User: mac03pat

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mac03pat10
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Posts by mac03pat

<prev • 14 results • page 1 of 2 • next >
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Error in MUSCLE
... Trying to run muscle on a file to build a tree. I successfully used muscle to align this file in .clw format yesterday. Now I tried running these two lines of code and received the same error each time. Anyone know what the error means and how to fix it? muscle -maketree -in seqs.afa -out seqs ...
phylogenetic fasta debian-stretch muscle written 22 days ago by mac03pat10 • updated 21 days ago by h.mon25k
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Trouble converting clustal to nexus
... Used this code: from Bio import AlignIO AlignIO.convert('aligned_KS1.clw', 'clustal', 'aligned_KS.nexus', 'nexus') On this file: https://drive.google.com/open?id=1UX7H1sDdRSVT0I3fXb-rGXbfRZx10hGZ And received this error: Traceback (most recent call last): File "C:\Users\ma ...
.clw clustalw nexus convert written 22 days ago by mac03pat10 • updated 22 days ago by SMK1.3k
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Comment: C: Bash not finding file
... Not sure why the error appeared but files were output! Good to go, thank you. ...
written 22 days ago by mac03pat10
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Comment: C: How to extract nucleotide sequence of select genes from a text file with Genbank
... This worked great, thank you again SMK. One more question if you don't mind. The previous results were generated by the online version of antiSMASH. I am now running a package version of antiSMASH from bash commandline and the output is different. I tried to change your code to process this slightl ...
written 22 days ago by mac03pat10
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Comment: C: Bash not finding file
... Seems to have worked, thank you!. I beleive now I'm running into problems with the package itself. The online version returns results for the same file that I'm trying to run on the downloaded package version of the program. However, the downloaded version is returning me this error: WARNING 25 ...
written 23 days ago by mac03pat10
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Comment: C: Bash not finding file
... (antismash) macpat@Debian9:~$ for infile in ~/inputs/*.gb; do echo $infile; done /home/macpat/inputs/DQ660910.gbor infile in ~/inputs/*.gb; do echo $infile; done /home/macpat/inputs/EU872212.gb /home/macpat/inputs/GU930713.gb /home/macpat/inputs/GU930714.gb /home/macpat/input ...
written 23 days ago by mac03pat10
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Bash not finding file
... I'm running Debian 9 as VM from serial console on Azure. Link to files I'm attempting to input: https://drive.google.com/open?id=1aIIjWO70clU8u4_gV2X_8c17HmEnqjr_ I was given some code from the help people at antiSMASH. It should iterate through genbank files in a folder and process them with the ...
debian9 bash linux written 23 days ago by mac03pat10
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Fasta with multiple sequences to alignment object which can by used to build a phylogenetic tree
... I attempting to take a single fasta file with multiple sequences of variable length as input and output aligned sequenes that I can use to build a phylogenetic tree with biopython phylo. Here's my file: https://drive.google.com/file/d/1QXXSJ2DJjJHz8K1WHuERFPQBTSvsWrcL/view?usp=sharing Things I've ...
fasta clustal alignment biopython phylo written 23 days ago by mac03pat10 • updated 23 days ago by jrj.healey12k
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Comment: C: How to extract nucleotide sequence of select genes from a text file with Genbank
... Thank you for your answer SMK! This code worked very well. There's one more piece of information I'd like included, the genus and species names included under "DEFINITION". For example, from this line I'd like just the words Cladonia grayi so that later on my final phylogenetic tree can include the ...
written 24 days ago by mac03pat10
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Comment: C: Trouble installing Bioconda
... Thanks for the tip! I successfully set up a Debian 9 VM and was able to get ddocent and antismash working. ...
written 25 days ago by mac03pat10

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