Hi,
I'm evaluating NCBI's EDirect command line tool for the first time (as an alternative to using E-utilities and parsing the XML). It looks pretty good so far but I'm having trouble dealing with cases where I attempt to extract individual fields from a docsum and one of the fields are empty. For example, when I do a very simple query of the bioproject database for all "Pseudomonas aeruginosa PAO1" records:
esearch -db bioproject -query "Pseudomonas aeruginosa PAO1" | efetch -format docsum | xtract -pattern DocumentSummary -element Organism_Strain Project_Acc
some of the records returned do not have an Organism_Strain value returned and the Project_Acc value gets shifted to the first column:
MPAO1 PRJNA273663
PRJEB8227
PRJNA268347
PAO1 PRJNA266474
PRJNA265367
PA01 PRJNA264943
PAO1 PRJNA258237
PRJNA256959
PRJNA252740
PRJNA252560
I would like to have xtract return an empty string or even "-" for cases where an Organism_name is missing so that it would have two columns instead of a combination of one or two column lines:
PA01 PRJNA264943
PAO1 PRJNA258237
- PRJNA256959
- PRJNA252740
- PRJNA252560
I've looked over the official NCBI documentation and tried to assign each field to an initialized variable doing different combinations of the following:
esearch -db bioproject -query "Pseudomonas aeruginosa PAO1" | efetch -format docsum | xtract -pattern DocumentSummary -element "&STRAIN" Organism_Strain -STRAIN "(-)" -element Bioproject_acc
but I can't seem to find the correct syntax to make things work the way I want. Does anyone have any experience with this kind of problem?
Thanks
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written
by
glwinsor •
Use the following XSLT stylesheet
curl -s 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=bioproject&id=273663,268347,266474,265367,264943,258237,256959,253371,252560,246577,246187,243443,243442,243441,243440,243439,243438,238552,234392,231042,229797,229796,228966,227545,225027,225026,222984,213568,213564,212862,212861,210078,209744,209743,206372,204979,203313,202063,201067,201024,197381,197270,186945,178535,169508,163909,153781,153301,152899,152815,152481,151585,150221,149213,149177,149097,148359,146229,144393,143701,141069,140783,140437,139731,139627,139393,134617,128339,127841,126779,125979,119669,117261,111043,109535,108523,108169,106267,103929,102875,102387,101467,100923,100723,99427,98977,98025,97617,96113,95321,95131,94055,93093,92577,91591,83447,66135,57945,331' | xsltproc stylesheet.xsl -
MPAO1 PRJNA273663
- PRJNA268347
PAO1 PRJNA266474
- PRJNA265367
PA01 PRJNA264943
PAO1 PRJNA258237
- PRJNA256959
- PRJNA253371
- PRJNA252560
PA01 PRJNA246577
- PRJNA246187
PAO1 PRJNA243443
PAO1 PRJNA243442
PAO1 PRJNA243441
PAO1 PRJNA243440
PAO1 PRJNA243439
PAO1 PRJNA243438
- PRJNA238552
- PRJNA234392
PAO1 PRJNA231042
PA01 PRJNA229797
PA01 PRJNA229796
- PRJNA228966
PAO1-GFP PRJNA227545
PAO1-VE13 PRJNA225027
PAO1-VE2 PRJNA225026
- PRJNA222984
PAO1 PRJNA213568
PA01 PRJNA213564
PAO1-VE13 PRJNA212862
PAO1-VE2 PRJNA212861
- PRJNA210078
PAO1 PRJNA209744
PAO1-CipR PRJNA209743
PAK PRJNA206372
- PRJNA204979
- PRJNA203313
PAO1-CipR PRJNA202063
- PRJNA201067
PAO1 PRJNA201024
PAO1 PRJNA197381
- PRJNA197270
- PRJNA186945
- PRJNA178535
PAO1 PRJNA169508
- PRJNA163909
- PRJNA153781
- PRJNA153301
- PRJNA152899
- PRJNA152815
- PRJNA152481
- PRJNA151585
- PRJNA150221
- PRJNA149213
- PRJNA149177
- PRJNA149097
- PRJNA148359
- PRJNA146229
- PRJNA144393
- PRJNA143701
- PRJNA141069
- PRJNA140783
- PRJNA140437
- PRJNA139731
- PRJNA139627
- PRJNA139393
- PRJNA134617
- PRJNA128339
- PRJNA127841
- PRJNA126779
- PRJNA125979
- PRJNA119669
- PRJNA117261
- PRJNA111043
- PRJNA109535
- PRJNA108523
- PRJNA108169
- PRJNA106267
- PRJNA103929
- PRJNA102875
- PRJNA102387
- PRJNA101467
- PRJNA100923
- PRJNA100723
- PRJNA99427
- PRJNA98977
- PRJNA98025
- PRJNA97617
- PRJNA96113
- PRJNA95321
- PRJNA95131
- PRJNA94055
- PRJNA93093
- PRJNA92577
- PRJNA91591
PAO1H2O PRJNA83447
PAK PRJNA66135
PAO1 PRJNA57945
PAO1 PRJNA331
Thanks for this. I overly simplified my example and requirements for the sake of clarity but it looks like the XLST approach will handle them very well!
•
written
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glwinsor •
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