In [101]:
!ls
biologydirect-1-1-19 jbiol-8-6-54.html
biologydirect-1-1-19.html LICENSE
biomedcentral1471-2164-7-151 parasitesandvectors-3-1-115
biomedcentral1471-2164-7-151.html parasitesandvectors-3-1-115.html
create_subfolders.sh README.md
genomebiology2013-14-6-122 trying-beautiful-soup.ipynb
genomebiology2013-14-6-122.html virologyj-11-1-26
get-figures.py virologyj-11-1-26.html
jbiol-8-6-54 whats-wrong-jbiol.ipynb
In [102]:
from bs4 import BeautifulSoup
In [103]:
import os, shutil
Having a look at one of the smaller files:
In [104]:
soup = BeautifulSoup (open("virologyj-11-1-26.html"))
In [105]:
print(soup.prettify())
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Virology Journal | Full text | Genome characterization of Long Island tick rhabdovirus, a new virus identified in Amblyomma americanum ticks
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<span class="articletype">
Research
</span>
<h1>
Genome characterization of Long Island tick rhabdovirus, a new virus identified in
<em>
Amblyomma americanum
</em>
ticks
</h1>
<div class="singleins">
<p class="authors">
<strong>
Rafal Tokarz
</strong>
<sup>
*
</sup>
,
<strong>
Stephen Sameroff
</strong>
,
<strong>
Maria Sanchez Leon
</strong>
,
<strong>
Komal Jain
</strong>
and
<strong>
W Ian Lipkin
</strong>
</p>
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<span>
*
</span>
Corresponding author: Rafal Tokarz
<a href="mailto:rt2249@cumc.columbia.edu">
rt2249@cumc.columbia.edu
</a>
</p>
</li>
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Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1701, New York, NY 10032, USA
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<section class="cit">
<div class="collapsible-content">
<p>
<em>
Virology Journal
</em>
2014,
<strong>
11
</strong>
:26
<span class="pseudotab">
doi:10.1186/1743-422X-11-26
</span>
</p>
<br/>
<p>
The electronic version of this article is the complete one and can be found online at:
<a href="http://www.virologyj.com/content/11/1/26">
http://www.virologyj.com/content/11/1/26
</a>
</p>
<br/>
<table cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td>
Received:
</td>
<td>
15 January 2014
</td>
</tr>
<tr>
<td>
Accepted:
</td>
<td>
10 February 2014
</td>
</tr>
<tr>
<td>
Published:
</td>
<td>
11 February 2014
</td>
</tr>
</tbody>
</table>
<!--<br/>-->
<div style="line-height:140%">
<p>
© 2014 Tokarz et al.; licensee BioMed Central Ltd.
<br/>
</p>
<p>
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (
<a href="http://creativecommons.org/licenses/by/2.0">
http://creativecommons.org/licenses/by/2.0
</a>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
</p>
</div>
</div>
<div id="article-body">
<section>
<a name="abs">
</a>
<h3>
Abstract
</h3>
<div class="collapsible-content">
<h4>
Background
</h4>
<p style="line-height:160%">
Ticks are implicated as hosts to a wide range of animal and human pathogens. The full
range of microbes harbored by ticks has not yet been fully explored.
</p>
<h4>
Methods
</h4>
<p style="line-height:160%">
As part of a viral surveillance and discovery project in arthropods, we used unbiased
high-throughput sequencing to examine viromes of ticks collected on Long Island, New
York in 2013.
</p>
<h4>
Results
</h4>
<p style="line-height:160%">
We detected and sequenced the complete genome of a novel rhabdovirus originating from
a pool of
<em>
Amblyomma americanum
</em>
ticks. This virus, which we provisionally name Long Island tick rhabdovirus, is distantly
related to Moussa virus from Africa.
</p>
<h4>
Conclusions
</h4>
<p style="line-height:160%">
The Long Island tick rhabdovirus may represent a novel species within family
<em>
Rhabdoviridae
</em>
.
</p>
</div>
</section>
<span id="keywords">
<h5 class="inline">
Keywords:
</h5>
Ticks; Rhabdovirus; High-throughput sequencing;
<em>
Amblyomma americanum
</em>
</span>
<section>
<a name="sec1">
</a>
<h3>
Background
</h3>
<div class="collapsible-content">
<p style="line-height:160%">
The family
<em>
Rhabdoviridae
</em>
consists of a large group of enveloped, single-stranded, negative sense RNA viruses
that infect a wide range of vertebrates, invertebrates, and plants
<a name="d43115e184">
</a>
[
<a href="#B1" onclick="LoadInParent('#B1'); return false;">
1
</a>
]. Their genome typically consists of at least five open reading frames (ORFs) organized
in a linear order 3′-N-P-M-G-L-5′, and encode the viral nucleocapsid (N), phosophoprotein
(P), matrixprotein (M), glycoprotein (G) and RNA polymerase (L). In addition to these
genes, many rhabdoviruses contain smaller ORFs that encode additional accessory proteins,
most without known function. Currently,
<em>
Rhabdoviridae
</em>
consists of nine named genera (
<em>
Cytorhabdovirus, Ephemerovirus, Lyssavirus, Novirhabdovirus, Nucleorhabdovirus, Perhabdovirus,
Sigmavirus, Tibrovirus, Vesiculovirus
</em>
), although many tentative rhabdoviruses still await taxonomic classification
<a name="d43115e194">
</a>
[
<a href="#B2" onclick="LoadInParent('#B2'); return false;">
2
</a>
].
