biopython

I have a FASTA file that can easily be parsed by SeqIO.parse . I am interested in extracting sequence ID's and sequence lengths. I used these lines to do it, but I feel it's waaaay too heavy (two iterations, conversions, etc.) from Bio import SeqIO import pandas as pd # parse sequence fasta file identifiers = [seq_record.id for seq_record in SeqIO.parse("sequence.fasta", "fasta")] lengths = [len(seq_record.seq) for seq_record in SeqIO.parse("sequence.fasta", "fasta")] #converting lists to pandas Series s1 = Series(identifiers, name='ID') s2 = Series(lengths, name='length') #Gathering Series

I'm trying to implement the Smith-Waterman algorithm for local sequence alignment using the affine gap penalty function. I think I understand how to initiate and compute the matrices required for calculating alignment scores, but am clueless as to how to then traceback to find the alignment. To generate the 3 matrices required I have the following code for j in range(1, len2): for i in range(1, len1): fxOpen = F[i][j-1] + gap xExtend = Ix[i][j-1] + extend Ix[i][j] = max(fxOpen, xExtend) fyOpen = F[i-1][j] + gap yExtend = Iy[i-1][j] + extend Iy[i][j] = max(fyOpen, yExtend) matchScore = (F[i-1]

I am trying to pass BioPython sequences to Ilya Stepanov's implementation of Ukkonen's suffix tree algorithm in iPython's notebook environment. I am stumbling on the argparse component. I have never had to deal directly with argparse before. How can I use this without rewriting main()? By the by, this writeup of Ukkonen's algorithm is fantastic . I've had a similar problem before, but using optparse instead of argparse . You don't need to change anything in the original script, just assign a new list to sys.argv like so: if __name__ == "__main__": from Bio import SeqIO path = '/path/to

I would like to extract chains from pdb files. I have a file named pdb.txt which contains pdb IDs as shown below. The first four characters represent PDB IDs and last character is the chain IDs. 1B68A 1BZ4B 4FUTA I would like to 1) read the file line by line 2) download the atomic coordinates of each chain from the corresponding PDB files. 3) save the output to a folder. I used the following script to extract chains. But this code prints only A chains from pdb files. for i in 1B68 1BZ4 4FUT do wget -c "http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId="

I trying to build a tree with BioPython, Phylo module. What I've done so far is this image: each name has a four digit number followed by - and a number: this number refer to the number of times that sequence is represented. That means 1578 - 22, that node should represent 22sequences. the file with the sequences aligned: file the file with the distance to build a tree: file So now I known how to change each size of the node. Each node has a different size, this is easy doing an array of the different values: fh = open(MEDIA_ROOT + "groupsnp.txt") list_size = {} for line in fh: if '>' in line:

I have two files. File 1: a FASTA file with gene sequences, formated like this example: >PITG_00002 | Phytophthora infestans T30-4 conserved hypothetical protein (426 nt) ATGCATCGCTCGGGTTCCGCACGGAAAGCCCAAGGTCTGGGATTACGGGGTGGTGGTCGG TTACACTTGGAATAACCTCGCAAATTCAGAATCTCTACAGGCTACGTTCGCGGATGGAAC >PITG_00003 | Phytophthora infestans T30-4 protein kinase (297 nt) ATGACGGCTGGGGTCGGTACGCCCTACTGGATCGCACCGGAGATTCTTGAAGGCAAACGG TACACTGAGCAAGCGGATATTTACTCGTTCGGAGTGGTTTTATCCGAGCTGGACACGTGC AAGATGCCGTTCTCTGACGTCGTTACGGCAGAGGGAAAGAAACCCAAACCAGTTCAGATC >PITG_00004 | Phytophthora infestans T30-4 protein kinase