06-13-2019
That's exactly what I meant!
Thanks RudiC!
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Hi, I have two files where 1 contains data and the other contains strings eg
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-0.00000 0.00000 0.00000
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T T T
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I would like to extract the sequences larger than 10 bases but shorter than 18 along with the identifier from a FASTA file that looks like this:
> Seq I
ACGACTAGACGATAGACGATAGA
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ACGATACGAT
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I have a fasta file that looks like this:
>Noname
ACCAAAATAATTCATGATATACTCAGATCCATCTGAGGGTTTCACCACTTGTAGAGCTAT
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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:
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Hi All,
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10. Shell Programming and Scripting
Input File:
>Seq1
ASDADAFASFASFADGSDGFSDFSDFSDFSDFSDFSDFSDFSDFSDFSDFSD
>Seq2
SDASDAQEQWEQeqAdfaasd
>Seq3
ASDSALGHIUDFJANCAGPATHLACJHPAUTYNJKG
......
Desired Output File
>Seq1
ASDADAFASF
ASFADGSDGF
SDFSDFSDFS
DFSDFSDFSD
FSDFSDFSDF
SD
>Seq2 (4 Replies)
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LEARN ABOUT DEBIAN
pynast
VERSION:(1) User Commands VERSION:(1)
NAME
PyNAST - alignment of short DNA sequences
SYNOPSIS
pynast [options] {-i input_fp -t template_fp}
DESCRIPTION
[] indicates optional input (order unimportant) {} indicates required input (order unimportant)
Example usage:
pynast -i my_input.fasta -t my_template.fasta
OPTIONS
--version
show program's version number and exit
-h, --help
show this help message and exit
-t TEMPLATE_FP, --template_fp=TEMPLATE_FP
path to template alignment file [REQUIRED]
-i INPUT_FP, --input_fp=INPUT_FP
path to input fasta file [REQUIRED]
-v, --verbose
Print status and other information during execution [default: False]
-p MIN_PCT_ID, --min_pct_id=MIN_PCT_ID
minimum percent sequence identity to consider a sequence a match [default: 75.0]
-l MIN_LEN, --min_len=MIN_LEN
minimum sequence length to include in NAST alignment [default: 1000]
-m PAIRWISE_ALIGNMENT_METHOD, --pairwise_alignment_method=PAIRWISE_ALIGNMENT_METHOD
method for performing pairwise alignment [default: uclust]
-a FASTA_OUT_FP, --fasta_out_fp=FASTA_OUT_FP
path to store resulting alignment file [default: derived from input filepath]
-g LOG_FP, --log_fp=LOG_FP
path to store log file [default: derived from input filepath]
-f FAILURE_FP, --failure_fp=FAILURE_FP
path to store file of seqs which fail to align [default: derived from input filepath]
-e MAX_E_VALUE, --max_e_value=MAX_E_VALUE
Depreciated. Will be removed in PyNAST 1.2
-d BLAST_DB, --blast_db=BLAST_DB
Depreciated. Will be removed in PyNAST 1.2
SEE ALSO
http://pynast.sourceforge.net
Version: pynast 1.1 August 2011 VERSION:(1)