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Proteomicslab57357 / UniprotR

Retrieving Information of Proteins from Uniprot
GNU General Public License v3.0
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GetProteinAnnontate function cannot parse the content of Column-Function #4

Closed panxiaoguang closed 4 years ago

panxiaoguang commented 4 years ago 
library(UniprotR)
library(httr)
ProteinAcc<-"P42293"
GetProteinAnnontate(ProteinAcc,"comment(CATALYTIC ACTIVITY)")
#Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
# no lines available in input
GetProteinAnnontate(ProteinAcc,c("feature(SIGNAL)","families"))
#                             Signal.peptide             Protein.families
#P42293 SIGNAL 1..26;  /evidence=ECO:0000255 Glycosyl hydrolase 43 family 
GetProteinAnnontate(ProteinAcc,c("feature(SIGNAL)","families","comment(CATALYTIC ACTIVITY)"))
#Error in curl::curl_fetch_memory(url, handle = handle) :

As seen in the code, once there is a call about the function column, the function will not work

MohmedSoudy commented 4 years ago

I think the problem is related to the internet connection as i run the same lines and have the output of the three lines.

ProteinAcc<-"P42293"
GetProteinAnnontate(ProteinAcc,"comment(CATALYTIC ACTIVITY)")
"CATALYTIC ACTIVITY: Reaction=Endohydrolysis of (1->5)-alpha-arabinofuranosidic linkages in (1->5)-arabinans.; EC=3.2.1.99; Evidence={ECO:0000269|PubMed:20883454};
Levels: CATALYTIC ACTIVITY: Reaction=Endohydrolysis of (1->5)-alpha-arabinofuranosidic linkages in (1->5)-arabinans.; EC=3.2.1.99; Evidence={ECO:0000269|PubMed:20883454};"
GetProteinAnnontate(ProteinAcc,c("feature(SIGNAL)","families"))
"                             Signal.peptide             Protein.families
P42293 SIGNAL 1..26;  /evidence=ECO:0000255 Glycosyl hydrolase 43 family"
GetProteinAnnontate(ProteinAcc,c("feature(SIGNAL)","families","comment(CATALYTIC ACTIVITY)"))
"                             Signal.peptide             Protein.families
P42293 SIGNAL 1..26;  /evidence=ECO:0000255 Glycosyl hydrolase 43 family
                                                                                                                                                       Catalytic.activity
P42293 CATALYTIC ACTIVITY: Reaction=Endohydrolysis of (1->5)-alpha-arabinofuranosidic linkages in (1->5)-arabinans.; EC=3.2.1.99; Evidence={ECO:0000269|PubMed:20883454};"
panxiaoguang commented 4 years ago

I think the problem is related to the internet connection as i run the same lines and have the output of the three lines.

ProteinAcc<-"P42293"
GetProteinAnnontate(ProteinAcc,"comment(CATALYTIC ACTIVITY)")
"CATALYTIC ACTIVITY: Reaction=Endohydrolysis of (1->5)-alpha-arabinofuranosidic linkages in (1->5)-arabinans.; EC=3.2.1.99; Evidence={ECO:0000269|PubMed:20883454};
Levels: CATALYTIC ACTIVITY: Reaction=Endohydrolysis of (1->5)-alpha-arabinofuranosidic linkages in (1->5)-arabinans.; EC=3.2.1.99; Evidence={ECO:0000269|PubMed:20883454};"
GetProteinAnnontate(ProteinAcc,c("feature(SIGNAL)","families"))
"                             Signal.peptide             Protein.families
P42293 SIGNAL 1..26;  /evidence=ECO:0000255 Glycosyl hydrolase 43 family"
GetProteinAnnontate(ProteinAcc,c("feature(SIGNAL)","families","comment(CATALYTIC ACTIVITY)"))
"                             Signal.peptide             Protein.families
P42293 SIGNAL 1..26;  /evidence=ECO:0000255 Glycosyl hydrolase 43 family
                                                                                                                                                       Catalytic.activity
P42293 CATALYTIC ACTIVITY: Reaction=Endohydrolysis of (1->5)-alpha-arabinofuranosidic linkages in (1->5)-arabinans.; EC=3.2.1.99; Evidence={ECO:0000269|PubMed:20883454};"

yes,it's the internet problem