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User: biohacker_tobe

gravatar for biohacker_tobe
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Posts by biohacker_tobe

<prev • 61 results • page 1 of 7 • next >
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Comment: C: How to retrieve sets of protein sequences?
... It was not executing since I am using a fish shell, I needed to add the bash command in front in order for it to run: bash -c 'for acc in `cat protein_ids.txt` ; do curl -s "https://www.uniprot.org/uniprot/$acc.fasta"; done > uniprot_seqs.fasta' ...
written 4 days ago by biohacker_tobe • 40
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Comment: C: How to retrieve sets of protein sequences?
... running this from my command line: for acc in `cat uniprot_ids.txt` ; do curl -s "https://www.uniprot.org/uniprot/$acc.fasta" ; done > uniprot_seqs.fasta does not actually do anything :s I have the file saved exactly as listed. it just stays in one state. ...
written 5 days ago by biohacker_tobe • 40
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Comment: C: Retrieve Protein Sequences from Uniprot
... I saw that this uses linux command directly, was curious if I could do it directly from a python command. ...
written 5 days ago by biohacker_tobe • 40
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Retrieve Protein Sequences from Uniprot
... I have a list of protein id's, these all traceback to Uniprot. However, I wanted to know if I can obtain sequence information from these proteins from uniprot protein ids.. Is there any package in biopython to do this? I found this snippet of code online and it does give the sequence information bu ...
python sequence biopython uniprot written 5 days ago by biohacker_tobe • 40 • updated 5 days ago by Shalu Jhanwar • 470
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Comment: C: get organism name from fasta file header (PYTHON)
... Thanks, this is exactly what I was looking for :D ...
written 9 days ago by biohacker_tobe • 40
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Comment: C: get organism name from fasta file header (PYTHON)
... Fair enough, thanks for the pointer :) ...
written 10 days ago by biohacker_tobe • 40
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Comment: C: get organism name from fasta file header (PYTHON)
... With linux I am aware on how to do it, but is it possible directly with python? ...
written 10 days ago by biohacker_tobe • 40
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get organism name from fasta file header (PYTHON)
... For example, is it possible to get the organism name as one gets the sequence and gene id for example: >sp|Q09305|AAR2_CAEEL Protein AAR2 homolog OS=Caenorhabditis elegans GN=F10B5.2 PE=3 SV=1 MGGALPPEIVDYMYRNGAFLLFLGFPQASEFGIDYKSWKTGEKFMGLKMIPPGVHFVYCS IKSAPRIGFFHNFKAGEILVKKWNTESETF ...
genome fasta sequence written 10 days ago by biohacker_tobe • 40 • updated 10 days ago by Joe ♦ 18k
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Comment: C: Downloading Proteomic Data (FTP FIles)
... For some reason I am not able to,. That's really strange... ...
written 10 days ago by biohacker_tobe • 40
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Downloading Proteomic Data (FTP Files)
... I'm trying to download protein information associated to specific melting temperatures, but am not successfull downloading the ftp files from the Proteomics Identification Database (PRIDE). I was wondering if anyone has tried doing this in the past. Below is the link to the data I am trying to acc ...
proteomics sequence written 10 days ago by biohacker_tobe • 40

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