attributes Instrument,total size of experiment are not present in the metadata fetched through flags

[saketkc]

attributes Instrument,total size of experiment are not present in the metadata fetched through flags

[saketkc]

Hi @deepthi888,

Sorry for the delay in my response.

Thank you for pointing this out. It was indeed missing from the metadata response.

The recent release prints instrument and total size by default in the SRAweb mode. I am slowly planning to retire the SRAdb mode, which means we will no longer require the SQLite file as it seems to be no longer updated and is missing a lot of SRA projects.

Here is the output for your query:

> pysradb metadata SRP063732
experiment_accession experiment_title                                                       experiment_desc                                                        organism_taxid  organism_name   library_strategy library_source library_selection instrument           total_spots total_size   sample_accession sample_title study_accession run_accession run_total_spots run_total_bases
 SRX1249861           Bisulfite-seq of rhesus macaque 26168_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 26168_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  89051187    11830170462  SRS1071080                    SRP063732       SRR2420581    89051187        17988339774   
 SRX1249860           Bisulfite-seq of rhesus macaque 26148_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 26148_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  87335402    11763248173  SRS1071081                    SRP063732       SRR2420580    87335402        17641751204   
 SRX1249859           Bisulfite-seq of rhesus macaque 25822_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 25822_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  83544130    9481342835   SRS1071082                    SRP063732       SRR2420579    83544130        13784781450   
 SRX1249858           Bisulfite-seq of rhesus macaque 25154_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 25154_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  115476876   13003165573  SRS1071083                    SRP063732       SRR2420578    115476876       19053684540   
 SRX1249857           Bisulfite-seq of rhesus macaque 23784_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 23784_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  101539017   13697691917  SRS1071084                    SRP063732       SRR2420577    101539017       20510881434   
 SRX1249856           Bisulfite-seq of rhesus macaque 23779_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 23779_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  98394582    13326784419  SRS1071085                    SRP063732       SRR2420576    98394582        19875705564   
 SRX1249855           Bisulfite-seq of rhesus macaque 23773_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 23773_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  84442355    11218164664  SRS1071086                    SRP063732       SRR2420575    84442355        17057355710   
 SRX1249854           Bisulfite-seq of rhesus macaque 23764_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 23764_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  87197006    11291883405  SRS1071087                    SRP063732       SRR2420574    87197006        17613795212   
 SRX1249853           Bisulfite-seq of rhesus macaque 23762_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 23762_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  89455608    11917710767  SRS1071088                    SRP063732       SRR2420573    89455608        18070032816   
 SRX1249852           Bisulfite-seq of rhesus macaque 25811_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 25811_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  88216999    10285962574  SRS1071089                    SRP063732       SRR2420572    88216999        14555804835   
 SRX1249851           Bisulfite-seq of rhesus macaque 25790_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 25790_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  94731241    10748979142  SRS1071090                    SRP063732       SRR2420571    94731241        15630654765   
 SRX1249850           Bisulfite-seq of rhesus macaque 25742_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 25742_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  113512952   17943763654  SRS1071091                    SRP063732       SRR2420570    113512952       22929616304   
 SRX1249849           Bisulfite-seq of rhesus macaque 25240_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 25240_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  81002663    9232986327   SRS1071092                    SRP063732       SRR2420569    81002663        13365439395   
 SRX1249848           Bisulfite-seq of rhesus macaque 25184_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 25184_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  110228135   12594727479  SRS1071093                    SRP063732       SRR2420568    110228135       18187642275   
 SRX1249847           Bisulfite-seq of rhesus macaque 25157_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 25157_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  97249804    11026452312  SRS1071094                    SRP063732       SRR2420567    97249804        16046217660   
 SRX1249846           Bisulfite-seq of rhesus macaque 21119_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 21119_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  68899204    9241244635   SRS1071095                    SRP063732       SRR2420566    68899204        13917639208   
 SRX1249845           Bisulfite-seq of rhesus macaque 26104_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 26104_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  84859783    9604170375   SRS1071096                    SRP063732       SRR2420565    84859783        14001864195   
 SRX1249844           Bisulfite-seq of rhesus macaque 26082_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 26082_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  73346886    8248399265   SRS1071097                    SRP063732       SRR2420564    73346886        12102236190   
 SRX1249843           Bisulfite-seq of rhesus macaque 25207_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 25207_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  77306973    12235827725  SRS1071098                    SRP063732       SRR2420563    77306973        15616008546   
 SRX1249842           Bisulfite-seq of rhesus macaque 25407_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 25407_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  83985968    13355795218  SRS1071099                    SRP063732       SRR2420562    83985968        16965165536   
 SRX1249841           Bisulfite-seq of rhesus macaque 24818_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 24818_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  72782928    8484613123   SRS1071100                    SRP063732       SRR2420561    72782928        12009183120   
 SRX1249840           Bisulfite-seq of rhesus macaque 24698_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 24698_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  79414016    12627204820  SRS1071101                    SRP063732       SRR2420560    79414016        16041631232   
 SRX1249839           Bisulfite-seq of rhesus macaque 24340_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 24340_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  84772576    13436053136  SRS1071102                    SRP063732       SRR2420559    84772576        17124060352   
 SRX1249838           Bisulfite-seq of rhesus macaque 22770_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 22770_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  83310630    13224887149  SRS1071103                    SRP063732       SRR2420558    83310630        16828747260   

