[python项目一]查找输出fasta序列的gap的起始终止等信息

一、需要实现的程序内容及输出：

对于输入的fasta序列，编写程序查找里面N的起始，终止位置等信息，如下面的染色体test.fa序列为例：

>1 dna_sm:chromosome chromosome:UMD3.1:1:1:158337067:1 REF
aaattagacactgaagagacttggaaagagaggaagtcaaataacaaagaagaggaaacc
aaaagggcctatagaccttgagtattctcaaggtggaacaagaaactatctgaaattgaa
ccgacccccacgctgcccacaacagctccagagaaattcctagatatatttttactacta
tcataaAAAAAatgattgagtttattttgtatttttaatattgtatttttgagagtgtat
cttctctacttcactctgtgaatctctaggtgttctgggctgtggagaacacttagggaa
>2
ctgattactggctagatcagtctctccccttttgtttgcccttcttctcctcctggtcac
tccaaaacttgagaacaccaggaaactcctgactccaggaacattaatcaacaagagctc
atccaaaagcctccatacctacacggaaaccaagctccatccaagagccaacaagttcca
NNNTCTTTTGACTCTCCCTTTTCTCTCCCATGTCAGCTCTTTCTCCTCCCTCCCCCTTCT
gatcaagacataccatgctaattctccaacaacataggaacatagccctgaacattaaaa
tacaggctgcccaacgtcatgtcaaacccatagatgccccaaaactcactcctggacact
>3
tcattgcactccagagagaagagatccagttccaccgaccagaacacagatgcaagtttc
caaacccaatcaaaagaggaagagatagggagtctacctgaaaaagaattcagagtaatg
>4
gatcaataatgaataatgcaataacagatcaaaagaactctggagggaaacaacagtaga
ggcatgagaaaatacctgaggagataatagttgaaattttctctaaaatggggaaggaaa
atcctaagacatacattaatcaaattaatgaagaccaaacacaaagaacaaatattaaag
TTTTTTTTAATAAATGCCAATCTGTTTATGACTTAACTTGTCANNNNNNNNNNNNNNNNN
NNNNNNNNANNCCCTNNNNNNNNACTTCAGACAATAATGTTTTTTTAAAACCAGTCTAGT
TTCTTGGACTTCTAGTTGGATGGCTTCACCGACTTGAAGGACGTGAGTTTGAGTAAGTTC
CAAGAGTTAGTGATGGACAGGGAAGCCCGGTGTGCTGCAGTCCCTGGGGTGGCAAAGAGT

希望得到每一条染色体N的pos的起始位置，终止位置，长度以及中的Gap(N又称为Gap区域)的总长及总数目，输出结果为：

test.fa.pos:

ID=>2   180     182     3
ID=>4   223     247     25
ID=>4   249     250     2
ID=>4   255     262     8

test.fa.stat:

Total_gap_num=4,Total_gap_len=38

二、用perl的相应的程序如下：

#/user/bin/perl -w
use strict;
unless(@ARGV==1){
die"Usage:perl $0 <input.fa>\n";
}
my($infile)=@ARGV;
open IN,$infile||die"error:can't open infile:$infile";
my $outfile1=$infile."_out";
my $outfile2=$infile."_stat";
open OUT,">$outfile1"||die$!;
open OUTT,">$outfile2"||die$!;
$/=">";<IN>;
my $start=0;
my $skip=0;
my $step;
my $len=1;
my $stop;
my $end;
my $total_len=0;
my $number=0;
my $num_1bp=0;
my $line;
my $i;
while(my $seq=<IN>)
{
if(index($seq,"N")!=-1)
{#if-1
my $id=$1 if($seq=~/^(\S+)/);
chomp $seq;
$seq=~s/^.+?\n//;
$seq=~s/\s//g;
if(index($seq,"N")==-1)
{
last;
}
$step=0;
$stop=1;
$start=index($seq,"N",$step)+1;
$step=$start-1;
$skip=$step;
print "start=$start\tstep=$step\tskip=$skip\n";
while($stop)
{#while -2
$skip=index($seq,"N",$step+1);
print "in while:skip=$skip\tstep=$step\n";
if($skip==($step+1))
{#if skip (49)
print "in-while-if:skip=$skip\tstep=$step\n";
$len++;
$step++;
next;
}else{
print "in-while-else:skip=$skip\tstep=$step\n";
if($skip!=-1)
{#if skip != -1 (55)
print "else-if:skip=$skip\tstep=$step\n";
if($len!=1){
$end=$start+$len-1;
}
else{
$num_1bp++;
$end=$start;
}
$total_len+=$len;
$number++;
print OUT"if-$id\t$start\t$end\t$len\n";


$step=$skip;
$start=$skip+1;
$len=1;
}else{
print "else-else:skip=$skip\tstep=$step\n";
if($len!=1){
$end=$start+$len-1;
}
else{
$num_1bp++;
$end=$start;
}
$total_len+=$len;
$number++;
print OUT"else-$id\t$start\t$end\t$len\n";
$stop=0;
$len=1;


}#if-else- (56)
}#if-else- (49)
}#while -2
       }#if-1
}#while 
print OUTT "total_length\t $total_len\ngap_number\t$number\n1bp_gap_number\t$num_1bp\n";
$/="\n";
close IN;
close OUT;

三、用python编写的程序如下：

#-*- coding=utf-8 -*-
#输出gap的起始位置，终止位置，长度等位置信息
import os,sys
import re


class Fasta():
    def __init__(self,name,sequence):
        self.name=name
        self.sequence=sequence


def process_fasta(infile):
    reader=infile.readlines()
    index=0
    increace=[]
    for line in reader:
        line=line.strip()
        if line.startswith('>'):
            if index >=1:
                 increace.append(instance)
            id=line
            seq=''
            index += 1
        else:
            seq += line
            instance=Fasta(id,seq)
    increace.append(instance)
    return increace


def find_N(List):
    gap_num=0
    gap_len=0
    for t in List:
        str1=t.sequence
        start=0
        end=0
        length=1
        if(str1.find('N') != -1):
            indel = str1.find('N',start)
            start = indel
            step = start 
            skip = step
            flag=True
            N_array=re.split('[N+]{1,}',str1)
            while(flag):
                skip=str1.find('N',step+1)
                if(skip - 1 == step):
                    #前后两次查找的N的index相差1，说明N是连续的
                    step += 1
                    length +=1
                    continue 
                else:
                    #前后两次index相差不为1，说明N之间出现了其他碱基
                    if (skip != -1):
                        #说明后面还有N
                        end = bool(length !=1) and start+length -1 or start
                        step=skip
                        outfile1.write("ID=%s\t%d\t%d\t%d\n" %(t.name,start,end,length))
                        length=1
                        start=step
                    else:
                        #说明后面已经没有N了
                        end = bool(length !=1) and start+length -1 or start
                        outfile1.write("ID=%s\t%d\t%d\t%d\n" %(t.name,start,end,length))
                        length=1                           
                        flag=False
            gap_len += str1.count('N')
            gap_num += len(N_array) -1
    outfile2.write("Total_gap_num=%d,Total_gap_len=%d\n" %(gap_num,gap_len))
    
if __name__ == '__main__':
    infile=open(sys.argv[1],'r')
    outfile1=open(sys.argv[1]+'.pos','w')
    outfile2=open(sys.argv[1]+'.stat','w')


    List=process_fasta(infile)
    find_N(List) 


    infile.close()                           
    outfile1.close()
    outfile2.close()

四、总结：

      编程思路请见下面的逻辑图