</p>
<p style="line-height:160%">
Arthropods are essential in transmission of many pathogenic rhabdoviruses. In the
context of a program in viral surveillance and discovery in arthropods, we examined
viromes of ticks collected in New York State and identified a novel rhabdovirus associated
with the lone star tick,
<em>
Amblyomma americanum
</em>
. We provisionally name this virus Long Island tick rhabdovirus.
</p>
</div>
</section>
<section>
<a name="sec2">
</a>
<h3>
Results
</h3>
<div class="collapsible-content">
<p style="line-height:160%">
Analysis of high-throughput sequencing (HTS) data by BLASTx revealed sequences with
homology to all five prototypical rhabdovirus proteins. Homology searches indicated
these sequences were most similar to Moussa virus (MOUV) and therefore all were assembled
to MOUV as a reference genome
<a name="d43115e209">
</a>
[
<a href="#B3" onclick="LoadInParent('#B3'); return false;">
3
</a>
]. Amino acid analysis of the coding sequence suggested this virus likely represented
a novel rhabdovirus; hence, we tentatively named it Long Island tick rhabdovirus (LITRV),
after its geographical location and host.
</p>
<h4>
Genome
</h4>
<p style="line-height:160%">
The complete genome of LITRV comprises 11,176 nucleotides (nt), contains non-coding
3′ and 5′ sequences, and five main ORFs encoded in linear order (Figure
<a name="d43115e218">
</a>
<a href="http://www.virologyj.com/content/11/1/26/figure/F1" onclick="popup('http://www.virologyj.com/content/11/1/26/figure/F1','',800,470); return false;">
1
</a>
A). Characteristic of rhabdoviruses, the coding regions are flanked by conserved sequences
that likely serve as transcription initiation and transcription termination/polyadenylation
signals. The polyadenylation signal consists of 3′- GAACUUUUUUU, which is followed
by a 2 nt intergenic sequence and a putative transcription initiation sequence 3′-UUGUU(U/G)N(G/A/U)U
(Figure
<a name="d43115e221">
</a>
<a href="http://www.virologyj.com/content/11/1/26/figure/F1" onclick="popup('http://www.virologyj.com/content/11/1/26/figure/F1','',800,470); return false;">
1
</a>
B). Homology search of all five coding regions revealed that each ORF is most similar
to the corresponding ORF of MOUV (Table
<a name="d43115e224">
</a>
<a href="http://www.virologyj.com/content/11/1/26/table/T1" onclick="popup('http://www.virologyj.com/content/11/1/26/table/T1','',800,470); return false;">
1
</a>
). Both MOUV and LITRV cluster together and form a distinct phylogenetic clade within
<em>
Rhabdoviridae
</em>
(Figure
<a name="d43115e230">
</a>
<a href="http://www.virologyj.com/content/11/1/26/figure/F2" onclick="popup('http://www.virologyj.com/content/11/1/26/figure/F2','',800,470); return false;">
2
</a>
). Similar to MOUV, only ORFs 1, 4 and 5, encoding the putative N, G and L proteins
display homology to corresponding
<em>
Rhabdoviridae
</em>
proteins. ORFs 2 and 3, encoding the putative P and M proteins display no homology
to any rhabdovirus proteins outside of MOUV. The LITRV genome also contains four alternative
ORFs located within the P, M and G ORFs. These ORFs were designated P’, M’ and G1’
and G2’, and would encode proteins of 81, 98, 106 and 105 amino acids (aa), respectively,
with no significant sequence identity with any other
<em>
Rhabdoviridae
</em>
protein by BLASTp analysis. Of the four ORFs, only P’ and G2’ have an initiation
codon in suitable context for translation.
</p>
<div class="figs">
<div class="fig">
<p>
<a href="http://www.virologyj.com/content/11/1/26/figure/F1" onclick="popup('http://www.virologyj.com/content/11/1/26/figure/F1','F1',800,470); return false;">
<img align="top" alt="thumbnail" class="thumbnail" src="/content/figures/1743-422X-11-26-1.gif"/>
<strong>
Figure 1.
</strong>
</a>
<strong>
Organization of the LITRV genome. A)
</strong>
Schematic representation of LITRV ORFs.
<strong>
B)
</strong>
LITRV coding regions and corresponding transcription regulatory sequences.
</p>
</div>
<div class="table">
<p>
<a href="http://www.virologyj.com/content/11/1/26/table/T1" onclick="popup('http://www.virologyj.com/content/11/1/26/table/T1','T1',800,470); return false;">
<strong>
Table 1.
