Hi all !
I have a fasta file that looks like that:
>Sequence1
RTYIPLCASQHKLCPITFLAVK
(it's just an example, obviously in reality I have several pairs of lines like that)
Using UNIX command(s), would it be possible to replace all the characters except the "C" of the second line only by... (7 Replies)
Hi
I have an alignment file (.fasta) with ~80 sequences. They look like this-
>JV101.contig00066(+):25302-42404|sequence_index=0|block_index=4|species=JV101|JV101_4_0
GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT
TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT... (2 Replies)
I have fasta files with multiple sequences in each. I need to change the sequence name headers from:
>accD:_59176-60699
ATGGAAAAGTGGAGGATTTATTCGTTTCAGAAGGAGTTCGAACGCA
>atpA_(reverse_strand):_showing_revcomp_of_10525-12048
ATGGTAACCATTCAAGCCGACGAAATTAGTAATCTTATCCGGGAAC... (2 Replies)
Hi,
I want to match the sequence id (sub-string of line starting with '>' and extract the information upto next '>' line ). Please help .
input
> fefrwefrwef X900
AGAGGGAATTGG
AGGGGCCTGGAG
GGTTCTCTTC
> fefrwefrwef X932
AGAGGGAATTGG
AGGAGGTGGAG
GGTTCTCTTC
> fefrwefrwef X937... (2 Replies)
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
I have a fasta file as follows
>sp|O15090|FABP4_HUMAN Fatty acid-binding protein, adipocyte OS=Homo sapiens GN=FABP4 PE=1 SV=3
MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKN
TEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVM
KGVTSTRVYERA
>sp|L18484|AP2A2_RAT AP-2... (3 Replies)
Hi Guys,
i am having a csv file where i need to round off numerical column to 2 decimal precision in specific columns. i need to ignore the first two line i.e the header columns and manipulate rest of the lines of the csv file. My columns are specific i.e i need to round off only 2nd,4th and... (13 Replies)
I would like to extract all entries containing the following patterns: ccccta & ccccccccc from the following infile:
>P39PT-1224_Freq_900
cccctacgacggcattggtaatggctcccgcaagccatctctcttcagccaagg
>P39PT-784_Freq_2
cccctacgacggcattggtaatggcacccgcaagccatctctcttccccccccc
>P39PT-678_Freq_5... (4 Replies)
Hi,
I have a fasta file with multiple sequences. How can i get only unique sequences from the file.
For example
my_file.fasta
>seq1
TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC
>seq2... (3 Replies)
Discussion started by: Ibk
3 Replies
LEARN ABOUT SUNOS
num
Num(3o) OCaml library Num(3o)NAME
Num - Operation on arbitrary-precision numbers.
Module
Module Num
Documentation
Module Num
: sig end
Operation on arbitrary-precision numbers.
Numbers (type num ) are arbitrary-precision rational numbers, plus the special elements 1/0 (infinity) and 0/0 (undefined).
type num =
| Int of int
| Big_int of Big_int.big_int
| Ratio of Ratio.ratio
The type of numbers.
=== Arithmetic operations ===
val (+/) : num -> num -> num
Same as Num.add_num .
val add_num : num -> num -> num
Addition
val minus_num : num -> num
Unary negation.
val (-/) : num -> num -> num
Same as Num.sub_num .
val sub_num : num -> num -> num
Subtraction
val ( */ ) : num -> num -> num
Same as Num.mult_num .
val mult_num : num -> num -> num
Multiplication
val square_num : num -> num
Squaring
val (//) : num -> num -> num
Same as Num.div_num .
val div_num : num -> num -> num
Division
val quo_num : num -> num -> num
Euclidean division: quotient.
val mod_num : num -> num -> num
Euclidean division: remainder.
val ( **/ ) : num -> num -> num
Same as Num.power_num .
val power_num : num -> num -> num
Exponentiation
val abs_num : num -> num
Absolute value.
val succ_num : num -> num
succ n is n+1
val pred_num : num -> num
pred n is n-1
val incr_num : num Pervasives.ref -> unit
incr r is r:=!r+1 , where r is a reference to a number.
val decr_num : num Pervasives.ref -> unit
decr r is r:=!r-1 , where r is a reference to a number.
val is_integer_num : num -> bool
Test if a number is an integer
=== The four following functions approximate a number by an integer : ===
val integer_num : num -> num
integer_num n returns the integer closest to n . In case of ties, rounds towards zero.
val floor_num : num -> num
floor_num n returns the largest integer smaller or equal to n .
val round_num : num -> num
round_num n returns the integer closest to n . In case of ties, rounds off zero.
val ceiling_num : num -> num
ceiling_num n returns the smallest integer bigger or equal to n .
val sign_num : num -> int
Return -1 , 0 or 1 according to the sign of the argument.
=== Comparisons between numbers ===
val (=/) : num -> num -> bool
val (</) : num -> num -> bool
val (>/) : num -> num -> bool
val (<=/) : num -> num -> bool
val (>=/) : num -> num -> bool
val (<>/) : num -> num -> bool
val eq_num : num -> num -> bool
val lt_num : num -> num -> bool
val le_num : num -> num -> bool
val gt_num : num -> num -> bool
val ge_num : num -> num -> bool
val compare_num : num -> num -> int
Return -1 , 0 or 1 if the first argument is less than, equal to, or greater than the second argument.
val max_num : num -> num -> num
Return the greater of the two arguments.
val min_num : num -> num -> num
Return the smaller of the two arguments.
=== Coercions with strings ===
val string_of_num : num -> string
Convert a number to a string, using fractional notation.
val approx_num_fix : int -> num -> string
See Num.approx_num_exp .
val approx_num_exp : int -> num -> string
Approximate a number by a decimal. The first argument is the required precision. The second argument is the number to approximate.
Num.approx_num_fix uses decimal notation; the first argument is the number of digits after the decimal point. approx_num_exp uses scien-
tific (exponential) notation; the first argument is the number of digits in the mantissa.
val num_of_string : string -> num
Convert a string to a number.
=== Coercions between numerical types ===
val int_of_num : num -> int
val num_of_int : int -> num
val nat_of_num : num -> Nat.nat
val num_of_nat : Nat.nat -> num
val num_of_big_int : Big_int.big_int -> num
val big_int_of_num : num -> Big_int.big_int
val ratio_of_num : num -> Ratio.ratio
val num_of_ratio : Ratio.ratio -> num
val float_of_num : num -> float
OCamldoc 2012-06-26 Num(3o)