cd ~
CWD=$(pwd)
perl -MNet::FTP -e \
'$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1);
$ftp->login; $ftp->binary;
$ftp->get("/entrez/entrezdirect/edirect.tar.gz");'
gunzip -c edirect.tar.gz | tar xf -
rm edirect.tar.gz
export PATH=${PATH}:$CWD/edirect >& /dev/null || setenv PATH "${PATH}:$CWD/edirect"
./edirect/setup.sh
# Setup path permamantly
echo "export PATH=\${PATH}:$CWD/edirect" >> $HOME/.bashrcPROJECT_WORKING_DIRECTORY='Documents/research/support/Arif_Malik/'
mkdir -p "${PROJECT_WORKING_DIRECTORY}"
cd "${PROJECT_WORKING_DIRECTORY}"
# Taxonomy
time esearch -db nuccore -query 'vertebrates[porgn] AND 12S ribosomal rna[Title] OR 12S rrna[Title] NOT partial [Title]' \
| efilter -location mitochondrion \
| efetch -format xml \
| xtract -pattern Seq-entry -element Textseq-id_accession -element Textseq-id_version -element OrgName_lineage \
| sed 's/\t/./' \
| awk '$1~/\./' \
> 12S_vertebrates.taxonomy
# Sequences
time esearch -db nuccore -query 'vertebrates[porgn] AND 12S ribosomal rna[Title] OR 12S rrna[Title] NOT partial [Title]' \
| efilter -location mitochondrion \
| efetch -format fasta \
| bgzip \
> 12S_vertebrates_all.fasta.gzEnsure we get the subset of sequences for which we have taxonomic information:
cut -f1 12S_vertebrates.taxonomy \
| xargs samtools faidx 12S_vertebrates_all.fasta.gz \
| bgzip \
> 12S_vertebrates.fasta.gz