</strong>
</a>
<strong>
Comparison of LITRV and MOUV ORFs
</strong>
</p>
</div>
<div class="fig">
<p>
<a href="http://www.virologyj.com/content/11/1/26/figure/F2" onclick="popup('http://www.virologyj.com/content/11/1/26/figure/F2','F2',800,470); return false;">
<img align="top" alt="thumbnail" class="thumbnail" src="/content/figures/1743-422X-11-26-2.gif"/>
<strong>
Figure 2.
</strong>
</a>
<strong>
Phylogeny of LITRV.
</strong>
Maximum likelihood phylogenetic tree based on full length L protein sequences of
currently recognized species of
<em>
Rhabdoviridae
</em>
. Gray boxes represent ICTV-accepted species within the genus. LITRV is indicated
by *. Accession numbers are provided next to the viral names. Due to excessive divergence,
only the type species for
<em>
Cytorhabdovirus
</em>
,
<em>
Novirhabdovirus
</em>
and
<em>
Nucleorhabdovirus
</em>
are included. The
<em>
Vesiculovirus
</em>
piry virus is not included due to limited available sequence.
</p>
</div>
</div>
<p style="line-height:160%">
As in all rhabdoviruses, the 3′ and 5′ terminal non-coding regions of LITRV contain
partially complementary regions, particularly at the terminal ends. The 3′ leader
sequence is 49 nt long while the length of the 5′ trailer sequence is 115 nt. The
terminal portions of the non-coding sequences are highly conserved in both LITRV and
MOUV with 13 out of 19 nt identical in both viruses.
</p>
<h4>
ORF analysis
</h4>
<p style="line-height:160%">
The 1413 nt ORF1 is predicted to encode a nucleoprotein of 470 aa that is 38% similar
to MOUV N and contains many conserved rhabdovirus N domains including the RNA binding
motif SPYS (Table
<a name="d43115e409">
</a>
<a href="http://www.virologyj.com/content/11/1/26/table/T1" onclick="popup('http://www.virologyj.com/content/11/1/26/table/T1','',800,470); return false;">
1
</a>
). ORF2, comprising 831 nt, and, in accordance with its position within the rhabdoviral
genome, is predicted to encode a 276 aa phosphoprotein. This protein shares 22.3%
identity with ORF2 of Moussa virus and is predicted to contain 17 serine, 6 threonine
and 1 tyrosine potential phosphorylation sites (
<a href="http://www.cbs.dtu.dk/services/NetPhos/">
http://www.cbs.dtu.dk/services/NetPhos/
</a>
<a alt="" class="xpushbutton" href="http://www.webcitation.org/query.php?url=http://www.cbs.dtu.dk/services/NetPhos/&refdoi=10.1186/1743-422x-11-26" title="Archive copy of webpage">
webcite
</a>
). The 618 nt ORF3 is predicted to encode a 206 aa protein. The protein shares 29.4%
identity with MOUV ORF3. No other known motifs or domains were recognized, although
a polyproline region, consisting of 8 consecutive proline residues was identified
at aa 43–50. ORF 4, comprising 1521 nt, is predicted to encode a 506 aa class I transmembrane
glycoprotein with 29.4% aa identity to MOUV G protein. The protein sequence contains
a predicted N terminal 18 aa signal peptidase cleavage site, a hydrophobic trans-membrane
domain at positions aa 458–480 followed by a C terminal 26 aa tail. It also contains
5 potential N-glycosylation sites at aa positions 58, 345, 359, 387, 424 and contains
all 12 cysteine residues conserved in other rhabdoviruses. The 6396 nt L ORF encodes
the RNA-dependent RNA polymerase, that in LITRV is predicted to encode a 2131 aa protein.
The LITRV L is 51.5% identical to MOUV and contains all the highly conserved residues
of negative strand RNA polymerases
<a name="d43115e416">
</a>
[
<a href="#B4" onclick="LoadInParent('#B4'); return false;">
4
</a>
].
</p>
<p style="line-height:160%">
To examine the presence of LITRV in ticks, we screened archived cDNA generated from
50 individual adult
<em>
A. americanum
</em>
by polymerase chain reaction. The ticks were collected in April of 2008 in the same
location as the ticks from the current study. LITRV sequence was successfully amplified
from one tick.
