Sponsored Content
Top Forums Shell Programming and Scripting Selecting sequences based on scores Post 302789603 by ahamed101 on Thursday 4th of April 2013 01:55:49 AM
Old 04-04-2013
Try this
Code:
awk 'NR==FNR{q=$1;getline;s=d=0;for(i=1;i<=NF;i++){if($i<20&&!d){d=1}s+=$i}a=s/NF;if(NF>=28&&!d&&a>=35){z[q]++}}
z[$1]{print;getline;print}' infile2 infile1

--ahamed
This User Gave Thanks to ahamed101 For This Post:
 

9 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

How to assign scores to rows based on column values

Hi, I'm trying to assign a score to each row which will allow me to identify which rows differ. In the example file below, I've used "," to indicate column separators (my actual file has tab separators). In this example, I'd like to identify that row 1 and row 5 are the same, and row 2 and row... (4 Replies)
Discussion started by: auburn
4 Replies

2. Shell Programming and Scripting

Trimming sequences based on specific pattern

My files look like this And I need to cut the sequences at the last "A" found in the following 'pattern' -highlighted for easier identification, the pattern is the actual file is not highlighted. The expected result should look like this Thus, all the sequences would end with AGCCCTA... (2 Replies)
Discussion started by: Xterra
2 Replies

3. Shell Programming and Scripting

Deleting sequences based on character frequency

This is what I would like to accomplish, I have an input file (file A) that consist of thousands of sequence elements with the same number of characters (length), each headed by a free text header starting with the chevron ‘>' character followed by the ID (all different IDs with different lenghts)... (9 Replies)
Discussion started by: Xterra
9 Replies

4. Shell Programming and Scripting

Trimming sequences based on Reference

My file looks something like this Wnat I need is to look for the Reference sequence (">Reference1") and based on the length of that sequence trim all the entries in that file. So, the rersulting file will contain all sequences with the same length, like this Thus, all sequences will keep... (5 Replies)
Discussion started by: Xterra
5 Replies

5. Shell Programming and Scripting

Extract sequences based on the list

Hi, I have a file with more than 28000 records and it looks like below.. >mm10_refflat_ABCD range=chr1:1234567-2345678 tgtgcacactacacatgactagtacatgactagac....so on >mm10_refflat_BCD range=chr1:3234567-4545678... tgtgcacactacacatgactagtatgtgcacactacacatgactagta . . . . . so on ... (2 Replies)
Discussion started by: Diya123
2 Replies

6. Shell Programming and Scripting

Randomly selecting sequences and generating specific output files

I have two files containing hundreds of different sequences with the same Identifiers (ID-001, ID-002, etc.,), something like this: Infile1: ID-001 ATGGGAGCGGGGGCGTCTGCCTTGAGGGGAGAGAAGCTAGATACA ID-002 ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACA ID-003... (18 Replies)
Discussion started by: Xterra
18 Replies

7. Shell Programming and Scripting

Eliminating sequences based on Distances

I have to remove sequences from a file based on the distance value. I am attaching the file containing the distances (Distance.xls) The second file looks something like this: Sequences.txt >Sample1 Freq 59 ggatatgatgatgaactggt >Sample1 Freq 54 ggatatgatgttgaactggt >Sample1 Freq 44... (2 Replies)
Discussion started by: Xterra
2 Replies

8. Shell Programming and Scripting

Create combinations based on scores

Hi experts, I have a score matrix like below, where the 3rd column ( 1 max, 0 min) says how close the 2nd column variable is to the 1st column variable a b 0.3 a c 0.87 a d 0.75 b x 0.67 b y 0.98 b z 0.24 c ... (4 Replies)
Discussion started by: jianp83
4 Replies

9. Shell Programming and Scripting

Outputting sequences based on length with sed

I have this file: >ID1 AA >ID2 TTTTTT >ID-3 AAAAAAAAA >ID4 TTTTTTGGAGATCAGTAGCAGATGACAG-GGGGG-TGCACCCC Add I am trying to use this script to output sequences longer than 15 characters: sed -r '/^>/N;{/^.{,15}$/d}' The desire output would be this: >ID4... (8 Replies)
Discussion started by: Xterra
8 Replies
sort(1) 							   User Commands							   sort(1)

