User: arsilan324

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arsilan32440
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Posts by arsilan324

<prev • 36 results • page 1 of 4 • next >
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Comment: C: how to extract/grep lines containing specific word?
... For some reason, the output file is still empty. Can you comment on it? Here is the link to the [file][1] [1]: https://www.dropbox.com/s/6bcwpfndmtkoes6/file.txt?dl=0 ...
written 5 weeks ago by arsilan32440
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how to extract/grep lines containing specific word?
... Hi all, I am trying to extract lines containing specific word from tabular file! I am using this command grep "[Sorghum bicolor]" file.txt Here [Sorghum bicolor] is the word (desired string) for the line which i want to retain. But this comamnd print everything as it is and doesn't filter. I ...
grep sed awk written 5 weeks ago by arsilan32440 • updated 5 weeks ago by Kevin Blighe16k
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Comment: C: How to retrieve single protein fasta file for multiple species?
... Here are examples, 1- Halodesulfurarchaeum formicicum 2- Methanosphaera cuniculi The whole list can be seen here... > https://gold.jgi.doe.gov/organisms?Organism.Domain=ARCHAEAL&Organism.Type%20Strain=Yes&Organism.Active=Yes ...
written 9 weeks ago by arsilan32440
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Comment: C: How to retrieve single protein fasta file for multiple species?
... I have prepared another list of archea this time but this command is not working. Is there any other assembly summary for archea? ...
written 9 weeks ago by arsilan32440
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Comment: C: Installing the new tool "table2asn_GFF"
... Here it is... ubt80:pre-req arslan$ file ./table2asn_GFF ./table2asn_GFF: cannot open `./table2asn_GFF' (No such file or directory) ubt80:pre-req arslan$ ls -lah ./table2asn_GFF ls: ./table2asn_GFF: No such file or directory when i entered the file name exactly, i got it... ...
written 9 weeks ago by arsilan32440
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Comment: C: Installing the new tool "table2asn_GFF"
... I am using macOS Sierra 10.12.6. Yes this is also not working... PS: Is there any installation step required after chmod +x ? ...
written 9 weeks ago by arsilan32440
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Installing the new tool "table2asn_GFF"
... Hi all, I am trying to install this tool "[table2asn_GFF][1]" but unable to do so. I have used chmod +x and still no help > -bash: table2asn: command not found There is no instructions given by NCBI as well about installation. Can you please guide how can I do it? Thank you very much in advan ...
ncbi installation table2asn written 9 weeks ago by arsilan32440
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Comment: C: NameError: name 'utils' is not defined
... Yes, I did install it using pip. What do you mean by? - What happens if you start the python interpreter and try to import biocode ...
written 9 weeks ago by arsilan32440
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Comment: C: NameError: name 'utils' is not defined
... Thank you for mentioning this tool. I am trying to install it using chmod +x but it is not helping me. I am using mac. I am unable to find instructions as well. Can you suggest how to install. Thanks ...
written 9 weeks ago by arsilan32440
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NameError: name 'utils' is not defined
... I am trying to run [convert_gff3_to_ncbi_tbl.py][1] script but getting this error. ubt80:EMBLmyGFF3 arslan$ python3 convert_gff3_to_ncbi_tbl.py -i juncus.fasta.transdecoder.refined.gff3 -o arslan.tbl -ln TEST -nap JE -gf juncus-rp.fasta INFO: splitting mRNA off gene Transcript_138016|g.1862 ...
gff3 python tbl ncbi written 9 weeks ago by arsilan32440 • updated 9 weeks ago by tdmurphy80

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