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edgardomortiz / vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
GNU General Public License v3.0
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output path issue #40

Open CHAOS324 opened 1 year ago

CHAOS324 commented 1 year ago

How to set a certain output path for the PHY? My VCF is too large and my C drive is too small to hold the output PHY. Thanks.

edgardomortiz commented 1 year ago

Hi, what was the error exactly? If you write the path to the output folder with the option --output-folder the output files will be saved there. This is described in the README page.

Edgardo

edgardomortiz commented 1 year ago

Also keep in mind that the code was tested on Linux and Mac, from your description of a C drive I guess you are using Windows, it should work too but you have to be careful as to how you type the route to the output folder

CHAOS324 commented 1 year ago

Thank you so much for replying. There's no error，actually the script runs well on Windows even if the VCF is as large as 1.7Tb.  I am a noob in bioinformatics and I don't even know how to use Linux!  I just want to process a whole genome sequence VCF data to draw a tree.   My Python is installed in the C drive, my VCF and the vcf2phylip are in the D drive. I used the Windows cmd and used the -i function of vcf2phylip, and it worked, but it seems that freespace of my C drive is reducing as the script keeps running.  So I guess the processed data is automatically output to the C drive. Because the remaining freespace of my C drive seems not enough to finish the convert, I wonder how to change the output path to my D drive, which should have enough freespace. Sorry for my amateurish question and my poor expression. Thank you so so much for your answer.  Chaos

---Original--- From: "Edgardo M. @.> Date: Thu, Dec 29, 2022 22:24 PM To: @.>; Cc: @.**@.>; Subject: Re: [edgardomortiz/vcf2phylip] output path issue (Issue #40)

Also keep in mind that the code was tested on Linux and Mac, from your description of a C drive I guess you are using Windows, it should work too but you have to be careful as to how you type the route to the output folder

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

edgardomortiz commented 1 year ago

I understand, in your command add the path to the destination you want with the option --output-folder

Python commands can take multiple options (-i ,--output-folder, etc). Your command will have to be something like the following, where you have to replace path_to_my_D by the actual path in your computer (that can be something like D://myfiles/ but I'm not sure exactly because I haven't used Windows in a while...)

vcf2phylip.py -i myfile.vcf --output-folder path_to_my_D

Edgardo

CHAOS324 commented 1 year ago

I got it. Again thanks for your help, it's a great encouragement for me to keep learning bioinformatics. : ) Chaos

---Original--- From: "Edgardo M. @.> Date: Sat, Dec 31, 2022 00:17 AM To: @.>; Cc: @.**@.>; Subject: Re: [edgardomortiz/vcf2phylip] output path issue (Issue #40)

I understand, in your command add the path to the destination you want with the option --output-folder

Python commands can take multiple options (-i ,--output-folder, etc). Your command will have to be something like the following, where you have to replace path_to_my_D by the actual path in your computer (that can be something like D://myfiles/ but I'm not sure exactly because I haven't used Windows in a while...) vcf2phylip.py -i myfile.vcf --output-folder path_to_my_D
Edgardo

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

edgardomortiz commented 1 year ago

Glad to have helped!