</p>
</div>
</section>
<section>
<a name="sec3">
</a>
<h3>
Discussion
</h3>
<div class="collapsible-content">
<p style="line-height:160%">
<em>
Rhabdoviridae
</em>
is a large family that includes over 100 viruses classified together on the basis
of genetic, serological or morphological analysis. The advent of high-throughput sequencing
has resulted in genome characterization of many novel and archived rhabdoviruses revealing
the vast diversity of this family
<a name="d43115e433">
</a>
<a name="d43115e435">
</a>
<a name="d43115e437">
</a>
<a name="d43115e439">
</a>
<a name="d43115e441">
</a>
<a name="d43115e443">
</a>
<a name="d43115e445">
</a>
[
<a href="#B3" onclick="LoadInParent('#B3'); return false;">
3
</a>
,
<a href="#B5" onclick="LoadInParent('#B5'); return false;">
5
</a>
-
<a href="#B10" onclick="LoadInParent('#B10'); return false;">
10
</a>
]. In this study we present the first complete genomic sequence of a tick-associated
rhabdovirus from the Western hemisphere. Although arthropods are frequently implicated
as hosts of rhabdoviruses, thus far relatively few of these viruses have been associated
with ticks
<a name="d43115e449">
</a>
<a name="d43115e451">
</a>
<a name="d43115e453">
</a>
[
<a href="#B1" onclick="LoadInParent('#B1'); return false;">
1
</a>
,
<a href="#B5" onclick="LoadInParent('#B5'); return false;">
5
</a>
,
<a href="#B11" onclick="LoadInParent('#B11'); return false;">
11
</a>
]. We detected LITRV in
<em>
A. americanum,
</em>
a common tick species with a broad range spanning eastern and south-central states
in the US. Along with
<em>
Ixodes scapularis
</em>
and
<em>
Dermacentor variablis, A. americanum
</em>
is the primary human-biting hard tick in the eastern part of the US and is implicated
in transmission of
<em>
Ehrlichia
</em>
species,
<em>
Borrelia lonestari
</em>
,
<em>
Francisella tularensis
</em>
, and the Heartland virus
<a name="d43115e476">
</a>
<a name="d43115e478">
</a>
[
<a href="#B12" onclick="LoadInParent('#B12'); return false;">
12
</a>
,
<a href="#B13" onclick="LoadInParent('#B13'); return false;">
13
</a>
].
</p>
<p style="line-height:160%">
Additional studies are needed to determine if
<em>
A. americanum
</em>
is the primary host for LITRV or if other arthropods, and particularly, other ticks,
have a role in its enzoonotic transmission. While sequences were obtained form
<em>
A. americanum
</em>
, this does not definitively implicate
<em>
A. americanum
</em>
as a biological host for LITRV. Detection of microbial nucleic acids in organisms
other than their presumed biological hosts has been reported and in a hematophagus
organism these can represent nucleic acid remains of microbes acquired as part of
a blood meal
<a name="d43115e493">
</a>
<a name="d43115e495">
</a>
[
<a href="#B14" onclick="LoadInParent('#B14'); return false;">
14
</a>
,
<a href="#B15" onclick="LoadInParent('#B15'); return false;">
15
</a>
]. However, our detection of LITRV in
<em>
A. americanum
</em>
collected at the same site five years apart is consistent with a role for this tick
species in the life cycle of this virus. Furthermore, deep sequencing analysis of
multiple pools of
<em>
I. scapularis
</em>
and
<em>
D. variabilis
</em>
collected from the same location and did not identify any LITRV-like sequences in
these two tick species. Our initial survey of LITRV in individual
<em>
A. americanum
</em>
suggests that the prevalence of this virus may be low in tick populations within
the examined area. Molecular surveys analyzing different life stages of
<em>
A. americanum
</em>
and other tick species in broader geographical areas are necessary to establish the
range and prevalence of LITRV.
</p>
<p style="line-height:160%">
Phylogenetically, LITRV forms a distinct clade with MOUV. MOUV was isolated from multiple
mosquito pools in Cote d’Ivoire, suggesting that arthropods are the likely hosts to
this clade of rhabdoviruses. LITRV and MOU share many genetic similarities, including
identical polyadenylation and terminal regions, as well as similar conserved 3′ and
5′ termini sequences. The high amino acid divergence of LITRV and MOUV relative to
other rhabdoviruses suggests that both viruses are unlikely to be associated with
any of the current ascribed genera and likely represent a unique taxonomic group within
<em>
Rhabdoviridae
</em>
. We anticipate that continued surveillance of arthropod vectors may uncover other
members of this clade.
</p>
</div>
</section>
<section>
<a name="sec4">
</a>
<h3>
Conclusions
</h3>
<div class="collapsible-content">
<p style="line-height:160%">
Using high-throughput sequencing analysis of tick viromes, we discovered a novel tick
associated rhabdovirus. This virus, which we provisionally name Long Island tick rhabdovirus,
may represent a novel species within family
<em>
Rhabdoviridae
</em>
.
</p>
</div>
</section>
<section>
<a name="sec5">
</a>
<h3>
Materials and methods
</h3>
<div class="collapsible-content">
<h4>
Nucleic acid extraction
</h4>
<p style="line-height:160%">
Adult ticks were collected in Heckscher State Park (Suffolk County, NY) in April,
2013. Ticks were pooled and homogenized in 500 μl of phosphate buffered saline. Five
tick pools were analyzed; one pool of
<em>
A. americanum
</em>
(N = 25), and two pools each (N = 30/pool) of
<em>
I. scapularis
</em>
and
<em>
D. variablis
</em>
. The homogenate was purified through 0.22 μM filter and treated with RNaseA and TurboDNase
exonucleases. 250 μl of the filtrate was added to 750 μl of NucliSens buffer and total
nucleic acid (TNA) was extracted with the EasyMag extraction platform (Biomerieux).
