SRA | Project based at the Bond University Center | Machine Learning library

When accessing google_patents_research.publications table from BigQuery I can filter results by the top_terms column. This column uses Google's machine learning algo to search the text inside a patent and extract the words it finds most meaningful. I was wondering if there is a similar search using BigQuery that can be done on PubMed's database. According to NCBI docs there is a dataset called nih-sra-datastore which should be accessible from BigQuery, but it doesn't show up when searching for it in BigQuery's console search box.

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I'm trying to use snakemake to download a list of files, and then rename them according to mapping given in the file. I first read a dictionary from a file that has the form of {ID_for_download : sample_name}, and I pass the list of its keys to first rule for download (because downloading is taxing, I'm just using a dummy script to generate empty files). For every file in the list, two files are downloaded in the form of {file_1.fastq} and {file_2.fastq} When those files are downloaded, I then rename them using the second rule - here I take advantage of being able to run python code in a rule using run key word. When I do a dry-run using -n flag, everything works. But when I do an actual run, I get an error of the form

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im am using Linux Ubuntu on a Virtual machine on Windows 10.

I have downloaded a IPython Notebook from dms_tools

Now when I try to run certain parts of the code I become the following error:

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I'm trying to import a json file in R (the downloaded file encoding is ANSI.), but the error below appears:

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I am using the checksum calculator from: https://github.com/Vi1i/OcarinaChecksumChecker

I downloaded the ocarina.h and checksumCalc.c files and was able to compile them using gcc checksumCalc.c in WSL for Windows (Debian Linux shell in Windows 10). It then outputs the file "a.out" which I am able to run using ./a.out "THE LEGEND OF ZELDA.sra" 0020 and which calculates the correct checksum for my Legend of Zelda save file that matches what I see in my hex editor.

Then I decided to play around and try compiling it using Windows. I've set up my Powershell so I can compile C programs simply using "cl" in Powershell. First, I tried doing cl checksumCalc.c and I got the following errors:

checksumCalc.c(49): error C2065: 'ushort': undeclared identifier

checksumCalc.c(49): error C2146: syntax error: missing ')' before identifier 'data'

checksumCalc.c(49): error C2059: syntax error: ')'

After Googling the first error, I changed "ushort" in the checksumCalc.c file to USHORT, and added #include at the top of the file. I tried compiling again and it actually compiled. However, when I try running the resulting exe in Windows, it gives an incorrect checksum. I used the same syntax as the a.out file, but replaced a.out with checksumCalc.exe. checksumCalc.exe "THE LEGEND OF ZELDA.sra" 0020

Does anyone have an idea of why the program is giving me a completely different result in Windows versus Linux? Here is a direct link to the checksumCalc.c code: https://github.com/Vi1i/OcarinaChecksumChecker/blob/master/checksumCalc.c

As mentioned above, the only thing I changed when trying in Windows was I added #include , and I made the ushort at the bottom all caps. I was hoping someone that understands the quirks of C programming and the differences between compiling in Windows and Linux could help me understand what might be going wrong.

For the record, I can just as easily accomplish what I'm trying to do by just getting the checksum from the Linux shell but I just want to understand what might be going on from a learning perspective. I'm a C noob, and to me I figured C was C, but apparently there must be commands that are exclusive to Linux/Windows where the code needs to be adapted to work properly.

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I've got a file that contains a list of file paths. I’m downloading them like this with wget:

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This was on an exam and I'll admit that I had no idea what was going on, shifts weren't discussed prior to the exam. They're both starting in hexadecimal and then the instructions shift one to the left logical and the other to the right arithmetic. For some reason the left logical one has every number plus 5 and then there's an 8 at the beginning, making the hex go from 7's to B's (12), and in the second one there's an E in the front but the numbers stay the same? My notes have the professor saying add two 0's or two 1's but I'm still not seeing where he got the answers from. The $t1 and $t0 values are given at the top and then below for each question is a different MIPS32 statement; sll $t2, $t1, 3 and sra $t2, $t0, 2. $t1 is in hex (0x7777 77777) and $t0 is (0x8888 88888).

