User: auninsaw

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auninsaw10
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2 years, 7 months ago
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4 years, 11 months ago
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a*******@mymail.vcu.edu

Posts by auninsaw

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Getting taxid from accession number
... This seems to get the job done, but there are probably still errors present or ways to make it shorter: #!/bin/bash file="accessions_out.txt" while read -r ACC do touch taxid_out.txt VAR=$(curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucco ...
written 2.7 years ago by auninsaw10
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Comment: C: Getting taxid from accession number
... Thanks for taking the time to respond to me, and the information about the unset versus empty variable, plus the error in the spacing in my code. I think I have it figured out and will post the updated code below. I will also look into the assembly summary files as well as an alternative to my ap ...
written 2.7 years ago by auninsaw10
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Getting taxid from accession number
... Hi - I have a question that is related to this thread: https://www.biostars.org/p/10959/ I assumed if I had a new question, I needed to open a new thread. I apologize if I should have posted under the original question. I have a file with a list of accession numbers in it: KU587513 KU5 ...
taxid efetch taxonomy genbank eutils written 2.7 years ago by auninsaw10
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Answer: A: Help with perl script to subset a fasta file?
... Okay, here is a well organized answer I received from stack overflow, that solves my question using Perl and may help others with a similar problem. It is similar to my original in spirit but with correct formatting, comments, and pragma. Thanks for those who offered help. #!/usr/bin/perl ...
written 3.1 years ago by auninsaw10
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Comment: C: Help with perl script to subset a fasta file?
... Thanks for the suggestion, I'm going to keep working at this and will post up when I get it working. ...
written 3.1 years ago by auninsaw10
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Comment: C: Help with perl script to subset a fasta file?
... Thanks, Pierre. I am not that familiar with awk, but I will try and work through what you posted and figure out how it is working. ...
written 3.1 years ago by auninsaw10
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Comment: C: Help with perl script to subset a fasta file?
... I've started on it, but its admittedly a mess. I was having some trouble getting it posted up correctly but it looks ok now. I may try Stackexchange, thanks for the suggestion. ...
written 3.1 years ago by auninsaw10
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Help with perl script to subset a fasta file?
... Hi - I have a large fasta file of ~500 sequences, each of which has a known to me target position with a SNP of interest. For each entry in the fasta file, I have a separate tab delimited text file that has on each line the fasta sequence name, start position, stop position, and SNP position. The f ...
perl fasta script snp written 3.1 years ago by auninsaw10
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Comment: C: Printing output for missing gids using blastdbcmd
... Okay, upgrading to the latest version fixed that, and I get the same output as you do now. I can run the commands as you suggested and append the output to the end of the tabular blast file and have the same number rows in each column. However, my goal was to be able to take the newly generated co ...
written 4.9 years ago by auninsaw10 • updated 2.3 years ago by _r_am32k
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Comment: C: Printing output for missing gids using blastdbcmd
... Thanks for the response. I need to clarify what I wrote above in that I made a mistake in what I wrote about output I am getting. If I run: $ blastdbcmd -db /path_to/nr -entry_batch ids -outfmt '%g %t' -out test.txt I get the following error: Error: XP_006633669.1: OID not found If I run ...
written 4.9 years ago by auninsaw10 • updated 2.3 years ago by _r_am32k

Latest awards to auninsaw

Popular Question 3.0 years ago, created a question with more than 1,000 views. For Printing output for missing gids using blastdbcmd
Scholar 3.1 years ago, created an answer that has been accepted. For A: Help with perl script to subset a fasta file?

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