fasta.qual
Written by Lucas Sinclair. MIT Licensed. Contact at www.sinclair.bio
1#!/usr/bin/env python3 2# -*- coding: utf-8 -*- 3 4""" 5Written by Lucas Sinclair. 6MIT Licensed. 7Contact at www.sinclair.bio 8""" 9 10# Built-in modules # 11 12# Internal modules # 13from fasta import FASTA 14 15############################################################################### 16class QualFile(FASTA): 17 """A single QUAL file somewhere in the filesystem.""" 18 19 format = 'qual' 20 ext = 'qual'
17class QualFile(FASTA): 18 """A single QUAL file somewhere in the filesystem.""" 19 20 format = 'qual' 21 ext = 'qual'
A single QUAL file somewhere in the filesystem.
Inherited Members
- autopaths.base_path.BasePath
- BasePath
- clean_path
- path
- short_prefix
- extension
- escaped
- absolute_path
- physical_path
- relative_path
- rel_path_from
- exists
- is_symlink
- permissions
- mdate
- mdate_iso
- cdate
- cdate_iso
- unix_style
- wsl_style
- win_style
- with_tilda
- with_home
- link_from
- link_to
- symlinks_on_linux
- symlinks_on_windows
- hard_link_win_to
- fasta.core.FASTA
- buffer_size
- gzipped
- first
- count
- lengths
- lengths_counter
- open
- close
- parse
- progress
- create
- add
- add_seq
- add_str
- add_fasta
- add_fastas
- flush
- write
- compress
- compress_slow
- compress_fast
- ids
- get_id
- sequences
- sql
- length_by_id
- subsample
- rename_with_num
- rename_with_prefix
- rename_sequences
- extract_length
- extract_sequences
- remove_trailing_stars
- remove_duplicates
- convert_U_to_T
- align
- template_align
- index_bowtie
- index_samtools
- graphs
- parse_primers
- autopaths.file_path.FilePath
- prefix_path
- prefix
- name
- filename
- directory
- count_bytes
- size
- contents
- contents_utf8
- md5
- might_be_binary
- contains_binary
- magic_number
- lines
- read
- touch
- writelines
- remove
- copy
- execute
- replace_extension
- new_name_insert
- make_directory
- must_exist
- head
- pretty_head
- tail
- pretty_tail
- move_to
- rename
- gzip_to
- gzip_internal
- gzip_external
- gzip_pigz
- ungzip_to
- ungzip_internal
- ungzip_external
- zip_to
- unzip_to
- untar_to
- untargz_to
- untargz_to_internal
- untargz_to_external
- append
- prepend
- remove_line
- remove_first_line
- replace_line
- replace_word
- sed_replace
- builtins.str
- encode
- replace
- split
- rsplit
- join
- capitalize
- casefold
- title
- center
- expandtabs
- find
- partition
- index
- ljust
- lower
- lstrip
- rfind
- rindex
- rjust
- rstrip
- rpartition
- splitlines
- strip
- swapcase
- translate
- upper
- startswith
- endswith
- removeprefix
- removesuffix
- isascii
- islower
- isupper
- istitle
- isspace
- isdecimal
- isdigit
- isnumeric
- isalpha
- isalnum
- isidentifier
- isprintable
- zfill
- format_map
- maketrans