[deepthi888]

Thanks for the response.
could you please let me know how to use this SRAweb mode in google colaboratory

thanks in advance.

[saketkc]

Here's one demonstrating relevant commands: https://colab.research.google.com/drive/1C60V-jkcNZiaCra_V5iEyFs318jgVoUR

[deepthi888]

thanks for your response@saketkc

[deepthi888]

@saketkc , could you please let me know about how to fetch attributes of a sample such as isolate, development stage,sex,tissue and treatment

[saketkc]

Currently missing from the SRAweb version, but I just got it working locally so it should be in the master branch sometime this week. Thank you for your patience!

[saketkc]

Hi @deepthi888, the latest commit on master bracnh will allow you to fetch these attributes:

> pysradb metadata SRP063732 --detailed
experiment_accession experiment_title                                                       experiment_desc                                                        organism_taxid  organism_name   library_strategy library_source library_selection instrument           total_spots total_size   sample_accession sample_title study_accession run_accession run_total_spots run_total_bases isolate                 dev_stage sex   tissue             treatment     BioSampleModel           
 SRX1249861           Bisulfite-seq of rhesus macaque 26168_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 26168_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  89051187    11830170462  SRS1071080                    SRP063732       SRR2420581    89051187        17988339774     26168_NucleusAccumbens  Adult     male  Nucleus accumbens  HeavyEthanol  Model organism or animal
 SRX1249860           Bisulfite-seq of rhesus macaque 26148_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 26148_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  87335402    11763248173  SRS1071081                    SRP063732       SRR2420580    87335402        17641751204     26148_NucleusAccumbens  Adult     male  Nucleus accumbens  HeavyEthanol  Model organism or animal
 SRX1249859           Bisulfite-seq of rhesus macaque 25822_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 25822_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  83544130    9481342835   SRS1071082                    SRP063732       SRR2420579    83544130        13784781450     25822_NucleusAccumbens  Adult     male  Nucleus accumbens  HeavyEthanol  Model organism or animal
 SRX1249858           Bisulfite-seq of rhesus macaque 25154_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 25154_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  115476876   13003165573  SRS1071083                    SRP063732       SRR2420578    115476876       19053684540     25154_NucleusAccumbens  Adult     male  Nucleus accumbens  HeavyEthanol  Model organism or animal
 SRX1249857           Bisulfite-seq of rhesus macaque 23784_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 23784_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  101539017   13697691917  SRS1071084                    SRP063732       SRR2420577    101539017       20510881434     23784_NucleusAccumbens  Adult     male  Nucleus accumbens  HeavyEthanol  Model organism or animal
 SRX1249856           Bisulfite-seq of rhesus macaque 23779_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 23779_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  98394582    13326784419  SRS1071085                    SRP063732       SRR2420576    98394582        19875705564     23779_NucleusAccumbens  Adult     male  Nucleus accumbens  HeavyEthanol  Model organism or animal
 SRX1249855           Bisulfite-seq of rhesus macaque 23773_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 23773_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  84442355    11218164664  SRS1071086                    SRP063732       SRR2420575    84442355        17057355710     23773_NucleusAccumbens  Adult     male  Nucleus accumbens  HeavyEthanol  Model organism or animal
 SRX1249854           Bisulfite-seq of rhesus macaque 23764_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 23764_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  87197006    11291883405  SRS1071087                    SRP063732       SRR2420574    87197006        17613795212     23764_NucleusAccumbens  Adult     male  Nucleus accumbens  HeavyEthanol  Model organism or animal
 SRX1249853           Bisulfite-seq of rhesus macaque 23762_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 23762_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  89455608    11917710767  SRS1071088                    SRP063732       SRR2420573    89455608        18070032816     23762_NucleusAccumbens  Adult     male  Nucleus accumbens  HeavyEthanol  Model organism or animal
 SRX1249852           Bisulfite-seq of rhesus macaque 25811_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 25811_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  88216999    10285962574  SRS1071089                    SRP063732       SRR2420572    88216999        14555804835     25811_NucleusAccumbens  Adult     male  Nucleus accumbens  LightEthanol  Model organism or animal
 SRX1249851           Bisulfite-seq of rhesus macaque 25790_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 25790_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  94731241    10748979142  SRS1071090                    SRP063732       SRR2420571    94731241        15630654765     25790_NucleusAccumbens  Adult     male  Nucleus accumbens  LightEthanol  Model organism or animal
