Using wget to recursively fetch .txt files in .php file, but filters break the command
I am looking to download all quality_variant_[accession_name].txt files from the Salk Arabidopsis 1001 Genomes site using wget in Bash shell.
- Main page with list of accessions: http://signal.salk.edu/atg1001/download.php
- Each accession links to a page (e.g., http://signal.salk.edu/atg1001/data/Salk/accession.php?id=Aa_0 where Aa_0 is the accession ID) containing three more links: unsequenced_[accession], quality_variant_[accession], and quality_variant_filtered_[accession]
- I am only interested in the quality_variant_[accession] link (not quality_variant_filtered_[accession] link), which takes you to to a
.txtfile with sequence data (e.g., http://signal.salk.edu/atg1001/data/Salk/quality_variant_Aa_0.txt)
Running the command below, the files of interest are eventually outputted (but not downloaded because of the --spider argument), demonstrating that wget can move through the page's hyperlinks to the files I want.
wget --spider --recursive "http://signal.salk.edu/atg1001/download.php
I have not let the command run long enough to determine whether the files of interest are downloaded, but the command below does begin to download the site recursively.
# Arguments in brackets do not impact the performance of the command
wget -r [-e robots=off] [-m] [-np] [-nd] "http://signal.salk.edu/atg1001/download.php"
However, whenever I try to apply filters to pull out the .txt files of interest, whether with --accept-regex, --accept, or many other variants, I cannot get past the initial .php file.
# This and variants thereof do not work
wget -r -A "quality_variant_*.txt" "http://signal.salk.edu/atg1001/download.php"
# Returns:
# Saving to: ‘signal.salk.edu/atg1001/download.php.tmp’
# Removing signal.salk.edu/atg1001/download.php.tmp since it should be rejected.
I could make a list of the accession names and loop through those names modifying the URL in the wget command, but I was hoping for a dynamic one-liner that could extract all files of interest even if accession IDs are added over time.
Thank you!
Note: the data files of interest are contained in the directory http://signal.salk.edu/atg1001/data/Salk/, which is also home to a .php or static HTML page that is displayed when that URL is visited. This URL cannot be used in the wget command because, although the data files of interest are contained here server side, the HTML page contains no reference to these files but rather links to a different set of .txt files that I don't want.
wget
edited Nov 14 '18 at 23:56
miken32
24k84972
asked Nov 14 '18 at 22:32
adirksadirks
114
add a comment |
I am looking to download all quality_variant_[accession_name].txt files from the Salk Arabidopsis 1001 Genomes site using wget in Bash shell.
- Main page with list of accessions: http://signal.salk.edu/atg1001/download.php
- Each accession links to a page (e.g., http://signal.salk.edu/atg1001/data/Salk/accession.php?id=Aa_0 where Aa_0 is the accession ID) containing three more links: unsequenced_[accession], quality_variant_[accession], and quality_variant_filtered_[accession]
- I am only interested in the quality_variant_[accession] link (not quality_variant_filtered_[accession] link), which takes you to to a
.txtfile with sequence data (e.g., http://signal.salk.edu/atg1001/data/Salk/quality_variant_Aa_0.txt)
Running the command below, the files of interest are eventually outputted (but not downloaded because of the --spider argument), demonstrating that wget can move through the page's hyperlinks to the files I want.
wget --spider --recursive "http://signal.salk.edu/atg1001/download.php
I have not let the command run long enough to determine whether the files of interest are downloaded, but the command below does begin to download the site recursively.
# Arguments in brackets do not impact the performance of the command
wget -r [-e robots=off] [-m] [-np] [-nd] "http://signal.salk.edu/atg1001/download.php"
However, whenever I try to apply filters to pull out the .txt files of interest, whether with --accept-regex, --accept, or many other variants, I cannot get past the initial .php file.