NAME
sort - sort, merge, or sequence check text files SYNOPSIS
/usr/bin/sort [-bcdfimMnru] [-k keydef] [-o output] [-S kmem] [-t char] [-T directory] [ -y [kmem]] [-z recsz] [ +pos1 [-pos2]] [file...] /usr/xpg4/bin/sort [-bcdfimMnru] [-k keydef] [-o output] [-S kmem] [-t char] [-T directory] [ -y [kmem]] [-z recsz] [ +pos1 [-pos2]] [file...] DESCRIPTION
The sort command sorts lines of all the named files together and writes the result on the standard output. Comparisons are based on one or more sort keys extracted from each line of input. By default, there is one sort key, the entire input line. Lines are ordered according to the collating sequence of the current locale. OPTIONS
The following options alter the default behavior: /usr/bin/sort -c Checks that the single input file is ordered as specified by the arguments and the collating sequence of the current locale. The exit code is set and no output is produced unless the file is out of sort. /usr/xpg4/bin/sort -c Same as /usr/bin/sort except no output is produced under any circumstances. -m Merges only. The input files are assumed to be already sorted. -o output Specifies the name of an output file to be used instead of the standard output. This file can be the same as one of the input files. -S kmem Specifies the maximum amount of swap-based memory used for sorting, in kilobytes (the default unit). kmem can also be spec- ified directly as a number of bytes (b), kilobytes (k), megabytes (m), gigabytes (g), or terabytes (t); or as a percentage (%) of the installed physical memory. -T directory Specifies the directory in which to place temporary files. -u Unique: suppresses all but one in each set of lines having equal keys. If used with the -c option, checks that there are no lines with duplicate keys in addition to checking that the input file is sorted. -y kmem (obsolete). This option was used to specify the amount of main memory initially used by sort. Its functionality is not appropriate for a virtual memory system; memory usage for sort is now specified using the -S option. -z recsz (obsolete). This option was used to prevent abnormal termination when lines longer than the system-dependent default buffer size are encountered. Because sort automatically allocates buffers large enough to hold the longest line, this option has no effect. Ordering Options The default sort order depends on the value of LC_COLLATE. If LC_COLLATE is set to C, sorting will be in ASCII order. If LC_COLLATE is set to en_US, sorting is case insensitive except when the two strings are otherwise equal and one has an uppercase letter earlier than the other. Other locales will have other sort orders. The following options override the default ordering rules. When ordering options appear independent of any key field specifications, the requested field ordering rules are applied globally to all sort keys. When attached to a specific key (see Sort Key Options), the specified ordering options override all global ordering options for that key. In the obsolescent forms, if one or more of these options follows a +pos1 option, it will affect only the key field specified by that preceding option. -d ``Dictionary'' order: only letters, digits, and blanks (spaces and tabs) are significant in comparisons. -f Folds lower-case letters into upper case. -i Ignores non-printable characters. -M Compares as months. The first three non-blank characters of the field are folded to upper case and compared. For example, in English the sorting order is "JAN" < "FEB" < ... < "DEC". Invalid fields compare low to "JAN". The -M option implies the -b option (see below). -n Restricts the sort key to an initial numeric string, consisting of optional blank characters, optional minus sign, and zero or more digits with an optional radix character and thousands separators (as defined in the current locale), which will be sorted by arithmetic value. An empty digit string is treated as zero. Leading zeros and signs on zeros do not affect ordering. -r Reverses the sense of comparisons. Field Separator Options The treatment of field separators can be altered using the following options: -b Ignores leading blank characters when determining the starting and ending positions of a restricted sort key. If the -b option is specified before the first sort key option, it is applied to all sort key options. Otherwise, the -b option can be attached independently to each -k field_start, field_end, or +pos1 or -pos2 option-argument (see below). -t char Use char as the field separator character. char is not considered to be part of a field (although it can be included in a sort key). Each occurrence of char is significant (for example, <char><char> delimits an empty field). If -t is not speci- fied, blank characters are used as default field separators; each maximal non-empty sequence of blank characters that fol- lows a non-blank character is a field