TNA was eluted in 35 μl volume followed by DNase treatment.
</p>
<h4>
Unbiased high throughput sequencing
</h4>
<p style="line-height:160%">
Total nucleic acid was subjected to first and second strand cDNA synthesis with Super
Script III reverse transcriptase (Invitrogen) and Klenow Fragment (New England Biolabs),
respectively. Ion Shear™ Plus Reagents Kit (Life Technologies) was used for double
stranded cDNA fragmentation. Ion Xpress™ Adapters and unique Ion Xpress™ Barcodes
(Life Technologies) were ligated to fragmented material by using the Ion Plus Fragment
Library kit, which also contained reagents for amplification of barcoded libraries.
Ion OneTouch™ 200 Template Kit v2 (Life Technologies) was used to bind barcoded libraries
to Ion Sphere™ particles (ISPS). Emulsion PCR of DNA linked ISPS was performed on
the Ion OneTouch™ 2 instrument (Life Technologies). Ion OneTouch™ ES instrument was
used to isolate template-positive ISPS. Ion PGM™ Sequencing 200 Kit v2 (Life Technologies)
was used for sequencing of templated ISPS which were loaded on the Ion 316™ Chip for
further processing on the Ion Personal Genome Machine® (PGM™) System (Life Technologies).
</p>
<p style="line-height:160%">
The de-multiplexed reads were preprocessed by trimming primers and adaptors, length
filtering, and masking of low complexity regions (WU-BLAST 2.0). The remaining reads
were subjected to homology search using BLASTn against a host genome database. The
host-subtracted reads were assembled using the Newbler assembler (454, v2.6). Contigs
and singletons were then subjected to a homology search against the entire GenBank
database using BLASTn and the viral GenBank database using BLASTx. Contigs and singletons
with similarity to viral sequences from the BLASTx analysis were again subjected to
a homology search against entire GenBank database to correct for biased e-values.
For potential viral candidates, close relatives were used to identify low homology
regions in the genome from BLASTx. Overall, out of approximately 190,000 sequence
reads obtained by HTS, 96 reads with a mean length of 182 nt were unique to LITRV.
Gaps were filled in by PCR using primers specific to the assembled sequence. The final
sequence was verified by classical dideoxy sequencing using primers designed to generate
overlapping PCR products. Genomic termini were obtained by 5′ and 3′ RACE kits (CloneTech).
Genome assembly was performed with Geneious v 6.1. All phylogenetic trees were constructed
with Mega 5.2 software.
</p>
<h4>
Tick screening
</h4>
<p style="line-height:160%">
To assess the presence of Long Island tick rhabdovirus in ticks, we used cDNA generated
from adult
<em>
A. americanum
</em>
ticks collected in April, 2008 at the same location. Tick cDNA was screened by PCR
with primers 5′-GGGACGATGCTCTAGTCACG-3′ (fwd), and 5′-TTTGTCTGTGAGGTCGGACG-3′ (rev)
targeting a 299 bp fragment of the N gene. PCR products were assessed by gel electrophoresis
and sequenced to confirm that they represent Long Island tick rhabdovirus.
</p>
<p style="line-height:160%">
The complete genome sequence of LITRV was deposited in Genebank under accession number
KJ396935.
</p>
</div>
</section>
<section>
<a name="sec6">
</a>
<h3>
Competing interests
</h3>
<div class="collapsible-content">
<p style="line-height:160%">
The authors declare that they have no competing interests.
</p>
</div>
</section>
<section>
<a name="sec7">
</a>
<h3>
Authors’ contributions
</h3>
<div class="collapsible-content">
<p style="line-height:160%">
RT and WIL conceived the study, analyzed data and wrote the manuscript. SS and MSL
performed all assays. KJ performed all bioinformatics analysis. All authors read and
approved the final manuscript.
</p>
</div>
</section>
<section>
<a name="ack">
</a>
<h3>
Acknowledgments
</h3>
<div class="collapsible-content">
<p style="line-height:160%">
This work was supported by grants from the National Institutes of Health AI057158
(Northeast Biodefense Center-Lipkin), USAID PREDICT and the Defense Threat Reduction
Agency.
</p>
</div>
</section>
<section>
<a name="refs">
</a>
<h3>
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<li id="B8">
<p>
<a name="B8">
</a>
Vasilakis N, Widen S, Mayer SV, Seymour R, Wood TG, Popov V, Guzman H, Travassos da Rosa , Ghedin E, Holmes EC, Walker PJ, Tesh RB:
<strong>
Niakha virus: a novel member of the family Rhabdoviridae isolated from phlebotomine
sandflies in Senegal.
</strong>
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<strong>
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</strong>
80-89.