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I have a dataset ('DF1') that has count data. It looks like this:

Species Date Site n AMCR 6/1/2021 SVC 14 AMCR 6/1/2021 BMA 1 AMCR 6/7/2021 SVA 2 AMCR 6/15/2021 SVA 9 AMCR 6/21/2021 SVA 18 AMCR 6/29/2021 SVA 18

However, my study actually has nine 'Sites' (SVC, BMA, SVA, BMC, TMA, TMC, SRA, SRC, and MCC) and each site has data collected on the same five dates (6/1/2021, 6/8/2021, 6/15/2021, 6/21/2021, and 6/29/2021). DF1 only shows rows for where there were counts in 'n', but if there were no counts, I want the dataframe to be populated with zero counts for each of those dates for each site so that it looks like this:

Species Date Site n AMCR 6/1/2021 SVC 14 AMCR 6/7/2021 SVC 0 AMCR 6/15/2021 SVC 0 AMCR 6/21/2021 SVC 0 AMCR 6/29/2021 SVC 0 AMCR 6/1/2021 BMA 1 AMCR 6/7/2021 BMA 0 AMCR 6/15/2021 BMA 0 AMCR 6/21/2021 BMA 0 AMCR 6/29/2021 BMA 0 AMCR 6/1/2021 SVA 0 AMCR 6/7/2021 SVA 2 AMCR 6/15/2021 SVA 9 AMCR 6/21/2021 SVA 18 AMCR 6/29/2021 SVA 18 AMCR 6/1/2021 BMC 0 AMCR 6/7/2021 BMC 0 AMCR 6/15/2021 BMC 0 AMCR 6/21/2021 BMC 0 AMCR 6/29/2021 BMC 0 AMCR 6/1/2021 TMA 0 AMCR 6/7/2021 TMA 0 AMCR 6/15/2021 TMA 0 AMCR 6/21/2021 TMA 0 AMCR 6/29/2021 TMA 0 AMCR 6/1/2021 TMC 0 AMCR 6/7/2021 TMC 0 AMCR 6/15/2021 TMC 0 AMCR 6/21/2021 TMC 0 AMCR 6/29/2021 TMC 0 AMCR 6/1/2021 SRA 0 AMCR 6/7/2021 SRA 0 AMCR 6/15/2021 SRA 0 AMCR 6/21/2021 SRA 0 AMCR 6/29/2021 SRA 0 AMCR 6/1/2021 SRC 0 AMCR 6/7/2021 SRC 0 AMCR 6/15/2021 SRC 0 AMCR 6/21/2021 SRC 0 AMCR 6/29/2021 SRC 0 AMCR 6/1/2021 MCC 0 AMCR 6/7/2021 MCC 0 AMCR 6/15/2021 MCC 0 AMCR 6/21/2021 MCC 0 AMCR 6/29/2021 MCC 0

Is there a way to add rows with 0 counts by checking to see if those date and site combinations don't exist?

Thank you.

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In order to extract some fastq data from NCBI's sequence read archive I've downloaded and installed the sra toolkit for Windows. In order to test if it is setup correctly, I opened cmd, navigated to the directory and typed in the command fasterq-dump --split-files SRR7647019. It downloads the file SRR7647019.sra as expected and splits it into fastq files.

Then I've tried the same command in RStudio, wrapping the system() command around it: system(fasterq-dump --split-files SRR7647019). However, R always returns

An error occured: unrecognized tool FASTER~2.EXE If this continues to happen, please contact the SRA Toolkit at https://trace.ncbi.nlm.nih.gov/Traces/sra/

as well as the number 75 (probably an error code).

Any idea why I'm not able to run fasterq-dump.exe from R? How could it be solved?

Thanks a lot for suggestions in advance!

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