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Beginning Perl for Bioinformatics | |
Beginning Perl for Bioinformatics
[Symbol][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][X]
! (bang) ! (logical negation) operator , 2nd
!= (not equal to) operator
!~ (binding) operator
#! (shebang) notation
" (quotes, double) within double-quoted strings
empty strings, representing with
string interpolation
in strings , 2nd
"exclusive-OR" operator (xor) , 2nd
"point-and-click" interaction with data
# (sharp) #! (shebang notation), command interpretation line
in Perl comments
$ (dollar sign) for scalar variable names , 2nd
$$, returning Perl program ID number
$& variables , 2nd
$' variables
$/ (input record separator)
$_ variables , 2nd
, 3rd
$` variables
before embedded newlines
metacharacter
metacharacter in regular expressions
$PATH or $path variable
% (percent sign) in directives
for hash names , 2nd
& (ampersand) && (logical and) operator , 2nd
(bitwise and) operator
subroutine names, starting with
' (quotes, single) empty strings, representing with
in strings , 2nd
() (parentheses) for capturing in patterns
enclosing subroutine arguments
grouping in regular expressions , 2nd
in regular expressions
metacharacter in regular expressions
order of operations, specifying with
variables from @_ array, enclosing with
(angle brackets)> (right angle bracket) right justification
< (left angle bracket) less than operator
line input (angle) operator , 2nd
, 3rd
, 4th
* (asterisk) *? quantifier
character wildcard
quantifier
in regular expressions
+ (plus sign) ++ (autoincrement) operator , 2nd
+= (add assignment) operator
quantifier
, (comma) separating items in lists
separating subroutine arguments
-- (minus sign), autodecrement operator
-d (debug) command-line switch
-e (exists) file test
-w command-line switch, turning on warnings
. (dot) .. (range) operator
character wildcard , 2nd
metacharacter in regular expressions
string concatenation operator , 2nd
/ (forward slash)// (double slash) end-of-record separator
in pattern modifiers
s/// (substitution) operator
/g (global) pattern modifier , 2nd
/i (case-insensitive) matching , 2nd
/m pattern modifier , 2nd
program to extract annotation from sequence
/s pattern modifier program to extract annotation from sequence
; (semicolon), ending Perl statements , 2nd
= (equal sign) == (equal to) operator
==> current line marker
=~ (pattern binding) operator , 2nd
, 3rd
assignment operator , 2nd
? (question mark), in quantifiers
@ (at sign) @_ arrays , 2nd
@ARGV array variables
beginning array variables with
for array names
@ARGV arrays
[] (brackets) array element lookups
enclosing character class in
\\\\ (backslash) escaping metacharacters
escaping quotes within quoted strings
metasymbols, use in
references, use in
\\\\n or \\\\n\\\\n (newlines)
^ (caret) beginning of string, anchoring to
bitwise xor operator
end of line assertion (in matching)
for filled text in formats
metacharacter in regular expressions , 2nd
, 3rd
restriction enzyme cut site (REBASE)
` (backticks), command input operator
{} (curly braces) hash lookups, use in
quantifier
for statement blocks
in string interpolation
| (vertical bar) (bitwise OR) operator , 2nd
|| (logical or) operator , 2nd
alternation
for centering
debugger commands
regular expressions, use in
~~ (tildes), for multiline data in fields
3' (three prime) end, nucleotides
3D protein structure , 2nd
, 3rd
5' (five prime) end, nucleotides
A
See : adenine A
accession numbers (GenBank records), storing as keys
active site of a protein
ActivePerl from ActiveState
adenine (A) , 2nd
algorithmsbinary search using with sorted arrays
data structures and gene expression database
graph, modelling biological networks
resource materials
sequence alignment and
string matching , 2nd
alignment (sequence), algorithms and
alignment of text
alignments, BLAST extracting
parsing
alpha helices, beta-strands, and turns
alpha-alpha units (protein supersecondary structure)
alphabetical sorting, array of strings
alphabets (nucleic acid and amino acid codes)
alternation , 2nd
amino acids , 2nd
codes for (standard IUB/IUPAC)
lacking stop codons
translating DNA into representing with codons
amino group
and operator bitwise and (&) operator
logical and control flow, using for
See : , under Symbols angle brackets ()
angle operator , 2nd
, 3rd
, 4th
annotations, BLAST files extracting
HSPs
annotations, GenBank files information in
parsing using regular expressions
separating from DNA sequences
applications (Perl), programming language vs.
Applied Biosystems (ABI) sequencer output
approximation
argument line
arguments , 2nd
, 3rd
@_ arrays, passing into subroutines with
command-line @ARGV array variables
passing by reference dereferencing
scoping and
separating with commas
arithmetic operators order of evaluation
array context, putting variables into
arrays , 2nd
, 3rd
@_ arrays , 2nd
@ARGV
associative
converting to scalar variables
elements numbering positions of
exploding strings into
GenBank annotations, parsing with
GenBank records, using with
of hash key/value pairs
initializing and accessing individual elements
inserting element at arbitrary position in
in list context
multiline strings, converting to
passing by reference into or out of subroutines
printing
randomly selecting elements from subroutines for
reversing
in scalar context
size, determining (scalar function)
sorted, for gene expression data
as subroutine arguments
unsorted, for gene expression data
using with push and pop functions
using with push and shift functions
ASCIIflat files PDB (Protein Data Bank)
assignment , 2nd
= operator, use in statements
array to scalar variable
arrays to lists
in concatenation of DNA fragments
in DNA to RNA transcription
scalar and list context
assignment operators , 2nd
See : hashes associative arrays
atomic coordinates, finding in PDB filesATOM record type parsing from input file
attributes, file
autoincrement and autodecrement operators
automating programs secondary structure predictor
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