04-04-2013
Build an array with only elements of those records in file 2 that have those criteria. Then use that array to print the corresponding records in file 1,
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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)
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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
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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)
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4. Shell Programming and Scripting
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
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5. Shell Programming and Scripting
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
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6. Shell Programming and Scripting
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)
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7. Shell Programming and Scripting
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
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8. Shell Programming and Scripting
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
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9. Shell Programming and Scripting
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
LEARN ABOUT DEBIAN
recsel
RECSEL(1) User Commands RECSEL(1)
NAME
recsel - print records from a recfile
SYNOPSIS
recsel [OPTION]... [-t TYPE] [-n INDEXES | -e RECORD_EXPR | -q EXPR | -m NUM] [-c | (-p|-P) FIELD_EXPR] [FILE]...
DESCRIPTION
Select and print rec data.
-d, --include-descriptors
print record descriptors along with the matched records.
-C, --collapse
do not section the result in records with newlines.
-S, --sort=FIELD
sort the output by the specified field.
-U, --uniq
remove duplicated fields in the output records.
-s, --password=STR
decrypt confidential fields with the given password.
--help print a help message and exit.
--version
show version and exit.
Record selection options:
-i, --case-insensitive
make strings case-insensitive in selection expressions.
-t, --type=TYPE
operate on records of the specified type only.
-e, --expression=EXPR
selection expression.
-q, --quick=STR
select records with fields containing a string.
-n, --number=NUM,...
select specific records by position, with ranges.
-R, --random=NUM
select a given number of random records.
Output options:
-p, --print=FIELDS
comma-separated list of fields to print for each matching record.
-P, --print-values=FIELDS
as -p, but print only the values of the selected fields.
-R, --print-row=FIELDS
as -P, but separate the values with spaces instead of newlines.
-c, --count
print a count of the matching records instead of the records themselves.
Special options:
--print-sexps
print the data in sexps instead of rec format.
AUTHOR
Written by Jose E. Marchesi.
REPORTING BUGS
Report bugs to: bug-recutils@gnu.org
GNU recutils home page: <http://www.gnu.org/software/recutils/>
General help using GNU software: <http://www.gnu.org/gethelp/>
COPYRIGHT
Copyright (C) 2010, 2011, 2012 Jose E. Marchesi. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.
SEE ALSO
The full documentation for recsel is maintained as a Texinfo manual. If the info and recsel programs are properly installed at your site,
the command
info recsel
should give you access to the complete manual.
recsel 1.4.93 January 2012 RECSEL(1)