Moderator: a.zielezinski

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a.zielezinski9.2k
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Andrzej Zielezinski

Posts by a.zielezinski

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Comment: C: Printing for each specific sequence and its residue in msa , every msa position
... Glad I could help. I just updated my answer to show all ids at once. ...
written 23 days ago by a.zielezinski9.2k
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Answer: A: Printing for each specific sequence and its residue in msa , every msa position
... Maybe this will help. from Bio.Align import MultipleSeqAlignment from Bio.Alphabet import generic_dna from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord def map_positions(aln, id): rec = next((r for r in aln if r.id==id), None) seq_pos = 0 f ...
written 23 days ago by a.zielezinski9.2k
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Comment: C: How to combine p-values of differentially expressed genes from different timepoi
... Can't you just take the maximum p-value (max_p) from these few genes and report it as p <= max_p. You can do the same with the foldchange. ...
written 5 weeks ago by a.zielezinski9.2k
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Comment: C: Calculate Ka/Ks using examples of two sequences.
... Do you want to calculate Ka/Ks ratio by hand or just use a tool? There are at least six different methods to calculate Ka/Ks ratio. ...
written 5 weeks ago by a.zielezinski9.2k
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Answer: A: python 3.8 'No module named pip'
... Download `get-pip.py` script to install pip: curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py Install pip: python3 get-pip.py Install biopython: python3 -m pip install biopython or pip3 install biopython ...
written 3 months ago by a.zielezinski9.2k
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Comment: C: Comparing multiple columns from 2 files using awk, perl or python
... Are sure the output is correct? I think that only "SpoScf_15890 12 2376" fulfils the criteria (start or end in the file1 should be less than in file2, and the difference shouldn't be greater than 1000) ...
written 4 months ago by a.zielezinski9.2k
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Comment: C: Comparing multiple columns from 2 files using awk, perl or python
... import sys d = {} for argv in [2, 1]: with open(sys.argv[argv]) as fh: for line in fh: sl = line.split() id = sl[0] st = int(sl[1]) en = int(sl[2]) if argv == 2: d ...
written 4 months ago by a.zielezinski9.2k
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Answer: A: Comparing multiple columns from 2 files using awk, perl or python
... Here's Python script: import sys d = {} for argv in [2, 1]: with open(sys.argv[argv]) as fh: for line in fh: sl = line.split() id = sl[0] st = int(sl[1]) en = int(sl[2]) if argv == 2 ...
written 4 months ago by a.zielezinski9.2k
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Comment: C: ID query with entrez -- invalid ID - rllib.error.HTTPError: HTTP Error 400: Bad
... Thank you for sharing! ...
written 4 months ago by a.zielezinski9.2k
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Answer: A: ID query with entrez -- invalid ID - rllib.error.HTTPError: HTTP Error 400: Bad
... You can modify your script to try downloading the sequence record three times until all fail. If all three attempts fail, skip this record. from urllib.request import urlopen from Bio import Entrez import time Entrez.email = "xxxx@xxxxx.com" IDs = ['AY851612', 'hahdshjhdasd ...
written 4 months ago by a.zielezinski9.2k

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Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Great Question 6 weeks ago, created a question with more than 5,000 views. For Hmmsearch (Hmmer) Tblout Format
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
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Scholar 4 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
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Scholar 6 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Appreciated 7 months ago, created a post with more than 5 votes. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Scholar 7 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Scholar 8 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
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Commentator 13 months ago, created a comment with at least 3 up-votes. For C: 200Bp Long Query Returning 201Bp
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
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Commentator 14 months ago, created a comment with at least 3 up-votes. For C: 200Bp Long Query Returning 201Bp
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Appreciated 14 months ago, created a post with more than 5 votes. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
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