separator. Sort Key Options Sort keys can be specified using the options: -k keydef The keydef argument is a restricted sort key field definition. The format of this definition is: -k field_start [type] [,field_end [type] ] where: field_start and field_end define a key field restricted to a portion of the line. type is a modifier from the list of characters bdfiMnr. The b modifier behaves like the -b option, but applies only to the field_start or field_end to which it is attached and characters within a field are counted from the first non-blank character in the field. (This applies separately to first_character and last_character.) The other modifiers behave like the corresponding options, but apply only to the key field to which they are attached. They have this effect if specified with field_start, field_end or both. If any modifier is attached to a field_start or to a field_end, no option applies to either. When there are multiple key fields, later keys are compared only after all earlier keys compare equal. Except when the -u option is specified, lines that otherwise compare equal are ordered as if none of the options -d, -f, -i, -n or -k were present (but with -r still in effect, if it was specified) and with all bytes in the lines significant to the comparison. The notation: -k field_start[type][,field_end[type]] defines a key field that begins at field_start and ends at field_end inclusive, unless field_start falls beyond the end of the line or after field_end, in which case the key field is empty. A missing field_end means the last character of the line. A field comprises a maximal sequence of non-separating characters and, in the absence of option -t, any preceding field separator. The field_start portion of the keydef option-argument has the form: field_number[.first_character] Fields and characters within fields are numbered starting with 1. field_number and first_character, interpreted as positive decimal integers, specify the first character to be used as part of a sort key. If .first_character is omitted, it refers to the first character of the field. The field_end portion of the keydef option-argument has the form: field_number[.last_character] The field_number is as described above for field_start. last_character, interpreted as a non-negative decimal integer, specifies the last character to be used as part of the sort key. If last_character evaluates to zero or .last_character is omitted, it refers to the last character of the field specified by field_number. If the -b option or b type modifier is in effect, characters within a field are counted from the first non-blank character in the field. (This applies separately to first_character and last_character.) [+pos1 [-pos2]] (obsolete). Provide functionality equivalent to the -kkeydef option. pos1 and pos2 each have the form m.n optionally followed by one or more of the flags bdfiMnr. A starting position specified by +m.n is interpreted to mean the n+1st character in the m+1st field. A missing .n means .0, indicating the first charac- ter of the m+1st field. If the b flag is in effect n is counted from the first non-blank in the m+1st field; +m.0b refers to the first non-blank character in the m+1st field. A last position specified by -m.n is interpreted to mean the nth character (including separators) after the last character of the mth field. A missing .n means .0, indicating the last character of the mth field. If the b flag is in effect n is counted from the last leading blank in the m+1st field; -m.1b refers to the first non-blank in the m+1st field. The fully specified +pos1 -pos2 form with type modifiers T and U: +w.xT -y.zU is equivalent to: undefined (z==0 & U contains b & -t is present) -k w+1.x+1T,y.0U (z==0 otherwise) -k w+1.x+1T,y+1.zU (z > 0) Implementations support at least nine occurrences of the sort keys (the -k option and obsolescent +pos1 and -pos2) which are significant in command line order. If no sort key is specified, a default sort key of the entire line is used. OPERANDS
The following operand is supported: file A path name of a file to be sorted, merged or checked. If no file operands are specified, or if a file operand is -, the standard input will be used. USAGE
See largefile(5) for the description of the behavior of sort when encountering files greater than or equal to 2 Gbyte ( 2**31 bytes). EXAMPLES
