Grab Lat_Lon for SRA accessions. about edirectcookbook HOT 4 CLOSED

esearch -db sra -query SRR5381359 | elink -target biosample | efetch -format docsum | xtract -pattern DocumentSummary -element Attribute

@mikeadavidson -- any idea why Attribute@lat_lon doesnt work?

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I'm by no means an expert on sra (I'm not even sure what it stands for), but Attribute@lat_lon would only identify <Attribute> elements (putting in angle brackets to differentiate from XML attributes...this is an unfortunately named element!) with an attribute named "lat_lon".

In this case, "lat_lon" is the value of the "attribute_name" attribute.

Try something like this for your xtract:

xtract -pattern DocumentSummary -block Attribute -if Attribute@attribute_name -equals lat_lon -element Attribute

from edirectcookbook.

Thanks Mike!

esearch -db sra -query SRR5381359 | elink -target biosample | efetch -format docsum | xtract -pattern DocumentSummary -block Attribute -if Attribute@attribute_name -equals lat_lon -element Attribute

so:

for i in cat <ACCN_LIST>; do echo -n $i; esearch -db sra -query $i | elink -target biosample | efetch -format docsum | xtract -pattern DocumentSummary -block Attribute -if Attribute@attribute_name -equals lat_lon -element Attribute; done (not tested)

Ill push after I test.

from edirectcookbook.

yes, that works.

for i in $(cat sra_ids.txt); do ll=$(esearch -db sra -query $i | elink -target biosample | efetch -format docsum | xtract -pattern DocumentSummary -block Attribute -if Attribute@attribute_name -equals lat_lon -element Attribute); echo -e "$i\t$ll"; done

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