01-03-2014
Append file name to fasta file headers in Linux
How do we append the file name to fasta file headers in multiple fasta-files in Linux?
Last edited by Mauve; 01-05-2014 at 02:36 PM..
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Hi ,
I have a typical situation. I have 4 files and with different headers (number of headers is varible ).
I need to make such a merged file which will have headers combined from all files (comman coluns should appear once only).
For example -
File 1
H1|H2|H3|H4
11|12|13|14
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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.
input.fasta:
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GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT
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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
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RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
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I have the following script:
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cccctacgacggcattggtaatggctcagctgctccggatcccgcaagccatcttggatatgagggttcgtcggcctcttcagccaagg-cccccagcagaacatccagctgatcg
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>P39PT-1224_Freq_900
cccctacgacggcattggtaatggctcccgcaagccatctctcttcagccaagg
>P39PT-784_Freq_2
cccctacgacggcattggtaatggcacccgcaagccatctctcttccccccccc
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I have two fasta files as shown below,
File:1
>Contig_1:90600-91187
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGGAATTGATGACGGTC
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG
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I have 5 sequences in a fasta file namely gene1.fasta as follows,
gene1.fasta
>1256
ATGTAGC
>GEP
TAGAG
>GTY578
ATGCATA
>67_iga
ATGCTGA
>90_ld
ATGCTG
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list.txt
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LEARN ABOUT DEBIAN
kalign
KALIGN(1) Kalign User Manual KALIGN(1)
NAME
kalign - performs multiple alignment of biological sequences.
SYNOPSIS
kalign [infile.fasta] [outfile.fasta] [Options]
kalign [-i infile.fasta] [-o outfile.fasta] [Options]
kalign [< infile.fasta] [> outfile.fasta] [Options]
DESCRIPTION
Kalign is a command line tool to perform multiple alignment of biological sequences. It employs the Muth?Manber string-matching algorithm,
to improve both the accuracy and speed of the alignment. It uses global, progressive alignment approach, enriched by employing an
approximate string-matching algorithm to calculate sequence distances and by incorporating local matches into the otherwise global
alignment.
OPTIONS
-s -gpo -gapopen -gap_open x
Gap open penalty .
-e -gpe -gap_ext -gapextension x
Gap extension penalty.
-t -tgpe -terminal_gap_extension_penalty x
Terminal gap penalties.
-m -bonus -matrix_bonus x
A constant added to the substitution matrix.
-c -sort <input, tree, gaps.>
The order in which the sequences appear in the output alignment.
-g -feature
Selects feature mode and specifies which features are to be used: e.g. all, maxplp, STRUCT, PFAM-A?
-same_feature_score
Score for aligning same features.
-diff_feature_score
Penalty for aligning different features.
-d -distance <wu, pair>
Distance method
-b -tree -guide-tree <nj, upgma>
Guide tree method.
-z -zcutoff
Parameter used in the wu-manber based distance calculation.
-i -in -input
Name of the input file.
-o -out -output
Name of the output file.
-a -gap_inc
Increases gap penalties depending on the number of existing gaps.
-f -format <fasta, msf, aln, clu, macsim>
The output format.
-q -quiet
Print nothing to STDERR. Read nothing from STDIN.
REFERENCES
o Timo Lassmann and Erik L.L. Sonnhammer (2005) Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics
6:298
o Timo Lassmann, Oliver Frings and Erik L. L. Sonnhammer (2009) Kalign2: high-performance multiple alignment of protein and nucleotide
sequences allowing external features. Nucleic Acid Research 3:858?865.
AUTHORS
Timo Lassmann <timolassmann@gmail.com>
Upstream author of Kalign.
Charles Plessy <plessy@debian.org>
Wrote the manpage.
COPYRIGHT
Copyright (C) 2004, 2005, 2006, 2007, 2008 Timo Lassmann
Kalign is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the
Free Software Foundation.
This manual page was written by Charles Plessy <plessy@debian.org> for the Debian(TM) system (but may be used by others). Permission is
granted to copy, distribute and/or modify this document under the same terms as kalign itself.
On Debian systems, the complete text of the GNU General Public License version 2 can be found in /usr/share/common-licenses/GPL-2.
kalign 2.04 February 25, 2009 KALIGN(1)