In the following examples, first the preferred and then the obsolete way of specifying sort keys are given as an aid to understanding the relationship between the two forms. Example 1: Sorting with the second field as a sort key Either of the following commands sorts the contents of infile with the second field as the sort key: example% sort -k 2,2 infile example% sort +1 -2 infile Example 2: Sorting in reverse order Either of the following commands sorts, in reverse order, the contents of infile1 and infile2, placing the output in outfile and using the second character of the second field as the sort key (assuming that the first character of the second field is the field separator): example% sort -r -o outfile -k 2.2,2.2 infile1 infile2 example% sort -r -o outfile +1.1 -1.2 infile1 infile2 Example 3: Sorting using a specified character in one of the files Either of the following commands sorts the contents of infile1 and infile2 using the second non-blank character of the second field as the sort key: example% sort -k 2.2b,2.2b infile1 infile2 example% sort +1.1b -1.2b infile1 infile2 Example 4: Sorting by numeric user ID Either of the following commands prints the passwd(4) file (user database) sorted by the numeric user ID (the third colon-separated field): example% sort -t : -k 3,3n /etc/passwd example% sort -t : +2 -3n /etc/passwd Example 5: Printing sorted lines excluding lines that duplicate a field Either of the following commands prints the lines of the already sorted file infile, suppressing all but one occurrence of lines having the same third field: example% sort -um -k 3.1,3.0 infile example% sort -um +2.0 -3.0 infile Example 6: Sorting by host IP address Either of the following commands prints the hosts(4) file (IPv4 hosts database), sorted by the numeric IP address (the first four numeric fields): example$ sort -t . -k 1,1n -k 2,2n -k 3,3n -k 4,4n /etc/hosts example$ sort -t . +0 -1n +1 -2n +2 -3n +3 -4n /etc/hosts Since '.' is both the field delimiter and, in many locales, the decimal separator, failure to specify both ends of the field will lead to results where the second field is interpreted as a fractional portion of the first, and so forth. ENVIRONMENT VARIABLES
See environ(5) for descriptions of the following environment variables that affect the execution of sort: LANG, LC_ALL, LC_COLLATE, LC_MES- SAGES, and NLSPATH. LC_CTYPE Determine the locale for the interpretation of sequences of bytes of text data as characters (for example, single- versus multi-byte characters in arguments and input files) and the behavior of character classification for the -b, -d, -f, -i and -n options. LC_NUMERIC Determine the locale for the definition of the radix character and thousands separator for the -n option. EXIT STATUS
The following exit values are returned: 0 All input files were output successfully, or -c was specified and the input file was correctly sorted. 1 Under the -c option, the file was not ordered as specified, or if the -c and -u options were both specified, two input lines were found with equal keys. >1 An error occurred. FILES
/var/tmp/stm??? temporary files ATTRIBUTES
See attributes(5) for descriptions of the following attributes: /usr/bin/sort +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWesu | +-----------------------------+-----------------------------+ |CSI |Enabled | +-----------------------------+-----------------------------+ /usr/xpg4/bin/sort +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWxcu4 | +-----------------------------+-----------------------------+ |CSI |Enabled | +-----------------------------+-----------------------------+ |Interface Stability |Standard | +-----------------------------+-----------------------------+ SEE ALSO
comm(1), join(1), uniq(1), nl_langinfo(3C), strftime(3C), hosts(4), passwd(4), attributes(5), environ(5), largefile(5), standards(5) DIAGNOSTICS
Comments and exits with non-zero status for various trouble conditions (for example, when input lines are too long), and for disorders dis- covered under the -c option. NOTES
When the last line of an input file is missing a new-line character, sort appends one, prints a warning message, and continues. sort does not guarantee preservation of relative line ordering on equal keys. One can tune sort performance for a specific scenario using the -S option. However, one should note in particular that sort has greater knowledge of how to use a finite amount of memory for sorting than the virtual memory system. Thus, a sort invoked to request an extremely large amount of memory via the -S option could perform extremely poorly. As noted, certain of the field modifiers (such as -M and -d) cause the interpretation of input data to be done with reference to locale- specific settings. The results of this interpretation can be unexpected if one's expectations are not aligned with the conventions estab- lished by the locale. In the case of the month keys, sort does not attempt to compensate for "approximate" month abbreviations. The precise month abbreviations from nl_langinfo(3C) or strftime(3C) are the only ones recognized. For printable or dictionary order, if these concepts are not well-defined by the locale, an empty sort key may be the result, leading to the next key being the significant one for determining the appropriate ordering. SunOS 5.10 19 Nov 2001 sort(1)
All times are GMT -4. The time now is 07:18 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy