from jcvi.utils.cbook import tile from jcvi.utils.console import printf from jcvi.apps.base import ( OptionParser, ActionDispatcher, get_email_address, mkdir, ls_ftp, download, sh, last_updated, which, ) myEmail = get_email_address() Entrez.email = myEmail PHYTOZOME_COOKIES = ".phytozome_cookies" def batch_taxonomy(list_of_taxids): """ Convert list of taxids to Latin names """ for taxid in list_of_taxids: handle = Entrez.efetch(db="Taxonomy", id=taxid, retmode="xml") records = Entrez.read(handle) yield records[0]["ScientificName"] def batch_taxids(list_of_names):
import sys import time import logging import urllib2 from Bio import Entrez, SeqIO from jcvi.formats.base import must_open from jcvi.formats.fasta import print_first_difference from jcvi.utils.cbook import tile from jcvi.utils.iter import grouper from jcvi.apps.console import green from jcvi.apps.base import OptionParser, ActionDispatcher, get_email_address, \ mkdir, ls_ftp, download myEmail = get_email_address(user=True) Entrez.email = myEmail def batch_taxonomy(list_of_taxids): """ Convert list of taxids to Latin names """ for taxid in list_of_taxids: handle = Entrez.efetch(db='Taxonomy', id=taxid, retmode="xml") records = Entrez.read(handle) yield records[0]["ScientificName"] def batch_taxids(list_of_names): """
import urllib2 import re from os.path import join as urljoin from Bio import Entrez, SeqIO from jcvi.formats.base import must_open from jcvi.formats.fasta import print_first_difference from jcvi.utils.cbook import tile from jcvi.utils.iter import grouper from jcvi.apps.console import green from jcvi.apps.base import OptionParser, ActionDispatcher, get_email_address, \ mkdir, ls_ftp, download myEmail = get_email_address(user=True) Entrez.email = myEmail def batch_taxonomy(list_of_taxids): """ Convert list of taxids to Latin names """ for taxid in list_of_taxids: handle = Entrez.efetch(db='Taxonomy', id=taxid, retmode="xml") records = Entrez.read(handle) yield records[0]["ScientificName"] def batch_taxids(list_of_names): """
import re from os.path import join as urljoin from Bio import Entrez, SeqIO from jcvi.formats.base import must_open from jcvi.formats.fasta import print_first_difference from jcvi.formats.fastq import fromsra from jcvi.utils.cbook import tile from jcvi.utils.iter import grouper from jcvi.apps.console import green from jcvi.apps.base import OptionParser, ActionDispatcher, get_email_address, \ mkdir, ls_ftp, download, sh, last_updated myEmail = get_email_address() Entrez.email = myEmail def batch_taxonomy(list_of_taxids): """ Convert list of taxids to Latin names """ for taxid in list_of_taxids: handle = Entrez.efetch(db='Taxonomy', id=taxid, retmode="xml") records = Entrez.read(handle) yield records[0]["ScientificName"] def batch_taxids(list_of_names): """