metadata for SRA study accession (SRP metadata)#
To obtain concise metadata for a SRP ID, we can use metadata.
The default metadata returned includes:
experiment accession (SRX)
sample accession (SRS)
run accession (SRR)
$ pysradb metadata SRP026005
study_accession experiment_accession sample_accession run_accession
SRP026005 SRX305245 SRS444476 SRR900108
SRP026005 SRX305246 SRS444467 SRR900109
SRP026005 SRX305247 SRS444468 SRR900110
SRP026005 SRX305247 SRS444468 SRR900111
SRP026005 SRX305248 SRS444470 SRR900112
SRP026005 SRX305249 SRS444471 SRR900113
SRP026005 SRX305250 SRS444472 SRR900114
SRP026005 SRX305250 SRS444472 SRR900115
SRP026005 SRX305251 SRS444473 SRR900116
SRP026005 SRX305251 SRS444473 SRR900117
SRP026005 SRX305252 SRS444474 SRR900118
SRP026005 SRX305252 SRS444474 SRR900119
SRP026005 SRX305253 SRS444475 SRR900120
SRP026005 SRX305253 SRS444475 SRR900121
In order to subset only RNA-seq experiments, you can do this simple operation:
$ pysradb metadata SRP098789 --detailed| grep 'study|RNA-Seq'
Getting more detailed metadata#
A major chunk of metadata information is still hidden by default.
For example, how long are the reads for each experiment?
Is the sequencing run single end or paired end?
Detailed metadata can be obtained by adding the --detailed
flag:
$ pysradb metadata SRP098789 --detailed
Saving metadata to a file#
pysradb follows a consistent pattern for providing
an option to save output of any of its subcommands to a file
using the --saveto argument:
$ pysradb metadata --detailed --saveto SRP098789_metadata.tsv SRP098789