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 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)