bioplus.fasta
meta-tools for large FASTA files
-
bioplus.fasta.count(foo)[source]
takes a file named foo returns the number lines
-
bioplus.fasta.pad(x, y)[source]
takes two integers x and y, and returns str(x) with enough 0s to match
the length of str(y)
-
bioplus.fasta.permute_fasta(f)[source]
takes a FASTA file and returns a new FASTA file with each sequence randomly
permuted (separately, such that its % A,T,G,C doesn’t change)
-
bioplus.fasta.random_files(foo, n, R)[source]
takes a FASTA file foo and creates (in the current directory) R random
files each containing n random sequences from foo, named foo_random[0-R].fa
-
bioplus.fasta.random_seq(foo, n)[source]
takes a file foo and returns n random sequences from it
-
bioplus.fasta.reader(foo)[source]
generator yielding Bio.Seq.Seq objects from a FASTA file
-
bioplus.fasta.truncate_lines(f, n)[source]
truncate_lines(f,n) truncates lines in a file to at most n characters
See truncate_seqs to truncate sequences instead of lines
-
bioplus.fasta.truncate_seqs(f, n)[source]
truncate FASTA seqs truncates sequences in a FASTA file named f to at most
n bases, writing a new FASTA file named f.n.fa
-
bioplus.fasta.writer(foo, iterable)[source]
writes SeqRecord objects from iterable to FASTA file foo.
Warning: overwrites foo, does not append