In Biopython, “fastq” (or the alias “fastq-sanger”) refers to Sanger style FASTQ files which encode PHRED qualities using an ASCII offset of 33.
This refers to the input FASTA file format introduced for Bill Pearson’s FASTA tool, where each record starts with a “>” line.įASTA format variant with no line wrapping and exactly two lines per record.įASTQ files are a bit like FASTA files but also include sequencing qualities. The alignment format of Clustal X and Clustal W. Reads a macromolecular Crystallographic Information File (mmCIF) file to determine the complete protein sequence as defined by the _pdbx_poly_seq_scheme records. Uses to determine the (partial) protein sequence as it appears in the structure based on the atomic coordinates. Reads the contig sequences from an ACE assembly file. Same as “abi” but with quality trimming with Mott’s algorithm. Note each ABI file contains one and only one sequence (so there is no point in indexing the file). Reads the ABI “Sanger” capillary sequence traces files, including the PHRED quality scores for the base calls. Possible we use the same name as BioPerl’s The format name is a simple lowercase string. Git to indicate this is supported in our latest inĭevelopment code). Index, with the Biopython version where this was first supported (or This table lists the file formats that Bio.SeqIO can read, write and Requirements, I hope this should suffice. My vision is that for manipulating sequence data you should tryīio.SeqIO as your first choice. ForĮxample, Bio.Nexus will also read sequences from Nexus files - butīio.Nexus can also do much more, for example reading any phylogenetic
#Bioedit convert txt to fasta how to#
Note that the inclusion of Bio.SeqIO (andīio.AlignIO) in Biopython does lead to someĭuplication or choice in how to deal with some file formats. The design was partly inspired by the simplicity of BioPerl’sīioPerl’s impressive list of supported sequence file There is a sister interface Bio.AlignIOįor working directly with sequence alignment files as Alignment objects. (which you can read online, or from within Python with the helpīio.SeqIO provides a simple uniform interface to input and outputĪssorted sequence file formats (including multiple sequence alignments),īut will only deal with sequences as SeqRecord Start with working with sequence files using SeqIO.īio.SeqIO, and although there is some overlap it is well worth reading Python novices might find Peter’s introductory Biopython The MEGA file converter looks for a line that begin with a greater-than sign (‘ >’), replaces it with a pound sign (‘ #’), takes the word following the pound sign as the sequence name, deletes the rest of the line, and takes the following lines (up to the next line beginning with a ‘>’) as the sequence data.This page describes Bio.SeqIO, the standard Sequence Input/Output TTGCTGCTTAGAGTCAAAGCATGTACTTAGAGTTGGTATGATTTATCTTTTTGGTCTTCT
GTAGGACTTCATTCTAGTCATTATAGCTGCTGGCAGTATAACTGGCCAGCCTTTAATACA GGTATGATTTATCTTTTTGGTCTTCTATAGCCTCCTTCCCCATCCCCATCAGTCTTAATCĪGTCTTGTTACGTTATGACTAATCTTTGGGGATTGTGCAGAATGTTATTTTAGATAAGCAĬATAAGCTCCTTTTAACTTGTTAAAGTCTTGCTTGAATTAAAGACTTGTTTAAACACAAAĪTTTAGACTTTTACTCAACAAAAGTGATTGATTGATTGATTGATTGATTGATGGTTTACA This is an example of a sample input file:ĪTACATCATAACACTACTTCCTACCCATAAGCTCCTTTTAACTTGTTAAAGTCTTGCTTGĪATTAAAGACTTGTTTAAACACAAAAATTTAGAGTTTTACTCAACAAAAGTGATTGATTGĪTTGATTGATTGATTGATGGTTTACAGTAGGACTTCATTCTAGTCATTATAGCTGCTGGCĪGTATAACTGGCCAGCCTTTAATACATTGCTGCTTAGAGTCAAAGCATGTACTTAGAGTT The FASTA file format is very simple and is quite similar to the MEGA file format. Converting FASTA format Converting FASTA format