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PubMed Abstract
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<p>
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</p>
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<li id="B12">
<p>
<a name="B12">
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<a href="/sfx_links?ui=1743-422X-11-26&bibl=B12" onclick="popup('/sfx_links?ui=1743-422X-11-26&bibl=B12','SFXMenu','460','420'); return false;">
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<p class="totext">
<script type="text/javascript">
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</script>
</p>
</li>
<li id="B13">
<p>
<a name="B13">
</a>
Savage HM, Godsey MS, Lambert A, Panella NA, Burkhalter KL, Harmon JR, Lash RR, Ashley DC, Nicholson WL:
<strong>
First detection of heartland virus (Bunyaviridae: Phlebovirus) from field collected
arthropods.
</strong>
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<p>
<em>
Am J Trop Med Hyg
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<strong>
89
</strong>
(3)
<strong>
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</strong>
445-452.
<a href="/pubmed/23878186" target="_blank">
PubMed Abstract
</a>
|
<a href="http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&cmd=prlinks&retmode=ref&id=23878186" target="_blank">
Publisher Full Text
</a>
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PubMed Central Full Text
</a>
<a href="/sfx_links?ui=1743-422X-11-26&bibl=B13" onclick="popup('/sfx_links?ui=1743-422X-11-26&bibl=B13','SFXMenu','460','420'); return false;">
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</a>
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<script type="text/javascript">
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</p>
</li>
<li id="B14">
<p>
<a name="B14">
</a>
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<strong>
Bartonella spp. transmission by ticks not established.
</strong>
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<em>
Emerg Infect Dis
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<strong>
16
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<strong>
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</strong>
379-384.
<a href="/pubmed/20202410" target="_blank">
PubMed Abstract
</a>
|
<a href="http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&cmd=prlinks&retmode=ref&id=20202410" target="_blank">
Publisher Full Text
</a>
|
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PubMed Central Full Text
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<a href="/sfx_links?ui=1743-422X-11-26&bibl=B14" onclick="popup('/sfx_links?ui=1743-422X-11-26&bibl=B14','SFXMenu','460','420'); return false;">
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<li id="B15">
<p>
<a name="B15">
</a>
Whitehouse CA:
<strong>
Crimean-Congo hemorrhagic fever.
</strong>
</p>
<p>
<em>
Antiviral Res
</em>
2004,
<strong>
64
</strong>
(3)
<strong>
:
</strong>
145-160.
<a href="/pubmed/15550268" target="_blank">
PubMed Abstract
</a>
|
<a href="http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&cmd=prlinks&retmode=ref&id=15550268" target="_blank">
Publisher Full Text
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I want figure caption text. And also perhaps separately, the URL link to the figure images:
------------ Rendered sample HTML below -----------------
-------------- Rendered HTML above, raw below ----------------
In [106]:
strong = soup.find_all('strong')
In [107]:
for link in strong:
print link
<strong>Virology Journal</strong>
<strong>Full text</strong>
<strong>Rafal Tokarz</strong>
<strong>Stephen Sameroff</strong>
<strong>Maria Sanchez Leon</strong>
<strong>Komal Jain</strong>
<strong>W Ian Lipkin</strong>
<strong>11</strong>
<strong>Figure 1.</strong>
<strong>Organization of the LITRV genome. A)</strong>
<strong>B)</strong>
<strong>Table 1.</strong>
<strong>Comparison of LITRV and MOUV ORFs</strong>
<strong>Figure 2.</strong>
<strong>Phylogeny of LITRV.</strong>
<strong> The rhabdoviruses: biodiversity, phylogenetics, and evolution. </strong>
<strong>9</strong>
<strong>:</strong>
<strong> Moussa virus: a new member of the Rhabdoviridae family isolated from Culex decens
mosquitoes in Cote d’Ivoire. </strong>
<strong>147</strong>
<strong>:</strong>
<strong> Sequence comparison of five polymerases (L proteins) of unsegmented negative-strand
RNA viruses: theoretical assignment of functional domains. </strong>
<strong>71</strong>
<strong>:</strong>
<strong> Kolente virus, a rhabdovirus species isolated from ticks and bats in the Republic
of Guinea. </strong>
<strong>94</strong>
<strong>:</strong>
<strong> Isolation and molecular characterization of Fikirini rhabdovirus, a novel virus from
a Kenyan bat. </strong>
<strong>94</strong>
