I am trying to run a basic biopython script to rename sequences within a fasta file. I have only ever ran this on a server; i am trying to do it on my macbook but I can’t work out what the correct path to the file should be. on the server is worked as follows:… Read More How are paths meant to be denoted on for Biopython on mac?

Hi I want to check the score value of the Amino acid sequence, for which I wrote the following code which works absolutely fine. But the problem is every time I have to edit the file. is there any way I can give the the amino acid sequence from the command interface. AA_seq=’AVTLSPQRS’ # this… Read More editing python script file again and again

I’d like to loop through every file in a directory given by the user and apply a specific transformation for every file that ends with ".fastq". Basically this would be the pipeline: User puts the directory of where those files are (in command line) Script loops through every file that has the format ".fastq" and… Read More Loop through every file with specific format in a directory using sys argv

I am doing simply queries on a csv document about a genome. I have the following code: locus_example = ‘Rv0001’ for locus in tuberculosis_data1["Locus"].values: if locus_example.rfind(locus): result = tuberculosis_data1.loc[tuberculosis_data1[‘Locus’] == locus][‘Sequences’].values for r in result: print(r) break That gives me the following sequence: ATGGACGCGGCTACGACAAGAGTTGGCCTCACCGACTTGACGTTTCGTTTGCTACGAGAGTCTTTCGCCGATGCGGTGTCGTGGGTGGCTAAAAATCTGCCAGCCAGGCCCGCGGTGCCGGTGCTCTCCGGCGTGTTGTTGACCGGCTCGGACAACGGTCTGACGATTTCCGGATTCGACTACGAGGTTTCCGCCGAGGCCCAGGTTGGCGCTGAAATTGTTTCTCCTGGAAGCGTTTTAGTTTCTGGCCGATTGTTGTCCGATATTACCCGGGCGTTGCCTAACAAGCCCGTAGACGTTCATGTCGAAGGTAACCGGGTCGCATTGACCTGCGGTAACGCCAGGTTTTCGCTACCGACGATGCCAGTCGAGGATTATCCGACGCTGCCGACGCTGCCGGAAGAGACCGGATTGTTGCCTGCGGAATTATTCGCCGAGGCAATCAGTCAGGTCGCTATCGCCGCCGGCCGGGACGACACGTTGCCTATGTTGACCGGCATCCGGGTCGAAATCCTCGGTGAGACGGTGGTTTTGGCCGCTACCGACAGGTTTCGCCTGGCTGTTCGAGAACTGAAGTGGTCGGCGTCGTCGCCAGATATCGAAGCGGCTGTGCTGGTCCCGGCCAAGACGCTGGCCGAGGCCGCCAAAGCGGGCATCGGCGGCTCTGACGTTCGTTTGTCGTTGGGTACTGGGCCGGGGGTGGGCAAGGATGGCCTGCTCGGTATCAGTGGGAACGGCAAGCGCAGCACCACGCGACTTCTTGATGCCGAGTTCCCGAAGTTTCGGCAGTTGCTACCAACCGAACACACCGCGGTGGCCACCATGGACGTGGCCGAGTTGATCGAAGCGATCAAGCTGGTTGCGTTGGTAGCTGATCGGGGCGCGCAGGTGCGCATGGAGTTCGCTGATGGCAGCGTGCGGCTTTCTGCGGGTGCCGATGATGTTGGACGAGCCGAGGAAGATCTTGTTGTTGACTATGCCGGTGAACCATTGACGATTGCGTTTAACCCAACCTATCTAACGGACGGTTTGAGTTCGTTGCGCTCGGAGCGAGTGTCTTTCGGGTTTACGACTGCGGGTAAGCCTGCCTTGCTACGTCCGGTGTCCGGGGACGATCGCCCTGTGGCGGGTCTGAATGGCAACGGTCCGTTCCCGGCGGTGTCGACGGACTATGTCTATCTGTTGATGCCGGTTCGGTTGCCGGGCTGA I also have the following code that is supposed to give… Read More Simply queries in pandas give different results