How to link two python scripts

[Larz60+]

Strange, the ftp I sent to you didn't work for you but did for me,
this one doesn't work for me, but did for you.
I can't find that sequence on the url you sent to me, probably because I don't know where or what to look for (on left side)

what is common name, scientific name, or tax id?

[berthenet]

It seems we are cursed. ^^

I used a genome from a whole genome shotgun project from a strain of Campylobacter jejuni containing 215 contigs, with some of them less than 1000 basepair.
The accession number for the project is AINZ01000000.
The strain id is 51494.

Will this info help you?

[Larz60+]

I can get to the page: https://www.ncbi.nlm.nih.gov/Traces/wgs/...igs&page=1,
just don't know what to download. My knowledge of the subject is quite limited.
Have used before, but with very specific instructions.

I have a large fasta file I downloade earlier for ecoli should work for sorting test, is that correct?
As before, I need sleep, so will be gone for 4 or 5 hours.

[berthenet]

Ok I'll try a step-by-step to guide you through.

So from the link I got in your last post: https://www.ncbi.nlm.nih.gov/Traces/wgs/...igs&page=1

Here is a printscreen for you to follow (I added small numbers in red):

So you start by selecting the "strain" option (number 1 on my prinscreen)
Then you type the strain id "51494" (number 2 on my printscreen) and press Enter
Then you check the box corresponding to the strain id you typed in (number 3 on my printscreen)
Only two lines should remain in the center of the page, you click on the "AINZ01" (number 4 on my printcreen)

This will take you to a page with 5 tabs.
You click on the "download" tab, then select the fasta file containing the contigs, which is the second one on the left side (under "Contigs:" ), named "AINZ01.1.fsa_nt.gz"

[buran]

ftp://ftp.ncbi.nlm.nih.gov/sra/wgs_aux/A....fsa_nt.gz
isn't it the file from the ftp link you posted few post back?

[Larz60+]

berthenet -> Got it, thanks.
I'll be on again later today.

Buran-> the ftp link didn't work for me.
But I have the data now.

[buran]

the ftp link didn't work for me.

because OP just copy/paste the url and it auto convert it to http. I just fixed that by adding url tag thus keeping ftp - see my post above

[berthenet]

Thank you buran!

So to avoid this in the future I should always use the BBCode URL tags instead of copy and paste directly into my message, is that it?

[buran]

So to avoid this in the future I should always use the BBCode URL tags instead of copy and paste directly into my message, is that it?

yes, paste the link, select it, then click on chain icon to add url tag and again paste the url in the pop-up window for url address
I also was not aware that forum auto convert ftp links to http. obviously if it does not detect http schema in the link, it add it. it will look like this:

[url=ftp://ftp.ncbi.nlm.nih.gov/sra/wgs_aux/AI/NZ/AINZ01/AINZ01.1.fsa_nt.gz]ftp://ftp.ncbi.nlm.nih.gov/sra/wgs_aux/AI/NZ/AINZ01/AINZ01.1.fsa_nt.gz[/url]

[Larz60+]

Will get back 10:00 - 11:00 GMT with sort.