Hello,
A bioperl problem I thought could be done with awk: convert the fasta format (Note: the length of each row is not the same for each entry as they were combined from different files!) to tabular format.
i.e. each row has two columns: the first one is the header for the sequence name and description, the second column is the DNA sequence. This is quite common in bioinformatics daily task.
I am aware bioperl is the right tool to do the job, but I am trying to level up my awk when I read the RS variable. Not sure how to handle this situation for the RS and the FS variables.
Thanks a lot!
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)
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)
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
Please provide script/commands to convert text file to HTML tabular format.
No need of styles and colours, just output and a heading in table is required.
Output file will be send via email and will be seen from outlook.
(script required without using awk).
output file content: (sar... (7 Replies)
Hi
How can I extract sequences from a fasta file with respect a certain criteria? The beginning of my file (containing in total more than 1000 sequences) looks like this:
>H8V34IS02I59VP
SDACNDLTIALLQIAREVRVCNPTFSFRWHPQVKDEVMRECFDCIRQGLG
YPSMRNDPILIANCMNWHGHPLEEARQWVHQACMSPCPSTKHGFQPFRMA... (6 Replies)
I have the following script:
awk 'FNR==NR{s+=$3;next;} { print $1 , $2, 100*$3/s }'
and the following file:
>P39PT-1224 Freq 900
cccctacgacggcattggtaatggctcagctgctccggatcccgcaagccatcttggatatgagggttcgtcggcctcttcagccaagg-cccccagcagaacatccagctgatcg
>P39PT-784 Freq 2... (2 Replies)
I would like to extract all entries containing the following patterns: ccccta & ccccccccc from the following infile:
>P39PT-1224_Freq_900
cccctacgacggcattggtaatggctcccgcaagccatctctcttcagccaagg
>P39PT-784_Freq_2
cccctacgacggcattggtaatggcacccgcaagccatctctcttccccccccc
>P39PT-678_Freq_5... (4 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)
Discussion started by: Ibk
3 Replies
LEARN ABOUT DEBIAN
bp_search2alnblocks
BP_SEARCH2ALNBLOCKS(1p) User Contributed Perl Documentation BP_SEARCH2ALNBLOCKS(1p)NAME
search2alnblocks - Turn SearchIO parseable reports(s) into a set of aligned blocks
SYNOPSIS
search2alnblocks --minid PERCENTID --minlen LEN --minevalue EVALUE file1.
blast file2.blast ...> out.fas
DESCRIPTION
This script will parse and filter BLAST (or other formats Bio::SearchIO can parse) output and format the alignment as blocks of alignments
based on the HSPs. Note this can only work if the input file parsed contains the necessary.
Typically this can be used to turn BLAST output into a FASTA alignment format for input into the QRNA comparative gene finder for RNA genes
(E.Rivas).
OPTIONS --maxevalue Maximum E-value for an HSP
--minevalue Minimum E-value for an HSP
--minlen Minimum length of an HSP [default 0]
--maxid Maximum Percent Id [default 100]
(to help remove sequences which are really close)
--minid Minimum Percent Identity for an HSP [default 0]
-i/--input An optional input filename (expects input on STDIN by default)
-o/--output An optional output filename (exports to STDOUT by default)
-f/--format Specify a different Search Alignment format-
{fasta, axt, waba, blast, blastxml} are all permitted
although the format must have actual alignment
sequence for this script to work
See L<Bio::SearchIO> for more information.
-of/--outformat Output format for the alignment blocks, anything
L<Bio::AlignIO> supports.
-v/--verbose Turn on debugging
AUTHOR - Jason Stajich
Jason Stajich, jason-at-bioperl-dot-org.
perl v5.14.2 2012-03-02 BP_SEARCH2ALNBLOCKS(1p)