User: jamesdong

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jamesdong0
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Posts by jamesdong

<prev • 16 results • page 1 of 2 • next >
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Comment: C: How to retain the row or line with longest protein isoform from csv table
... It is awesome ! I use `datamash --sort --header-out groupby 3 max 5 -f < aa.txt > ab.txt ` it will creat all columns data including deduplicated column 3 and their conresponding max value columns, the header will be retained but changed name to `field-1 field-2 field-3 field-4 field-5 max(fie ...
written 1 day ago by jamesdong0
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Comment: C: How to retain the row or line with longest protein isoform from csv table
... The header can be handled by other script offered by https://stackoverflow.com/questions/14562423/is-there-a-way-to-ignore-header-lines-in-a-unix-sort and https://stackoverflow.com/questions/21876640/last-line-to-first-line, the piped script is: cat aa.txt | awk 'NR<2{print $0;next}{print $0| ...
written 1 day ago by jamesdong0
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Comment: C: How to retain the row or line with longest protein isoform from csv table
... It works, it is great answer! Many thanks! ...
written 6 days ago by jamesdong0
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Comment: C: How to retain the row or line with longest protein isoform from csv table
... Many thanks. I am learning the amazing command datamash, and run it successfully, however, when I use > datamash --sort --header-out groupby 3 max 5 < aa.txt > ab.txt > it ignored other columns, only left the deduplicated column 3 and their conresponding max value columns, I want al ...
written 7 days ago by jamesdong0
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Comment: C: How to retain the row or line with longest protein isoform from csv table
... Thanks for kind reply. These days I learned the command sort, and I used >sort -k 5nr aa.txt > bb.txt > as your suggested to decrease by Protein_length successfully, however, when I use > sort -k 5 -u bb.txt > no changes happened, is there a problem? ...
written 7 days ago by jamesdong0
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How to retain the row or line with longest protein isoform from csv table
... I have 5 columns of data in csv format, the data title includes Organism, Accession_number, GeneID, Chromosome,and Protein_length, if different accession_numbers have same geneID, the line or row with longest protein length will be retained. Although there are many items and great answers about sele ...
linux command python csv protein isoform written 9 days ago by jamesdong0
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Comment: C: Retrieve GFF3 file from Ensembl
... Thank you for reminding me, I have edited. ...
written 11 months ago by jamesdong0
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Comment: A: Retrieve GFF3 file from Ensembl
... The solutions are great! ...
written 11 months ago by jamesdong0
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Retrieve GFF3 file from Ensembl
... I have a bunch of Ensembl mRNA IDs of homologous genes from different species: ENSGACT00000003747,ENSMLUT00000000343,ENSMICT00000005631,......, I want to retrieve conresponding gff3 files respectively from ensembl site. I have searched the Biostars and found the link https://www.biostars.org/p/29682 ...
gene assembly genome ensembl written 12 months ago by jamesdong0
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Comment: C: multiple DNA file Sliced to a fixed length substring by index/location
... Thanks for your good question about map parameter, if you use seqkit sliding -s 1 -W 5, it will also achieve that goal partially. ...
written 18 months ago by jamesdong0

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