Ejemplos de get_email_address en Python

Ejemplo n.º 1

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):

Ejemplo n.º 2

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):
    """

Ejemplo n.º 3

Archivo: fetch.py Proyecto: yangjl/jcvi

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):
    """

Ejemplo n.º 4

Archivo: fetch.py Proyecto: tanghaibao/jcvi

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):
    """