User: alowi33

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alowi330
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Posts by alowi33

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Extract fasta sequences from a file using a list in another file.
... `grep -w -A 2 -f test.txt test.fa --no-group-separator` doesn't work if there are special characters in the header, which is common. Use `grep -w -A 2 -Ff test.txt test.fa --no-group-separator` instead. -F searchers for a fixed string. For anyone that only has one sequence per header in their fa ...
written 6 months ago by alowi330
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Comment: C: How to download sample attributes (sample metadata) file from the European nucle
... Worked great :) Anyway to include each attribute's category in the first line? ...
written 2.7 years ago by alowi330
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Comment: C: How to download sample attributes (sample metadata) file from the European nucle
... How can you make the xslt stylesheet so that sample names are rows and sample attributes are columns, and tab delimited? Example: age age_units ... ERS1887136 61 years ... ERS1887137 61 years ... ERS1887138 44 years ...
written 2.7 years ago by alowi330
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Comment: C: How to download sample attributes (sample metadata) file from the European nucle
... That is what I was looking for. Usually bioprojects in NCBI contain a file with all metadata. This file is available in other bioprojects but I couldn't find it in this project. I didn't know about the option you described. Very simple yet useful. Many thanks. ...
written 2.7 years ago by alowi330
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Comment: C: How to download sample attributes (sample metadata) file from the European nucle
... I am ssh-ed in to a remote server. I didnt ssh using a key - that is the "key" to solving my problem ;) ...
written 2.7 years ago by alowi330
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Comment: C: How to download sample attributes (sample metadata) file from the European nucle
... Astounding! Much appreciated. I wonder why It didnt fully work for my machine.... ...
written 2.7 years ago by alowi330
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Comment: C: How to download sample attributes (sample metadata) file from the European nucle
... Exquisite solution. However, it only works for the first 3 samples and then the following error code is repeated many times: unable to parse - -:1: parser error : Document is empty ^ -:1: parser error : Start tag expected, '<' not found Perhaps the site stoped granting us a ...
written 2.7 years ago by alowi330
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Comment: C: How to download sample attributes (sample metadata) file from the European nucle
... Unfortunately NCBI does not contain metadata for this project. I get the error "Unable to establish SSL connection" using your codes. I have tried pythons request function but after one successful xml reading the connection fails when I try to read again. You can see my sample codes here: [https://w ...
written 2.7 years ago by alowi330
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How to download sample attributes (sample metadata) file from the European nucleotide archive (EMBL-EBI)?
... Project PRJEB99111 has 147 samples. I want to download the metadata (age, sex, disease status, etc) of each sample, not fastq. The only way I can download the metadata is by downloading the xml file of each sample accession one by one - is there a way to bulk download all 147 metadata files? I can w ...
european nucleotide archive embl-ebi attributes written 2.7 years ago by alowi330 • updated 2.7 years ago by genomax85k
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Comment: C: python stopped opening xml url, connection closed.
... 'TEXT" does not contain metadata (age, sex, disease status, etc). The metadata can be found by clicking on the "Attributes" tab for each sample individually (147 samples all together). This page contains the metadata for one of the samples: [https://www.ebi.ac.uk/ena/data/view/SAMEA104228118][1] ...
written 2.7 years ago by alowi330

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