# This and variants thereof do not work
wget -r -A "quality_variant_*.txt" "http://signal.salk.edu/atg1001/download.php"
# Returns:
# Saving to: ‘signal.salk.edu/atg1001/download.php.tmp’
# Removing signal.salk.edu/atg1001/download.php.tmp since it should be rejected.
I could make a list of the accession names and loop through those names modifying the URL in the wget command, but I was hoping for a dynamic one-liner that could extract all files of interest even if accession IDs are added over time.
Thank you!
Note: the data files of interest are contained in the directory http://signal.salk.edu/atg1001/data/Salk/, which is also home to a .php or static HTML page that is displayed when that URL is visited. This URL cannot be used in the wget command because, although the data files of interest are contained here server side, the HTML page contains no reference to these files but rather links to a different set of .txt files that I don't want.
wget
edited Nov 14 '18 at 23:56
miken32
24k84972
asked Nov 14 '18 at 22:32
adirksadirks
114
Perhaps you'd be better off pulling a list of the URLs in question, and then passing those to wget?
– miken32
Nov 14 '18 at 23:38
parsing directly the links in the page with regexp is maybe an option : stackoverflow.com/questions/1881237/…
– SachaDee
Nov 14 '18 at 23:45
add a comment |
I am looking to download all quality_variant_[accession_name].txt files from the Salk Arabidopsis 1001 Genomes site using wget in Bash shell.
- Main page with list of accessions: http://signal.salk.edu/atg1001/download.php
- Each accession links to a page (e.g., http://signal.salk.edu/atg1001/data/Salk/accession.php?id=Aa_0 where Aa_0 is the accession ID) containing three more links: unsequenced_[accession], quality_variant_[accession], and quality_variant_filtered_[accession]
- I am only interested in the quality_variant_[accession] link (not quality_variant_filtered_[accession] link), which takes you to to a
.txtfile with sequence data (e.g., http://signal.salk.edu/atg1001/data/Salk/quality_variant_Aa_0.txt)
Running the command below, the files of interest are eventually outputted (but not downloaded because of the --spider argument), demonstrating that wget can move through the page's hyperlinks to the files I want.
wget --spider --recursive "http://signal.salk.edu/atg1001/download.php
I have not let the command run long enough to determine whether the files of interest are downloaded, but the command below does begin to download the site recursively.
# Arguments in brackets do not impact the performance of the command
wget -r [-e robots=off] [-m] [-np] [-nd] "http://signal.salk.edu/atg1001/download.php"
However, whenever I try to apply filters to pull out the .txt files of interest, whether with --accept-regex, --accept, or many other variants, I cannot get past the initial .php file.
# This and variants thereof do not work
wget -r -A "quality_variant_*.txt" "http://signal.salk.edu/atg1001/download.php"
# Returns:
# Saving to: ‘signal.salk.edu/atg1001/download.php.tmp’
# Removing signal.salk.edu/atg1001/download.php.tmp since it should be rejected.
I could make a list of the accession names and loop through those names modifying the URL in the wget command, but I was hoping for a dynamic one-liner that could extract all files of interest even if accession IDs are added over time.
Thank you!
Note: the data files of interest are contained in the directory http://signal.salk.edu/atg1001/data/Salk/, which is also home to a .php or static HTML page that is displayed when that URL is visited. This URL cannot be used in the wget command because, although the data files of interest are contained here server side, the HTML page contains no reference to these files but rather links to a different set of .txt files that I don't want.
wget
edited Nov 14 '18 at 23:56
miken32
24k84972
asked Nov 14 '18 at 22:32
adirksadirks
114
I am looking to download all quality_variant_[accession_name].txt files from the Salk Arabidopsis 1001 Genomes site using wget in Bash shell.
