fasta

问题 I am trying to parse a large fasta file and I am encountering out of memory errors. Some suggestions to improve the data handling would be appreciated. Currently the program correctly prints out the names however partially through the file I get a MemoryError Here is the generator def readFastaEntry( fp ): name = "" seq = "" for line in fp: if line.startswith( ">" ): tmp = [] tmp.append( name ) tmp.append( seq ) name = line seq = "" yield tmp else: seq = seq.join( line ) and here is the

问题 I have a 2 files. One is a fasta file contain multiple fasta sequences, while another file includes the names of candidate sequences I want to search (file Example below). seq.fasta >Clone_18 GTTACGGGGGACACATTTTCCCTTCCAATGCTGCTTTCAGTGATAAATTGAGCATGATGGATGCTGATAATATCATTCCCGTGT >Clone_23 GTTACGGGGGGCCGAAAAACACCCAATCTCTCTCTCGCTGAAACCCTACCTGTAATTTGCCTCCGATAGCCTTCCCCGGTGA >Clone_27-1 GTTACGGGGACCACACCCTCACACATACAAACACAAACACTTCAAGTGACTTAGTGTGTTTCAGCAAAACATGGCTTC >Clone_27-2

问题 Firstly I can't use BioPython :( I need to translate a bunch of FASTA sequences from a FASTA file and translate them to protein sequence. FASTA file is like this; >some info ACCGGGCTAAA >other info ACCGCCAATTT So I can create a function that outputs only the DNA sequence but when I try to translate it I get the following error; "TypeError: object of type '_io.TextIOWrapper' has no len()" I have no ide how to resolve this. Any help is immensely appreciated!!!!! Also I am taking my first Python

问题 I am processing text files with thousands of records per file. Each record is made up of two lines: a header that starts with ">" and followed by a line with a long string of characters "-AGTCNR". Here is how a simple file looks like: >ACML500-12|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_-2 ----TAAGATTTTGACTTCTTCCCCCATCATCAAGAAGAATTGT------- >ACRJP458-10|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_N -----------TCCCTTTAATACTAGGAGCCCCTGACATAGCCTTTCCTAAATAAT----- >ASILO303-17|Dip|gs-Par|sp

问题 This is my first question on Stack Overflow and so I want to apologise first if my question is not formatted correctly. I am not particularly experienced with coding, but am trying to solve a specific problem with my work. I am trying to replace the headers of a large fasta file (used for aligning DNA sequences). I have a txt file containing the fasta alignment (alignment.txt), which has contents like this: >418035201_b1_168_m12_gag__Assembly_8 ATGGGTGCGAGAGCGTCAGTATTAAGTGGGGGAAA......

问题 I want to merge two fasta file and remove the duplicate information. Here is some example >Symbiotaphrina_buchneri|DQ248313|SH1641879.08FU|reps|k__Fungi;p__Ascomycota;c__Xylonomycetes;o__Symbiotaphrinales;f__Symbiotaphrinaceae;g__Symbiotaphrina;s__Symbiotaphrina_buchneri

问题 I currently want to sort a hudge fasta file (+10**8 lines and sequences) by sequence size. fasta is a clear defined format in biology use to store sequence (genetic or proteic): >id1 sequence 1 # could be on several line >id2 sequence 2 ... I have run a tools that give me in tsv format: the Identifiant, the length, and the position in bytes of the identifiant. for now what I am doing is to sort this file by the length column then I parse this file and use seek to retrieve the corresponding

问题 The code below extract short sequence in every sequence with the window size 4. How to shift the window by step size 2 and extract 4 base pairs? Example code from Bio import SeqIO with open("testA_out.fasta","w") as f: for seq_record in SeqIO.parse("testA.fasta", "fasta"): i = 0 while ((i+4) < len(seq_record.seq)) : f.write(">" + str(seq_record.id) + "\n") f.write(str(seq_record.seq[i:i+4]) + "\n") i += 2 Example Input of testA.fasta >human1 ACCCGATTT Example Output of testA_out >human1 ACCC

问题 I have a file (mydata.txt) that contains many exon sequences with fasta format. I want to find start ('atg') and stop ('taa','tga','tag') codons for each DNA sequence (considering the frame). I tried using matchPattern ( a function from the Biostrings R package) to find theses amino acids: As an example mydata.txt could be: >a atgaatgctaaccccaccgagtaa >b atgctaaccactgtcatcaatgcctaa >c atggcatgatgccgagaggccagaataggctaa >d atggtgatagctaacgtatgctag >e atgccatgcgaggagccggctgccattgactag file=read

问题 I have the following FASTA file: >header1 CGCTCTCTCCATCTCTCTACCCTCTCCCTCTCTCTCGGATAGCTAGCTCTTCTTCCTCCT TCCTCCGTTTGGATCAGACGAGAGGGTATGTAGTGGTGCACCACGAGTTGGTGAAGC >header2 GGT >header3 TTATGAT My desired output: >header1 117 >header2 3 >header3 7 # 3 sequences, total length 127. This is my code: awk '/^>/ {print; next; } { seqlen = length($0); print seqlen}' file.fa The output I get with this code is: >header1 60 57 >header2 3 >header3 7 I need a small modification in order to deal with