cut command is not working properly.. its splicing whole file in to 10 frament length lines
Yes.The given cut command is intended to work as you said. You would need to change the start and end character index accordingly. If you need to only match certain lines to extract characters, provide more information.
Hi Everyone,
I am new in the world of UNIX and Shell scripting.
I am working with a sequence file that looks like this:
>contig00001 length=128 numreads=2
aTGTGCTGGgTGGGTGCCTGTTgCCccATGCTCCAGTtCAGGATTtCAGGCAttCTCATG
TCCAGCATTTCTATTTAATCCTGCTGCTGGACTTGGGTGGtCTCAGTCtGGGAAGTGAGC
tGTCTGTG... (8 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)
Hi,
I am trying to remove lines once a string is found till another string is found including the start string and end string. I want to basically grab all the lines starting with color (closing bracket). PS: The line after the closing bracket for color could be anything (currently 'more').... (1 Reply)
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)
Hello,
I have 10 fasta files with sequenced reads information with read sizes from 15 - 35 . I have combined the reads and collapsed in to unique reads and filtered for sizes 18 - 26 bp long unique reads. Now i wanted to count each unique read appearance in all the fasta files and make a table... (5 Replies)
HI,
I have a Complete genome fasta file and I have list of sub sequence regions
in the format as :
4353..5633
6795..9354
1034..14456
I want a script which can mask these region in a single complete genome fasta file with the alphabet N
kindly help (2 Replies)
I would like to take a fasta file formated like
>0001
agttcgaggtcagaatt
>0002
agttcgag
>0003
ggtaacctga
and use command line perl to move the all sample gt 8 in length to a new file. the result would be
>0001
agttcgaggtcagaatt
>0003
ggtaacctga
cat ${sample}.fasta | perl -lane... (2 Replies)
I have to mine the following sequence pattern from a large fasta file namely gene.fasta (contains multiple fasta sequences) along with the flanking sequences of 5 bases at starting position and ending position,
AAGCZ-N16-AAGCZ
Z represents A, C or G (Except T)
N16 represents any of the four... (3 Replies)
Below are my custom period start and end dates based on a calender, these dates are placed in a file, for each period i need to split into three weeks for each period row, example is given below.
Could you please help out to achieve solution through shell script..
File content:
... (2 Replies)
Discussion started by: nani2019
2 Replies
LEARN ABOUT ULTRIX
cut
cut(1) General Commands Manual cut(1)Name
cut - cut out selected fields of each line of a file
Syntax
cut -clist [file1 file2...]
cut -flist [-dchar] [-s] [file1 file2...]
Description
Use the command to cut out columns from a table or fields from each line of a file. The fields as specified by list can be fixed length,
that is, character positions as on a punched card (-c option), or the length can vary from line to line and be marked with a field delim-
iter character like tab (-f option). The command can be used as a filter. If no files are given, the standard input is used.
Use to make horizontal ``cuts'' (by context) through a file, or to put files together in columns. To reorder columns in a table, use and
Options
list Specifies ranges that must be a comma-separated list of integer field numbers in increasing order. With optional - indicates
ranges as in the -o option of nroff/troff for page ranges; for example, 1,4,7; 1-3,8; -5,10 (short for 1-5,10); or 3- (short
for third through last field).
-clist Specifies character positions to be cut out. For example, -c1-72 would pass the first 72 characters of each line.
-flist Specifies the fields to be cut out. For example, -f1,7 copies the first and seventh field only. Lines with no field delim-
iters are passed through intact (useful for table subheadings), unless -s is specified.
-dchar Uses the specified character as the field delimiter. Default is tab. Space or other characters with special meaning to the
shell must be quoted. The -d option is used only in combination with the -f option, according to XPG3 and SVID2/SVID3.
-s Suppresses lines with no delimiter characters. Unless specified, lines with no delimiters are passed through untouched.
Either the -c or -f option must be specified.
Examples
Mapping of user IDs to names:
cut -d: -f1,5 /etc/passwd
To set name to the current login name for the csh shell:
set name=`who am i | cut -f1 -d" "`
To set name to the current login name for the sh, sh5, and ksh shells:
name=`who am i | cut -f1 -d" "`
Diagnostics
"line too long" A line can have no more than 511 characters or fields.
"bad list for c/f option"
Missing -c or -f option or incorrectly specified list. No error occurs if a line has fewer fields than the list calls
for.
"no fields" The list is empty.
See Alsogrep(1), paste(1)cut(1)