Body: <p>I have just started using BlastKOALA KEGG which has been useful in annotating (aminoacid) sequences. This is their website: <a href="https://www.kegg.jp/blastkoala/" rel="nofollow noreferrer">https://www.kegg.jp/blastkoala/</a></p>
  
  <p>When you get results, there are links for downloading. However these links will not download all detailed query search results, but just general notes already on the screen. To get these results I need to manually click on each query result on the page, which becomes impracticable with >500 entries. Thus I think need is a tool to download all linked contents from a webpage. I have been trying 'wget' however it doesn't work. It says 'Requested Job Not Found' whatever I do.</p>
  
  <p>Please, did anyone every try to achieve this? Thanks in advance.</p>
  
  <p>P.S. I have provided a working link as an example, below:</p>
  
  <p><a href="https://www.kegg.jp/kegg-bin/blastkoala_result_list?id=7345faab3969a3ef10a4a7542ba749386068138f&amp;passwd=NKfm46&amp;type=blastkoala&amp;code=user" rel="nofollow noreferrer">https://www.kegg.jp/kegg-bin/blastkoala_result_list?id=7345faab3969a3ef10a4a7542ba749386068138f&amp;passwd=NKfm46&amp;type=blastkoala&amp;code=user</a></p>
  
  <p>I think it should remain active for a week. </p>
  
  <p>I have inserted a picture showing examples of query result links below:</p>
  
  <p><a href="https://i.sstatic.net/WrVtw.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/WrVtw.png" alt="Picture showing a fraction of results table, where each sequence number is a link to detailed search results; clicking on &quot;Download Detail&quot; merely returns the table as showing on screen already."></a></p>
  
  <p>At this moment I would like to end up with the listed hit results for each of the queries, whose links are showing in blue; one result per file. In short, it is using wget for downloading all links in the page into a dedicated folder.</p>
  
  <p>Thanks in advance!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-22T10:50:28.913Z
Comments.Text: Could you provide some links of the entries you want to download and the command with wget you tried? This would be useful to create a program or change the command line.
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-22T11:11:28.597Z
Comments.Text: @Llopis Sure, I'm adding that now to the question. I think they keep temporary links for results. Thanks!
Comments.UserDisplayName: Scientist
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-25T07:25:51.550Z
Comments.Text: I can't see any link to the entries you want to retry on the link you posted.  But you can download the annotations. Perhaps is that what you want?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-25T13:06:24.483Z
Comments.Text: Yes, please [edit] your question and show us an example of the data you want to download. I don't understand what you need from your question.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-25T15:07:23.687Z
Comments.Text: @terdon thanks, I have done just that. I may have found a workaround, but if anyone provides a better solution it would be great.
Comments.UserDisplayName: Scientist
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-25T15:09:57.250Z
Comments.Text: So you want to download the target of each of the links in the "Query" column? Do you also need the "Second best" ones? And how do you want them organized? One file per "query"? Everything in one file? Do you just want the "gene (Length)" column from the target? Please [edit] and give us an example of what you want to end up with.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-25T16:05:12.600Z
Comments.Text: Perhaps it might be easier for you to explain why your current "workaround" is not good enough for you.
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-25T16:28:57.440Z
Comments.Text: @Llopis Following scattered suggestions I've gathered from related download threads I am using the command line wget -r -l3 -H -t1 -nd -N -np -erobots=off "link_path" which is returning all hits, but in a very disorganised way and raw format. I am no programmer myself.
Comments.UserDisplayName: Scientist
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-25T16:37:31.437Z
Comments.Text: How would it be better organized? Not being a programmer doesn't prevent you to program (or to learn to do it :) and even less to explain yourself. Please continue clarifying the question by answering terdon answers
Comments.UserDisplayName: llrs
Tags: <blast><sequence-annotation><kegg><functional-annotation>
Title: Downloading full search results from BlastKOALA?
ThreadText: # Downloading full search results from BlastKOALA?
  
  (Asked by: username_0 on 2018-09-21)
  
  I have just started using BlastKOALA KEGG which has been useful in annotating (aminoacid) sequences. This is their website: <https://www.kegg.jp/blastkoala/>
  
  When you get results, there are links for downloading. However these links will not download all detailed query search results, but just general notes already on the screen. To get these results I need to manually click on each query result on the page, which becomes impracticable with >500 entries. Thus I think need is a tool to download all linked contents from a webpage. I have been trying 'wget' however it doesn't work. It says 'Requested Job Not Found' whatever I do.
  
  Please, did anyone every try to achieve this? Thanks in advance.
  
  P.S. I have provided a working link as an example, below:
  
  <https://www.kegg.jp/kegg-bin/blastkoala_result_list?id=7345faab3969a3ef10a4a7542ba749386068138f&passwd=NKfm46&type=blastkoala&code=user>
  
  I think it should remain active for a week.
  
  I have inserted a picture showing examples of query result links below:
  
  [![Picture showing a fraction of results table, where each sequence number is a link to detailed search results; clicking on "Download Detail" merely returns the table as showing on screen already.](https://i.sstatic.net/WrVtw.png)](https://i.sstatic.net/WrVtw.png)
  
  At this moment I would like to end up with the listed hit results for each of the queries, whose links are showing in blue; one result per file. In short, it is using wget for downloading all links in the page into a dedicated folder.
  
  Thanks in advance!
  
  **Tags:** blast, sequence-annotation, kegg, functional-annotation
  
  > **Comments:**
  > **username_1**: Could you provide some links of the entries you want to download and the command with wget you tried? This would be useful to create a program or change the command line.  
  > **username_0**: @Llopis Sure, I'm adding that now to the question. I think they keep temporary links for results. Thanks!  
  > **username_1**: I can't see any link to the entries you want to retry on the link you posted.  But you can download the annotations. Perhaps is that what you want?  
  > **username_2**: Yes, please [edit] your question and show us an example of the data you want to download. I don't understand what you need from your question.  
  > **username_0**: @username_2 thanks, I have done just that. I may have found a workaround, but if anyone provides a better solution it would be great.  
  > **username_2**: So you want to download the target of each of the links in the "Query" column? Do you also need the "Second best" ones? And how do you want them organized? One file per "query"? Everything in one file? Do you just want the "gene (Length)" column from the target? Please [edit] and give us an example of what you want to end up with.  
  > **username_1**: Perhaps it might be easier for you to explain why your current "workaround" is not good enough for you.  
  > **username_0**: @Llopis Following scattered suggestions I've gathered from related download threads I am using the command line wget -r -l3 -H -t1 -nd -N -np -erobots=off "link_path" which is returning all hits, but in a very disorganised way and raw format. I am no programmer myself.  
  > **username_1**: How would it be better organized? Not being a programmer doesn't prevent you to program (or to learn to do it :) and even less to explain yourself. Please continue clarifying the question by answering username_2 answers  
  
  ---
  
  ## 0 answers
  
  