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Full Discussion: Extract the part of sequences from a file
Top Forums Shell Programming and Scripting Extract the part of sequences from a file Post 302881033 by rahim42 on Thursday 26th of December 2013 07:25:05 AM
Old 12-26-2013
Extract the part of sequences from a file
I have a text file, input.fasta contains some protein sequences. input.fasta is shown below.

Code:
>P02649
MKVLWAALLVTFLAGCQAKVEQAVETEPEPELRQQTEWQSGQRWELALGRFWDYLRWVQT
LSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVAEETRARLSKELQAAQA
RLGADMEDVCGRLVQYRGEVQAMLGQSTEELRVRLASHLRKLRKRLLRDADDLQKRLAVY
QAGAREGAERGLSAIRERLGPLVEQGRVRAATVGSLAGQPLQERAQAWGERLRARMEEMG
SRTRDRLDEVKEQVAEVRAKLEEQAQQIRLQAEAFQARLKSWFEPLVEDMQRQWAGLVEK
VQAAVGTSAAPVPSDNH
>P17427
MPAVSKGDGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKYVC
KLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDL
ASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQSAALCLLRLYRTSP
DLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVTSA

I would like to extract the parts of the above sequences based on another file ids.txt . It is shown below.
Code:
P02649  3   23
P02649  130 162
P17427  25  27

For example, From the sequence P02649, I need to extract the positions from 3rd character to 23rd character. The output would be
Code:
>P02649:3-23
VLWAALLVTFLAGCQAKVEQA
>P02649:130-162
CGRLVQYRGEVQAMLGQSTEELRVRLASHLRKL
>P17427:25-27
SKE

I tried the following python code.

Code:
#!/usr/bin/python 
import sys 
import socket 
import string 
import random 
import os 
import re 
 
FASTA= sys.argv[1] 
BED= sys.argv[2] 
 
fasta= open(FASTA, 'U') 
fasta_dict= {} 
for line in fasta: 
    line= line.strip() 
    if line == '': 
        continue 
    if line.startswith('>'): 
        seqname= line.lstrip('>') 
        seqname= re.sub('\..*', '', seqname) 
        fasta_dict[seqname]= '' 
    else: 
        fasta_dict[seqname] += line 
fasta.close() 
 
bed= open(BED, 'U') 
for line in bed: 
    line= line.strip().split('\t') 
    outname= line[0] + ':' + line[1] + '-' + line[2] 
    print('>' + outname) 
    s= int(line[1]) 
    e= int(line[2]) 
    print(fasta_dict[line[0]][s:e]) 
bed.close() 
sys.exit()

But I got the error like this

Code:
Traceback (most recent call last):
  File "domainseq.py", line 29, in <module>
    outname= line[0] + ':' + line[1] + '-' + line[2]
IndexError: list index out of range

your help would be appreciated
 

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LEARN ABOUT CENTOS

locale::codes::langfam

Locale::Codes::LangFam(3)				User Contributed Perl Documentation				 Locale::Codes::LangFam(3)

NAME

       Locale::Codes::LangFam - standard codes for language extension identification

SYNOPSIS

	  use Locale::Codes::LangFam;

	  $lext = code2langfam('apa');		       # $lext gets 'Apache languages'
	  $code = langfam2code('Apache languages');    # $code gets 'apa'

	  @codes   = all_langfam_codes();
	  @names   = all_langfam_names();

DESCRIPTION

       The "Locale::Codes::LangFam" module provides access to standard codes used for identifying language families, such as those as defined in
       ISO 639-5.

       Most of the routines take an optional additional argument which specifies the code set to use. If not specified, the default ISO 639-5
       language family codes will be used.

SUPPORTED CODE SETS

       There are several different code sets you can use for identifying language families. A code set may be specified using either a name, or a
       constant that is automatically exported by this module.

       For example, the two are equivalent:

	  $lext = code2langfam('apa','alpha');
	  $lext = code2langfam('apa',LOCALE_LANGFAM_ALPHA);

       The codesets currently supported are:

       alpha
	   This is the set of three-letter (lowercase) codes from ISO 639-5 such as 'apa' for Apache languages.

	   This is the default code set.

ROUTINES

       code2langfam ( CODE [,CODESET] )
       langfam2code ( NAME [,CODESET] )
       langfam_code2code ( CODE ,CODESET ,CODESET2 )
       all_langfam_codes ( [CODESET] )
       all_langfam_names ( [CODESET] )
       Locale::Codes::LangFam::rename_langfam  ( CODE ,NEW_NAME [,CODESET] )
       Locale::Codes::LangFam::add_langfam  ( CODE ,NAME [,CODESET] )
       Locale::Codes::LangFam::delete_langfam  ( CODE [,CODESET] )
       Locale::Codes::LangFam::add_langfam_alias  ( NAME ,NEW_NAME )
       Locale::Codes::LangFam::delete_langfam_alias  ( NAME )
       Locale::Codes::LangFam::rename_langfam_code  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::LangFam::add_langfam_code_alias  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::LangFam::delete_langfam_code_alias  ( CODE [,CODESET] )
	   These routines are all documented in the Locale::Codes::API man page.

SEE ALSO

       Locale::Codes
	   The Locale-Codes distribution.

       Locale::Codes::API
	   The list of functions supported by this module.

       http://www.loc.gov/standards/iso639-5/id.php
	   ISO 639-5 .

AUTHOR

       See Locale::Codes for full author history.

       Currently maintained by Sullivan Beck (sbeck@cpan.org).

COPYRIGHT

	  Copyright (c) 2011-2013 Sullivan Beck

       This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

perl v5.16.3							    2013-02-27						 Locale::Codes::LangFam(3)
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