Breaking a fasta formatted file into multiple files containing each gene separately
Hey,
I've been trying to break a massive fasta formatted file into files containing each gene separately. Could anyone help me? I've tried to use the following code but i've recieved errors every time:
Last edited by Corona688; 03-16-2012 at 12:47 PM..
Hi,
I have a file that looks like this (tab deliminited).
MAT1 YKR2 3
MAT1 YMR1 2
MAT1 YFG2 2
MAT2 YLM4 4
MAT2 YHL2 1
BAR1 YKR2 3
BAR1 YFR1 4
BAR1 YMR1 1
What I want to do is break this file down into multiple files. So the result will look like this:
File 1... (2 Replies)
Hi,
I have a code as given below
Set -A _Category="A\
B\
C"
for _cat in ${_Category}
do
sed -e "s:<TABLE_NAME>:${_cat}:g" \
-e "s:<date>:${_dt}:g" \
${_home}/skl/sq1.sql >> ${_dest}/del_${_dt}.sql
fi
... (4 Replies)
Hi.,
My current script extracts only if the date and time are in 3rd and 4th pos.
#!/bin/bash
echo "Enter the file name to extract the timestamp"
read fname
IFILE=$fname
F=$IFILE
IFS="_."
f=($F)
echo "Date ${f} Time ${f}"
How to generalize the script to extract the... (3 Replies)
Hello Friends,
I am trying to implement the following using UNIX. I am getting a sequential file as input which would have two columns, "Name" and "Countries Visited". The "Countries Visisted" field will be multi-valued, each value separated by a space and also the number of values are not... (2 Replies)
I've been trying to write a command-line function to grab a website's MX records and their ip addresses. The code below works with domains that only have one MX record:
function kmx { mx=`host -t MX $1 | awk '{ print $7 }'`;
ip=`host $mx | sed '/IPv6/d;/handled/d' | awk '{ print $4 }'`; ... (8 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)
Dear all,
I have huge txt file with the input files for some setup_code. However for running my setup_code, I require txt files with maximum of 1000 input files
Please help me in suggesting way to break down this big txt file to small txt file of 1000 entries only.
thanks and Greetings,
Emily (12 Replies)
I have the following data set about the snps ID txt file
POS ID
78599583 rs987435
33395779 rs345783
189807684 rs955894
33907909 rs6088791
75664046 rs11180435
218890658 rs17571465
127630276 rs17011450
90919465 rs6919430
and a gene... (7 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)
I have two fasta files as shown below,
File:1
>Contig_1:90600-91187
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGGAATTGATGACGGTC
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG
>Contig_24:26615-28387... (11 Replies)
Discussion started by: dineshkumarsrk
11 Replies
LEARN ABOUT DEBIAN
bp_mask_by_search
BP_MASK_BY_SEARCH(1p) User Contributed Perl Documentation BP_MASK_BY_SEARCH(1p)NAME
mask_by_search - mask sequence(s) based on its alignment results
SYNOPSIS
mask_by_search.pl -f blast genomefile blastfile.bls > maskedgenome.fa
DESCRIPTION
Mask sequence based on significant alignments of another sequence. You need to provide the report file and the entire sequence data which
you want to mask. By default this will assume you have done a TBLASTN (or TFASTY) and try and mask the hit sequence assuming you've
provided the sequence file for the hit database. If you would like to do the reverse and mask the query sequence specify the -t/--type
query flag.
This is going to read in the whole sequence file into memory so for large genomes this may fall over. I'm using DB_File to prevent keeping
everything in memory, one solution is to split the genome into pieces (BEFORE you run the DB search though, you want to use the exact file
you BLASTed with as input to this program).
Below the double dash (--) options are of the form --format=fasta or --format fasta or you can just say -f fasta
By -f/--format I mean either are acceptable options. The =s or =n or =c specify these arguments expect a 'string'
Options:
-f/--format=s Search report format (fasta,blast,axt,hmmer,etc)
-sf/--sformat=s Sequence format (fasta,genbank,embl,swissprot)
--hardmask (booelean) Hard mask the sequence
with the maskchar [default is lowercase mask]
--maskchar=c Character to mask with [default is N], change
to 'X' for protein sequences
-e/--evalue=n Evalue cutoff for HSPs and Hits, only
mask sequence if alignment has specified evalue
or better
-o/--out/
--outfile=file Output file to save the masked sequence to.
-t/--type=s Alignment seq type you want to mask, the
'hit' or the 'query' sequence. [default is 'hit']
--minlen=n Minimum length of an HSP for it to be used
in masking [default 0]
-h/--help See this help information
AUTHOR - Jason Stajich
Jason Stajich, jason-at-bioperl-dot-org.
perl v5.14.2 2012-03-02 BP_MASK_BY_SEARCH(1p)