<strong>:</strong>
<strong> Characterization of Farmington virus, a novel virus from birds that is distantly related
to members of the family Rhabdoviridae. </strong>
<strong>10</strong>
<strong>:</strong>
<strong> Niakha virus: a novel member of the family Rhabdoviridae isolated from phlebotomine
sandflies in Senegal. </strong>
<strong>444</strong>
<strong>:</strong>
<strong> Genetic characterization of K13965, a strain of Oak Vale virus from Western Australia. </strong>
<strong>160</strong>
<strong>:</strong>
<strong> Characterisation of the genomes of four putative vesiculoviruses: tench rhabdovirus,
grass carp rhabdovirus, perch rhabdovirus and eel rhabdovirus European X. </strong>
<strong>158</strong>
<strong>:</strong>
<strong> Tick-borne viruses. </strong>
<strong>129</strong>
<strong>:</strong>
<strong> Role of the lone star tick, Amblyomma americanum (L.), in human and animal diseases. </strong>
<strong>160</strong>
<strong>:</strong>
<strong> First detection of heartland virus (Bunyaviridae: Phlebovirus) from field collected
arthropods. </strong>
<strong>89</strong>
<strong>:</strong>
<strong> Bartonella spp. transmission by ticks not established. </strong>
<strong>16</strong>
<strong>:</strong>
<strong> Crimean-Congo hemorrhagic fever. </strong>
<strong>64</strong>
<strong>:</strong>
<strong>Desktop view</strong>
In [108]:
strong = soup.find_all('em')
In [109]:
for link in strong:
print link
<em>Amblyomma americanum</em>
<em>Virology Journal</em>
<em>Amblyomma americanum</em>
<em>Rhabdoviridae</em>
<em>Amblyomma americanum</em>
<em>Rhabdoviridae</em>
<em>Rhabdoviridae</em>
<em>Cytorhabdovirus, Ephemerovirus, Lyssavirus, Novirhabdovirus, Nucleorhabdovirus, Perhabdovirus,
Sigmavirus, Tibrovirus, Vesiculovirus</em>
<em>Amblyomma americanum</em>
<em>Rhabdoviridae</em>
<em>Rhabdoviridae</em>
<em>Rhabdoviridae</em>
<em>Rhabdoviridae</em>
<em>Cytorhabdovirus</em>
<em>Novirhabdovirus</em>
<em>Nucleorhabdovirus</em>
<em>Vesiculovirus</em>
<em>A. americanum</em>
<em>Rhabdoviridae</em>
<em>A. americanum,</em>
<em>Ixodes scapularis</em>
<em>Dermacentor variablis, A. americanum</em>
<em>Ehrlichia</em>
<em>Borrelia lonestari</em>
<em>Francisella tularensis</em>
<em>A. americanum</em>
<em>A. americanum</em>
<em>A. americanum</em>
<em>A. americanum</em>
<em>I. scapularis</em>
<em>D. variabilis</em>
<em>A. americanum</em>
<em>A. americanum</em>
<em>Rhabdoviridae</em>
<em>Rhabdoviridae</em>
<em>A. americanum</em>
<em>I. scapularis</em>
<em>D. variablis</em>
<em>A. americanum</em>
<em>Infect Genet Evol</em>
<em>Virus Taxonomy; Ninth Report of the International Committee on Taxonomy of Viruses. </em>
<em>Virus Res</em>
<em>J Gen Virol</em>
<em>J Gen Virol</em>
<em>J Gen Virol</em>
<em>Virol J</em>
<em>Virology</em>
<em>Virus Res</em>
<em>Arch Virol</em>
<em>Parasitology</em>
<em>Vet Parasitol</em>
<em>Am J Trop Med Hyg</em>
<em>Emerg Infect Dis</em>
<em>Antiviral Res</em>
<em>Virology Journal</em>
Thanks StackOverflow for the syntax for the next one: http://stackoverflow.com/questions/19011613/using-beautifulsoup-to-select-div-blocks-withing-html
In [110]:
soup.find_all('div', class_="figs")
Out[110]:
[<div class="figs">
<div class="fig"><p><a href="http://www.virologyj.com/content/11/1/26/figure/F1" onclick="popup('http://www.virologyj.com/content/11/1/26/figure/F1','F1',800,470); return false;"><img align="top" alt="thumbnail" class="thumbnail" src="/content/figures/1743-422X-11-26-1.gif"/><strong>Figure 1.</strong></a> <strong>Organization of the LITRV genome. A)</strong> Schematic representation of LITRV ORFs. <strong>B)</strong> LITRV coding regions and corresponding transcription regulatory sequences.
</p></div>
<div class="table"><p><a href="http://www.virologyj.com/content/11/1/26/table/T1" onclick="popup('http://www.virologyj.com/content/11/1/26/table/T1','T1',800,470); return false;"><strong>Table 1.</strong></a> <strong>Comparison of LITRV and MOUV ORFs</strong></p></div>
<div class="fig"><p><a href="http://www.virologyj.com/content/11/1/26/figure/F2" onclick="popup('http://www.virologyj.com/content/11/1/26/figure/F2','F2',800,470); return false;"><img align="top" alt="thumbnail" class="thumbnail" src="/content/figures/1743-422X-11-26-2.gif"/><strong>Figure 2.</strong></a> <strong>Phylogeny of LITRV.</strong> Maximum likelihood phylogenetic tree based on full length L protein sequences of
currently recognized species of <em>Rhabdoviridae</em>. Gray boxes represent ICTV-accepted species within the genus. LITRV is indicated
by *. Accession numbers are provided next to the viral names. Due to excessive divergence,
only the type species for <em>Cytorhabdovirus</em>, <em>Novirhabdovirus</em> and <em>Nucleorhabdovirus</em> are included. The <em>Vesiculovirus</em> piry virus is not included due to limited available sequence.
