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Transfer GI to taxID by efetch in a loop

0

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6.9 years ago

wyc661217 ▴ 10

I am a new guy and want to add taxID to the fasta file (1.fa) which begins with GI for each line. So firstly I try to get the taxID by efetch through the following code.

cat 1.fa | while read line
do
GI=`grep ">" | cut -d '>' -f 2 | cut -d ' ' -f 1`
wget curl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=${GI}&rettype=fasta&retmode=xml"
done

But it did not work by saying:

--2017-06-01 16:10:48-- http://curl/ Resolving curl (curl)... failed: Name or service not known. wget: unable to resolve host address ‘curl’ URL transformed to HTTPS due to an HSTS policy --2017-06-01 16:10:48-- https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=X51700.1%0AX68321.1%0AX55027.1%0AZ12029.1%0AX52700.1&rettype=fasta&retmode=xml Resolving eutils.ncbi.nlm.nih.gov eutils.ncbi.nlm.nih.gov)... 130.14.29.110, 2607:f220:41e:4290::110 Connecting to eutils.ncbi.nlm.nih.gov eutils.ncbi.nlm.nih.gov)|130.14.29.110|:443... connected. HTTP request sent, awaiting response... 400 Bad Request 2017-06-01 16:10:49 ERROR 400: Bad Request.

However it works well when replacing the ${GI} to the real GI numbers, like

wget curl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=X51700.1&rettype=fasta&retmode=xml"

And could produce the correct GI no. by

cat 1.fa | while read line
do
GI=`grep ">" | cut -d '>' -f 2 | cut -d ' ' -f 1`
echo "$GI"
done

Could anyone tell me where is the mistake? Thank you guys!

efetch software error GI taxid • 2.3k views

ADD COMMENT • link 6.9 years ago by wyc661217 ▴ 10

score 0 · Answer 1 · 2017-06-01

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6.9 years ago

GenoMax 141k

Once you figure out how to get a clean single value for GI (looks like you have multiple values in the example you posted), use only curl with https. Redirect output to a file or use -o filename to save.

ADD COMMENT • link 6.9 years ago by GenoMax 141k

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Thanks! I have got the clean GI. And also I tried to curl the https, but it did not work even when I typed the GI manually:

curl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=X52700.1&rettype=fasta&retmode=xml"


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ADD REPLY • link 6.9 years ago by wyc661217 ▴ 10

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As I said above you need to use https. Try: curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=X52700.1&rettype=fasta&retmode=xml"