 SRX1249850           Bisulfite-seq of rhesus macaque 25742_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 25742_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  113512952   17943763654  SRS1071091                    SRP063732       SRR2420570    113512952       22929616304     25742_NucleusAccumbens  Adult     male  Nucleus accumbens  LightEthanol  Model organism or animal
 SRX1249849           Bisulfite-seq of rhesus macaque 25240_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 25240_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  81002663    9232986327   SRS1071092                    SRP063732       SRR2420569    81002663        13365439395     25240_NucleusAccumbens  Adult     male  Nucleus accumbens  LightEthanol  Model organism or animal
 SRX1249848           Bisulfite-seq of rhesus macaque 25184_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 25184_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  110228135   12594727479  SRS1071093                    SRP063732       SRR2420568    110228135       18187642275     25184_NucleusAccumbens  Adult     male  Nucleus accumbens  LightEthanol  Model organism or animal
 SRX1249847           Bisulfite-seq of rhesus macaque 25157_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 25157_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  97249804    11026452312  SRS1071094                    SRP063732       SRR2420567    97249804        16046217660     25157_NucleusAccumbens  Adult     male  Nucleus accumbens  LightEthanol  Model organism or animal
 SRX1249846           Bisulfite-seq of rhesus macaque 21119_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 21119_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  68899204    9241244635   SRS1071095                    SRP063732       SRR2420566    68899204        13917639208     21119_NucleusAccumbens  Adult     male  Nucleus accumbens  LightEthanol  Model organism or animal
 SRX1249845           Bisulfite-seq of rhesus macaque 26104_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 26104_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  84859783    9604170375   SRS1071096                    SRP063732       SRR2420565    84859783        14001864195     26104_NucleusAccumbens  Adult     male  Nucleus accumbens  Control       Model organism or animal
 SRX1249844           Bisulfite-seq of rhesus macaque 26082_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 26082_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  73346886    8248399265   SRS1071097                    SRP063732       SRR2420564    73346886        12102236190     26082_NucleusAccumbens  Adult     male  Nucleus accumbens  Control       Model organism or animal
 SRX1249843           Bisulfite-seq of rhesus macaque 25207_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 25207_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  77306973    12235827725  SRS1071098                    SRP063732       SRR2420563    77306973        15616008546     25207_NucleusAccumbens  Adult     male  Nucleus accumbens  Control       Model organism or animal
 SRX1249842           Bisulfite-seq of rhesus macaque 25407_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 25407_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  83985968    13355795218  SRS1071099                    SRP063732       SRR2420562    83985968        16965165536     25407_NucleusAccumbens  Adult     male  Nucleus accumbens  Control       Model organism or animal
 SRX1249841           Bisulfite-seq of rhesus macaque 24818_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 24818_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  72782928    8484613123   SRS1071100                    SRP063732       SRR2420561    72782928        12009183120     24818_NucleusAccumbens  Adult     male  Nucleus accumbens  Control       Model organism or animal
 SRX1249840           Bisulfite-seq of rhesus macaque 24698_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 24698_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  79414016    12627204820  SRS1071101                    SRP063732       SRR2420560    79414016        16041631232     24698_NucleusAccumbens  Adult     male  Nucleus accumbens  Control       Model organism or animal
 SRX1249839           Bisulfite-seq of rhesus macaque 24340_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 24340_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  84772576    13436053136  SRS1071102                    SRP063732       SRR2420559    84772576        17124060352     24340_NucleusAccumbens  Adult     male  Nucleus accumbens  Control       Model organism or animal
 SRX1249838           Bisulfite-seq of rhesus macaque 22770_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 22770_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             Illumina HiSeq 2000  83310630    13224887149  SRS1071103                    SRP063732       SRR2420558    83310630        16828747260     22770_NucleusAccumbens  Adult     male  Nucleus accumbens  Control       Model organism or animal

You can install the latest version using:
pip install git+https://github.com/saketkc/pysradb.git

Let me know if you face any issues.

[saketkc]

Hi @deepthi888,

This is now available in v0.9.9.
Please let me know if you run into issues.

Here's a colab version demonstrating --detailed output: https://colab.research.google.com/drive/1C60V-jkcNZiaCra_V5iEyFs318jgVoUR