Sponsored Content
Top Forums UNIX for Beginners Questions & Answers How to count the length of fasta sequences? Post 303033623 by dineshkumarsrk on Tuesday 9th of April 2019 09:04:53 AM
Old 04-09-2019
I have a multi fasta sequences in unique.fasta as given below,
Code:
>seq1
ATGCTA
>seq2
GCTAGTT
>seq3
TAGC

I need to count the length of following header's listed in id.txt as given below,
Code:
seq1
seq2

And the results(length) to be printed in csv file as shown below,
Code:
seq1   6
seq2   7

Moderator's Comments:
Mod Comment Changed QUOTE tags to CODE tags for sample Input_file.

Last edited by RavinderSingh13; 04-09-2019 at 10:16 AM..
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Extract length wise sequences from fastq file

I have a fastq file from small RNA sequencing with sequence lengths between 15 - 30. I wanted to filter sequence lengths between 21-25 and write to another fastq file. how can i do that? (4 Replies)
Discussion started by: empyrean
4 Replies

2. Shell Programming and Scripting

Shell script for changing the accession number of DNA sequences in a FASTA file

Hi, I am having a file of dna sequences in fasta format which look like this: >admin_1_45 atatagcaga >admin_1_46 atatagcagaatatatat with many such thousands of sequences in a single file. I want to the replace the accession Id "admin_1_45" similarly in following sequences to... (5 Replies)
Discussion started by: margarita
5 Replies

3. Shell Programming and Scripting

Extract sequences from a FASTA file based on another file

I have two files. File1 is shown below. >153L:B|PDBID|CHAIN|SEQUENCE RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM DIGTTHDDYANDVVARAQYYKQHGY >16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
Discussion started by: nelsonfrans
7 Replies

4. Shell Programming and Scripting

Count and search by sequence in multiple fasta file

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)
Discussion started by: empyrean
5 Replies

5. Shell Programming and Scripting

Shorten header of protein sequences in fasta file

I have a fasta file as follows >sp|O15090|FABP4_HUMAN Fatty acid-binding protein, adipocyte OS=Homo sapiens GN=FABP4 PE=1 SV=3 MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKN TEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVM KGVTSTRVYERA >sp|L18484|AP2A2_RAT AP-2... (3 Replies)
Discussion started by: alexypaul
3 Replies

6. UNIX for Dummies Questions & Answers

Select distinct sequences from fasta file and list

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)
Discussion started by: Marion MPI
6 Replies

7. Shell Programming and Scripting

Getting unique sequences from multiple fasta file

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

8. Shell Programming and Scripting

Outputting sequences based on length with sed

I have this file: >ID1 AA >ID2 TTTTTT >ID-3 AAAAAAAAA >ID4 TTTTTTGGAGATCAGTAGCAGATGACAG-GGGGG-TGCACCCC Add I am trying to use this script to output sequences longer than 15 characters: sed -r '/^>/N;{/^.{,15}$/d}' The desire output would be this: >ID4... (8 Replies)
Discussion started by: Xterra
8 Replies

9. Shell Programming and Scripting

Shorten header of protein sequences in fasta file to only organism name

I have a fasta file as follows >sp|Q8WWQ8|STAB2_HUMAN Stabilin-2 OS=Homo sapiens OX=9606 GN=STAB2 PE=1 SV=3 MMLQHLVIFCLGLVVQNFCSPAETTGQARRCDRKSLLTIRTECRSCALNLGVKCPDGYTM ITSGSVGVRDCRYTFEVRTYSLSLPGCRHICRKDYLQPRCCPGRWGPDCIECPGGAGSPC NGRGSCAEGMEGNGTCSCQEGFGGTACETCADDNLFGPSCSSVCNCVHGVCNSGLDGDGT... (3 Replies)
Discussion started by: jerrild
3 Replies

10. UNIX for Beginners Questions & Answers

How to add specific bases at the beginning and ending of all the fasta sequences?

Hi, I have to add 7 bases of specific nucleotide at the beginning and ending of all the fasta sequences of a file. For example, I have a multi fasta file namely test.fasta as given below test.fasta >TalAA18_Xoo_CIAT_NZ_CP033194.1:_2936369-2939570:+1... (1 Reply)
Discussion started by: dineshkumarsrk
1 Replies
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)
All times are GMT -4. The time now is 11:16 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy