# retrieve a single GenBank entry using GID
efetch -db nucleotide -id 13872713 -format gb


# retrieve a single GenBank entry using ACCESSION
efetch -db nucleotide -id AJ311046 -format gb


#retrieve a set of GenBank entries using GID
efetch -db nucleotide -id 7672660,13872713 -format gb > testgid.gen

#retrieve a set of GenBank entries using ACCESSION
efetch -db nucleotide -id AF141132,AJ311046 -format gb > testacc.gen

#This doesn't work
cat test.acc | efetch -db nuccore -format gb

cat test.gid | efetch -db nuccore -format gb

# this works for gid's
cat test.gid | epost -db nuccore | efetch -db nuccore -format gb | more

# this doesn't work for ACC numbers
cat test.acc | epost -db nuccore | efetch -db nuccore -format gb | more

# NCBI now tells me that you need to tell epost what you are 
# what you are feeding it using the -format option
cat test.acc | epost -db nuccore -format acc  | efetch -db nuccore -format gb | more



epost -db nuccore -id AF112443,AF128239 |more

#retrieves all sequences in the gi list whose length is less than 1000 bp
cat AF210069_1.gi | epost -db nuccore | efilter -query "1:1000 [SLEN]" | efetch -db nuccore -format gb | more

# Use seqfetch to retrieve sequences filtered with an Entrez query statement.
seqfetch.py AF210069_1.gi junk.gen -q '1:800 [SLEN]'


##### xtract ######

#prints all fields
cat AF210069.xml | xtract -pattern DocumentSummary

cat AF210069.xml | xtract -pattern DocumentSummary -element Gi,Title,Biomol,Slen


####  refine search ######

#steps to refine a previous entrez search

{venus:/home/psgendb/BIRCHDEV/temp/edirect}cat searchresult.esearch
<ENTREZ_DIRECT>
  <Db>nuccore</Db>
  <WebEnv>NCID_1_861923382_130.14.22.215_9001_1404945972_1472278226</WebEnv>
  <QueryKey>1</QueryKey>
  <Count>5</Count>
  <Step>1</Step>
</ENTREZ_DIRECT>


cat searchresult.esearch | esearch -db nuccore -query pi176 
<ENTREZ_DIRECT>
  <Db>nuccore</Db>
  <WebEnv>NCID_1_861923382_130.14.22.215_9001_1404945972_1472278226</WebEnv>
  <QueryKey>2</QueryKey>
  <Count>2</Count>
  <Step>2</Step>
</ENTREZ_DIRECT>
{venus:/home/psgendb/BIRCHDEV/temp/edirect}cat searchresult.esearch | esearch -db nuccore -query pi176 > pi176.esearch
{venus:/home/psgendb/BIRCHDEV/temp/edirect}cat pi176.esearch | efetch -db nuccore -format fasta
>gi|169077|gb|M18249.1|PEADRRA Pea (P.sativum) disease resistance response protein (PI176) mRNA, complete cds
TACACAACTAGGCAAGCAATTTCTTAGTTCTTTCTCACACTTTAGCAATATAAAACAATATCATCATGGG
TGTTTTTAATGTTGAAGATGAAATCACTTCTGTTGTAGCACCTGCTATACTCTACAAAGCTCTAGTTACA
GATGCTGACACTCTTACTCCAAAGGTTATTGATGCCATCAAAAGTATCGAAATTGTTGAAGGAAACGGAG
GTGCTGGAACCATCAAGAAACTCACTTTCGTTGAAGATGGTGAAACCAAACATGTGTTGCACAAAGTGGA
GTTAGTAGATGTTGCTAACTTGGCTTACAACTATAGCATAGTTGGTGGTGTTGGATTTCCAGACACAGTT
GAGAAGATCTCATTTGAGGCTAAACTGTCTGCAGGACCAAATGGAGGATCCATTGCAAAGCTGAGTGTGA
AATATTACACAAAAGGTGATGCTGCTGCTCCTACTGAAGAGCAACTCAAGAGTGACAAAGCTAAGGGTGA
TGGTCTTTTCAAGGCTCTTGAGCGTTACTGTTTGGCTCATCCTGATTACAACTAAACTATATAATCATCA
ACAAGTGTGTGTTGTTATGTATACTATATAATCATCATGTGTGCTTAATTTGGCTGCCAATGTAATCCCC
CTGTTTTGTTTTTTCCCTTTCCCTTTTCTTTGTGGACTAAAAGTGTGAGATTGTAAGTCATGTATACCTC
TCCTTCAATAAATTATAATCATTTATAT

>gi|78033574|emb|AM110016.1| Uncultured organism partial 16S rRNA gene, clone Pi176
ATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGTAACAGGTCTTCGGATGCTGACGAGTGG
CGAACGGGTGAGTAATACATCGGAACGTGCCCGATCGTGGGGGATAACGGAGCGAAAGCTTTGCTAATAC
CGCATACGACCTACGGATGAAAGCAGGGGACCGCAAGGCCTTGCGCGGACGGAGCGGCCGATGGCAGATT
AGGTAGTTGGTGGGATAAAAGCTTACCAAGCCGACGATCTGTAGCTGGTCTGAGAGGACGACCAGCCACA
CTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGC
CTGATCCAGCCATGCCGCGTGCAGGATGAAGGCCTTCGGGTTGTAAACTGCTTTTGTACGGAACGAAAAG
ACTCTGGTTAATACCTGGGGTCCATGACGGTACCGTAAGAATAAGCACCGGCTTAA

{venus:/home/psgendb/BIRCHDEV/temp/edirect}