Here is the set up of my list of lists of lists: please see the development code for the read.GenBank function here
#must be connected to internet for this to work
library(ape)
library(plyr)
gi_sample<-c(336087836, 336087835, 336087834)
#use the read.GenBank function with apply because we ultimately have more than the max at one time (400)
my_output <- apply(gi_sample, 1, function(x) read.GenBank(x))
str(my_output)
List of 3
$ :List of 1
..$ 336087836:Class 'DNAbin' raw [1:606] 00 00 00 00 ...
..- attr(*, "class")= chr "DNAbin"
..- attr(*, "species")= chr "Flavobacterium_johnsoniae"
..- attr(*, "references")=List of 1
.. ..$ 336087836:List of 2
.. .. ..$ :List of 4
.. .. .. ..$ pubmedid: chr(0)
.. .. .. ..$ authors : chr "Rusznyak,A., Akob,D.M., Nietzsche,S., Eusterhues,K., Totsche,K.U., Neu,T.R., Frosch,T., Popp,J., Keiner,R., Geletneky,J., Katzs"| __truncated__
.. .. .. ..$ title : chr "Calcite mineralization by karstic cave bacteria"
.. .. .. ..$ journal : chr "Unpublished"
.. .. ..$ :List of 4
.. .. .. ..$ pubmedid: chr(0)
.. .. .. ..$ authors : chr "Rusznyak,A."
.. .. .. ..$ title : chr "Direct Submission"
.. .. .. ..$ journal : chr "Submitted (13-APR-2011) to the INSDC. Institute of Ecology, Aquatic"
$ :List of 1
..$ 336087835:Class 'DNAbin' raw [1:991] 00 00 00 00 ...
..- attr(*, "class")= chr "DNAbin"
..- attr(*, "species")= chr "Rhodococcus_fascians"
..- attr(*, "references")=List of 1
.. ..$ 336087835:List of 2
.. .. ..$ :List of 4
.. .. .. ..$ pubmedid: chr(0)
.. .. .. ..$ authors : chr "Rusznyak,A., Akob,D.M., Nietzsche,S., Eusterhues,K., Totsche,K.U., Neu,T.R., Frosch,T., Popp,J., Keiner,R., Geletneky,J., Katzs"| __truncated__
.. .. .. ..$ title : chr "Calcite mineralization by karstic cave bacteria"
.. .. .. ..$ journal : chr "Unpublished"
.. .. ..$ :List of 4
.. .. .. ..$ pubmedid: chr(0)
.. .. .. ..$ authors : chr "Rusznyak,A."
.. .. .. ..$ title : chr "Direct Submission"
.. .. .. ..$ journal : chr "Submitted (13-APR-2011) to the INSDC. Institute of Ecology, Aquatic"
$ :List of 1
..$ 336087834:Class 'DNAbin' raw [1:690] 00 00 00 00 ...
..- attr(*, "class")= chr "DNAbin"
..- attr(*, "species")= chr "Serratia_plymuthica"
..- attr(*, "references")=List of 1
.. ..$ 336087834:List of 2
.. .. ..$ :List of 4
.. .. .. ..$ pubmedid: chr(0)
.. .. .. ..$ authors : chr "Rusznyak,A., Akob,D.M., Nietzsche,S., Eusterhues,K., Totsche,K.U., Neu,T.R., Frosch,T., Popp,J., Keiner,R., Geletneky,J., Katzs"| __truncated__
.. .. .. ..$ title : chr "Calcite mineralization by karstic cave bacteria"
.. .. .. ..$ journal : chr "Unpublished"
.. .. ..$ :List of 4
.. .. .. ..$ pubmedid: chr(0)
.. .. .. ..$ authors : chr "Rusznyak,A."
.. .. .. ..$ title : chr "Direct Submission"
.. .. .. ..$ journal : chr "Submitted (13-APR-2011) to the INSDC. Institute of Ecology, Aquatic"
What I would like out of this list:
GI authors title journal
336087836 "Rusznyak,A., Akob,D.M., Nietzsche,S., Eusterhues,K., Totsche,K.U., Neu,T.R., Frosch,T., Popp,J., Keiner,R., Geletneky,J., Katzs"| __truncated__ "Calcite mineralization by karstic cave bacteria" "Unpublished"
336087835 "Rusznyak,A., Akob,D.M., Nietzsche,S., Eusterhues,K., Totsche,K.U., Neu,T.R., Frosch,T., Popp,J., Keiner,R., Geletneky,J., Katzs"| __truncated__ "Calcite mineralization by karstic cave bacteria" "Unpublished"
336087834 "Rusznyak,A., Akob,D.M., Nietzsche,S., Eusterhues,K., Totsche,K.U., Neu,T.R., Frosch,T., Popp,J., Keiner,R., Geletneky,J., Katzs"| __truncated__ "Calcite mineralization by karstic cave bacteria" "Unpublished"
I am sorely in need of an explanation of how these lists are nested. How can I access the "title" and keep the name of each list? I have tinkered with all sorts of "[]" subsetting combinations and ultimately do not understand how to read this list. I have read many beginner explanations, and am still at a loss.
This is changed from the earlier question, although the data remain the same.
Thank you!