</p></div></div>]
In [111]:
divfig = soup.find_all('div', class_="fig")
print(divfig)
[<div class="fig"><p><a href="http://www.virologyj.com/content/11/1/26/figure/F1" onclick="popup('http://www.virologyj.com/content/11/1/26/figure/F1','F1',800,470); return false;"><img align="top" alt="thumbnail" class="thumbnail" src="/content/figures/1743-422X-11-26-1.gif"/><strong>Figure 1.</strong></a> <strong>Organization of the LITRV genome. A)</strong> Schematic representation of LITRV ORFs. <strong>B)</strong> LITRV coding regions and corresponding transcription regulatory sequences.
</p></div>, <div class="fig"><p><a href="http://www.virologyj.com/content/11/1/26/figure/F2" onclick="popup('http://www.virologyj.com/content/11/1/26/figure/F2','F2',800,470); return false;"><img align="top" alt="thumbnail" class="thumbnail" src="/content/figures/1743-422X-11-26-2.gif"/><strong>Figure 2.</strong></a> <strong>Phylogeny of LITRV.</strong> Maximum likelihood phylogenetic tree based on full length L protein sequences of
currently recognized species of <em>Rhabdoviridae</em>. Gray boxes represent ICTV-accepted species within the genus. LITRV is indicated
by *. Accession numbers are provided next to the viral names. Due to excessive divergence,
only the type species for <em>Cytorhabdovirus</em>, <em>Novirhabdovirus</em> and <em>Nucleorhabdovirus</em> are included. The <em>Vesiculovirus</em> piry virus is not included due to limited available sequence.
</p></div>]
Useful for later: print(soup.get_text())
In [112]:
dirname = os.path.splitext("virologyj-11-1-26.html")[0]
In [113]:
dirname = ("virologyj-11-1-26.html")
chomped = dirname[:-5]
print dirname
print chomped
virologyj-11-1-26.html
virologyj-11-1-26
In [114]:
file = open("./"+chomped+"/virology-fig-image-links.txt", "wb")
In [115]:
for tr in divfig:
for link in tr.find_all('a', href=True):
fullink = link.get ('href').encode("utf8")
#print fullink #print in terminal to verify results
dirname = os.path.splitext("sys.argv[1]")[0]
file.write(fullink+'\n')
In [116]:
file.flush()
file.close()
So, we can get the URLs (above) from divfig and the plaintext captions (below)
In [117]:
dirname = ("virologyj-11-1-26.html")
chomped = dirname[:-5]
print dirname
print chomped
virologyj-11-1-26.html
virologyj-11-1-26
In [118]:
file = open("./"+chomped+"/virologycaptions.txt", "wb")
In [119]:
for tr in divfig:
for link in tr.find_all('p'):
plaintext = link.get_text ()
oneline = plaintext.replace('\n',' ').replace(' ',' ').encode("utf8")
print oneline
file.write(oneline+'\n')
Figure 1. Organization of the LITRV genome. A) Schematic representation of LITRV ORFs. B) LITRV coding regions and corresponding transcription regulatory sequences.
Figure 2. Phylogeny of LITRV. Maximum likelihood phylogenetic tree based on full length L protein sequences of currently recognized species of Rhabdoviridae. Gray boxes represent ICTV-accepted species within the genus. LITRV is indicated by *. Accession numbers are provided next to the viral names. Due to excessive divergence, only the type species for Cytorhabdovirus, Novirhabdovirus and Nucleorhabdovirus are included. The Vesiculovirus piry virus is not included due to limited available sequence.
In [120]:
file.flush()
file.close()
In [121]:
dirname = ("virologyj-11-1-26.html")
chomped = dirname[:-5]
print dirname
print chomped
virologyj-11-1-26.html
virologyj-11-1-26
In [129]:
file = open("./"+chomped+"/"+chomped+"-gif.txt", "wb")
In [130]:
for link in soup.find('h5'):
print(link.get('href'))
baseurl = link.get('href')
print baseurl
http://www.virologyj.com
http://www.virologyj.com
In [131]:
for tr in divfig:
for link in tr.find_all('img', src=True):
fullink = link.get ('src').encode("utf8")
print fullink #print in terminal to verify results
dirname = os.path.splitext("sys.argv[1]")[0]
file.write(baseurl+fullink+'\n')
/content/figures/1743-422X-11-26-1.gif
/content/figures/1743-422X-11-26-2.gif
In [132]:
file.flush()
file.close()
In [125]:
for link in soup.find('h5'):
print(link.get('href'))
http://www.virologyj.com
In [135]:
jazzy = "/content/figures/1743-422X-11-26-1.gif"
print jazzy
/content/figures/1743-422X-11-26-1.gif
In [ ]:
Content source: rossmounce/Trying-beautiful-soup
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