User: erwan.scaon

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erwan.scaon570
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Limoges - CBRS - France
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http://www.unilim.fr/r...
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Posts by erwan.scaon

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Comment: C: edirect esearch : exclude given accessions
... Yes, I get what you mean. I just wanted to achieve my goal (retrieve all full length genome sequences of genus Salmonella in NCBI DBs) and understand how to do it best. ...
written 22 days ago by erwan.scaon570
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Answer: A: edirect esearch : exclude given accessions
... So, here we are : I want to retrieve all full length genome sequences of genus *Salmonella*. Get *Salmonella* taxid : taxid=$(esearch -db taxonomy \ -query 'Salmonella' \ | efetch -format xml \ | xtract -pattern Taxon \ ...
written 22 days ago by erwan.scaon570
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Comment: C: edirect esearch : exclude given accessions
... Ok, this "efilter -source insd" is working well ! If I compare my "dirty" solution with yours : taxid=$(esearch -db taxonomy \ -query 'Salmonella' \ | efetch -format xml \ | xtract -pattern Taxon \ -elemen ...
written 22 days ago by erwan.scaon570
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Comment: C: edirect esearch : exclude given accessions
... Did you download "prokaroytes.txt" today ? Do you mind sharing a file with full "grep -w "Complete" prokaryotes.txt | grep -w "Salmonella"" output so that we can run "comm" ? *Ps* : I am already quite confident that the previous solution yielding 420 sequences is not good enough, given that it's ...
written 24 days ago by erwan.scaon570
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Comment: C: edirect esearch : exclude given accessions
... Ubuntu 16.04 grep (GNU grep) 2.25 grep -w "Complete" prokaryotes.txt | grep -w "Salmonella" | head -2 > Salmonella enterica subsp. enterica serovar Typhi str. > CT18 220341 PRJNA236 236 Proteobacteria Gammaproteobacteria 5.13371 51.8776 chromosome:NC_003198.1/AL513382.1; > plasmid pH ...
written 24 days ago by erwan.scaon570
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Comment: C: edirect esearch : exclude given accessions
... axel -q ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/prokaryotes.txt; grep -w "Complete" prokaryotes.txt | grep -w "Salmonella" | awk 'BEGIN{FS="\t"}{print $21}' | awk 'BEGIN{OFS=FS="/"}{print "wget "$0,$NF"_genomic.fna.gz"}' | wc -l; > 458 ! ...
written 24 days ago by erwan.scaon570
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Comment: C: edirect esearch : exclude given accessions
... This returned 9 FASTA files for me, for a total of 15 sequences. My prokaryotes.txt file as 36129 lines. Did I miss something ? Edit : First download of "prokaryotes.txt" did break somehow, thus the weird results. ...
written 24 days ago by erwan.scaon570
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Comment: C: edirect esearch : exclude given accessions
... Any idea why this one "[AM933172][1]" is not returned with your command (despite being a GenBank accession) ? [1]: https://www.ncbi.nlm.nih.gov/nuccore/AM933172.1/ ...
written 24 days ago by erwan.scaon570
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Comment: C: edirect esearch : exclude given accessions
... I'll stop chatting with myself after this comment, but here is my final "dirty" solution : After checking for additional "duplicates", I found that NC_XXXXX sequences are derived from an identical sequence entry in the DB (thus need to be removed). Also found that "complete chromosome" is an acc ...
written 24 days ago by erwan.scaon570
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Comment: C: Edirect esearch exclude given accessions
... Ok, based on NZ_XX[0-9]* sequences IDs I have when downloading the non-filtered database, I came to this "dirty" solution : esearch -db nucleotide \ -query "salmonella[organism] \ AND complete genome[Title] \ NOT contig[Title] \ ...
written 24 days ago by erwan.scaon570

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