User: Promi

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Promi10
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3 years, 6 months ago
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3 years, 11 months ago
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p****@chalmers.se

Posts by Promi

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Retrieve Full Lineage From Taxon Id
... Hi Sophie, Can you tell me what's 'a' in v1 <- a[i,1] here? ...
written 3.7 years ago by Promi10
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Comment: C: Retrieve Full Lineage From Taxon Id
... Hi Pierre, What would be the script for a file (test_taxids.txt) having a list of taxids through this xml sheet to obtain the full taxonomic information? ...
written 3.7 years ago by Promi10
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How to create dictionary by reading lines from a file and find exact values inside another file through looping a defined path?
... Hello, I have a file containing gi's 103485576 **298489615** 103485741 10348579 And there is a directory home/documents/all.ptt/_Nostoc_azollae__0708_uid**49725**/**NC_014249**.ptt home/documents/all.ptt/_Ruminococcus__obeum_uid197165/NC_021022.ptt ...
python bash dictionary ptt linux written 3.7 years ago by Promi10 • updated 3.7 years ago by Pierre Lindenbaum134k
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Comment: C: Filtering rows based on specific conditions
... The desired output should be like: gi|336321007|ref|YP_004600975.1 adh_short_C2 gi|336321007|ref|YP_004600975.1 adh_short gi|336321007|ref|YP_004600975.1 KR ...
written 3.7 years ago by Promi10
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Comment: C: Accession number to taxonomy id after blasting
... Thanks for the reply Sej Modha. I tried to install: cd ~ perl -MNet::FTP -e \ '$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1); $ftp->login; $ftp->binary; $ftp->get("/entrez/entrezdirect/edirect.zip");' unzip -u -q edirect.zip rm edirect.zip export PATH=$ ...
written 3.7 years ago by Promi10
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Filtering rows based on specific conditions
... Hi, I have a tab-limited text file which has the IDs in column number 1 and the corresponding HMM name in column number 7 as shown below. gi|336321007|ref|YP_004600975.1| adh_short_C2 gi|336321007|ref|YP_004600975.1| adh_short gi|336321007|ref|YP_004600975.1| KR gi|5 ...
data filtering pfam written 3.7 years ago by Promi10 • updated 3.7 years ago by GenoMax96k
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Comment: C: Splitting NCBI Accession ID
... Worked perfectly! Thanks! Sorry I didn't get you about the assignment question. ...
written 3.7 years ago by Promi10
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Comment: C: Splitting NCBI Accession ID
... Worked perfectly. Thanks! ...
written 3.7 years ago by Promi10
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Splitting NCBI Accession ID
... Hi, I have a file 'ids.txt' containing IDs like this: gi|78062356|ref|YP_372264.1| gi|206563435|ref|YP_002234198.1| gi|402568881|ref|YP_006618225.1| gi|54024439|ref|YP_118681.1| gi|146275970|ref|YP_001166130.1| How can I have them into two columns one havi ...
ncbi R accessionid blast python written 3.7 years ago by Promi10 • updated 3.7 years ago by Sej Modha4.8k
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Comment: C: Accession number to taxonomy id after blasting
... Hi! Can you share the code that you used for converting the accession ids to taxids from the blast output file? ...
written 3.7 years ago by Promi10

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