User: bioinfoSeeker

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Posts by bioinfoSeeker

<prev • 20 results • page 1 of 2 • next >
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AttributeError: 'Hit' object has no attribute 'sacc_ver'
... Hi, I am trying to write a script to parse and summarize the ncbi web blast output (14 columns). I am using biopython searchIO on the tab delimited output file with the first seven lines commented by default. I get the following error : AttributeError: 'Hit' object has no attribute 'sacc_ver' In ...
python searchio biopython blast written 13 months ago by bioinfoSeeker20
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Answer: A: Blast parse script: ValueError: Required query and/or hit ID field not found.
... I looked at SearchIO documentation http://biopython.org/DIST/docs/api/Bio.SearchIO.BlastIO-pysrc.html, and used to the table in there to replace the corresponding fields from the blast report, in the script. custom_fields = 'qseqid, sseqid, qaccver, sacc_ver, nident, length, mismatch, gapopen, ...
written 13 months ago by bioinfoSeeker20
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Comment: A: Blast parse script: ValueError: Required query and/or hit ID field not found.
... In continuation to my post, i'm adding a snippet of my blast report file that I'm trying to parse. # blastn # Iteration: 0 # Query: 000000577|size:2297896 # RID: xxxxxx # Database: nr # Fields: query id, subject ids, query ...
written 13 months ago by bioinfoSeeker20
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Blast parse script: ValueError: Required query and/or hit ID field not found.
... Hi, I am trying to write a script to parse and summarize the ncbi web blast output (14 columns). I am using biopython searchIO on the tab delimited output file which is commented by default. I get the error ValueError: Required query and/or hit ID field not found. I tried to remove the further summ ...
python blast written 13 months ago by bioinfoSeeker20
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Comment: C: NCBI web Blastn csv headers
... Thank you. When I download the hittable(CSV) or hittable(txt), it doesn't have a header. Not sure if I am missing some option that I have to click. Anyway, i see in your example 14 column headers, a subset of the 21 headers from blast+ command line report. I shall go ahead and use that to match my n ...
written 13 months ago by bioinfoSeeker20
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Comment: C: NCBI web Blastn csv headers
... Thanks for your reply. I do already have the header names for the Blast+ report. Its the webserver report headers that I can't find. I had initially thought they matched with each other, but when I look at the content of the reports, they look different. See the sample rows below from two different ...
written 13 months ago by bioinfoSeeker20
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NCBI web Blastn csv headers
... Hi, I am looking for information about the blastn report headers. I can only find the info about the csv report headers from ncbi blast+ run from command line. I cannot find this information for the webserver blastn csv report. The link from the ncbi webserver blast page called "Blast report descri ...
blasn ncbi blast blastn written 13 months ago by bioinfoSeeker20 • updated 13 months ago by genomax58k
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Answer: A: Tool For Taxonomy Classification Of contigs and reads
... [CLARK][1] can be used for taxonomic classification of assembled reads. [1]: http://clark.cs.ucr.edu/ ...
written 16 months ago by bioinfoSeeker20
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Comment: C: Error when running PhiSpy
... Tried that command as suggested with the full path. It still gives the same error that I have captured in my earlier comment. I then tried running PhiSpy with another genome directory (10479.4 ) downloaded from the database linked in ReadMe.md. I continue to get the same errors. Moreover any genome ...
written 22 months ago by bioinfoSeeker20
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Comment: A: Error when running PhiSpy
... Bumping this post up, if it is okay. Pls see the thread above on my reply/query on this error. ...
written 22 months ago by bioinfoSeeker20

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For OrthoMcl - Orthologs.txt is empty. All output is present in inParalogs.txt
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Generating tree from Amphora2 for Synergytwo
Popular Question 5 weeks ago, created a question with more than 1,000 views. For NCBI web Blastn csv headers
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Scholar 4.3 years ago, created an answer that has been accepted. For A: probesets with identical values in Affymetrix Hugene 2.1 platform

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