- Main page with list of accessions: http://signal.salk.edu/atg1001/download.php
- Each accession links to a page (e.g., http://signal.salk.edu/atg1001/data/Salk/accession.php?id=Aa_0 where Aa_0 is the accession ID) containing three more links: unsequenced_[accession], quality_variant_[accession], and quality_variant_filtered_[accession]
- I am only interested in the quality_variant_[accession] link (not quality_variant_filtered_[accession] link), which takes you to to a
.txtfile with sequence data (e.g., http://signal.salk.edu/atg1001/data/Salk/quality_variant_Aa_0.txt)
Running the command below, the files of interest are eventually outputted (but not downloaded because of the --spider argument), demonstrating that wget can move through the page's hyperlinks to the files I want.
wget --spider --recursive "http://signal.salk.edu/atg1001/download.php
I have not let the command run long enough to determine whether the files of interest are downloaded, but the command below does begin to download the site recursively.
# Arguments in brackets do not impact the performance of the command
wget -r [-e robots=off] [-m] [-np] [-nd] "http://signal.salk.edu/atg1001/download.php"
However, whenever I try to apply filters to pull out the .txt files of interest, whether with --accept-regex, --accept, or many other variants, I cannot get past the initial .php file.
# This and variants thereof do not work
wget -r -A "quality_variant_*.txt" "http://signal.salk.edu/atg1001/download.php"
# Returns:
# Saving to: ‘signal.salk.edu/atg1001/download.php.tmp’
# Removing signal.salk.edu/atg1001/download.php.tmp since it should be rejected.
I could make a list of the accession names and loop through those names modifying the URL in the wget command, but I was hoping for a dynamic one-liner that could extract all files of interest even if accession IDs are added over time.
Thank you!
Note: the data files of interest are contained in the directory http://signal.salk.edu/atg1001/data/Salk/, which is also home to a .php or static HTML page that is displayed when that URL is visited. This URL cannot be used in the wget command because, although the data files of interest are contained here server side, the HTML page contains no reference to these files but rather links to a different set of .txt files that I don't want.
wget
wget
edited Nov 14 '18 at 23:56
miken32
24k84972
asked Nov 14 '18 at 22:32
adirksadirks
114
edited Nov 14 '18 at 23:56
miken32
24k84972
asked Nov 14 '18 at 22:32
adirksadirks
114
edited Nov 14 '18 at 23:56
miken32
24k84972
edited Nov 14 '18 at 23:56
miken32
24k84972
edited Nov 14 '18 at 23:56
miken32
24k84972
24k84972
asked Nov 14 '18 at 22:32
adirksadirks
114
asked Nov 14 '18 at 22:32
adirksadirks
114
asked Nov 14 '18 at 22:32
adirksadirks
114
114
Perhaps you'd be better off pulling a list of the URLs in question, and then passing those to wget?
– miken32
Nov 14 '18 at 23:38
parsing directly the links in the page with regexp is maybe an option : stackoverflow.com/questions/1881237/…
– SachaDee
Nov 14 '18 at 23:45
add a comment |
Perhaps you'd be better off pulling a list of the URLs in question, and then passing those to wget?
– miken32
Nov 14 '18 at 23:38
parsing directly the links in the page with regexp is maybe an option : stackoverflow.com/questions/1881237/…
– SachaDee
Nov 14 '18 at 23:45
Perhaps you'd be better off pulling a list of the URLs in question, and then passing those to wget?
– miken32
Nov 14 '18 at 23:38
Perhaps you'd be better off pulling a list of the URLs in question, and then passing those to wget?
– miken32
Nov 14 '18 at 23:38
parsing directly the links in the page with regexp is maybe an option : stackoverflow.com/questions/1881237/…
– SachaDee
Nov 14 '18 at 23:45
parsing directly the links in the page with regexp is maybe an option : stackoverflow.com/questions/1881237/…
– SachaDee
Nov 14 '18 at 23:45
add a comment |
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Perhaps you'd be better off pulling a list of the URLs in question, and then passing those to wget?
– miken32
Nov 14 '18 at 23:38
parsing directly the links in the page with regexp is maybe an option : stackoverflow.com/questions/1881237/…
– SachaDee
Nov 14 '18 at 23:45