Question

Objective: Practice Displaying Output with print Function, Comments, Variable, Reading Input from the Keyboard, format output, if statement, if-else statement, loop structure. import, functions, file handling. and string methods. Lab Description: You are given a file containing protein sequences with the task of finding motifs. Motifs are certain patterns of amino acids that appear many times in protein sequences that act as indictors or markers for special regions, genes, mutations, etc. An example of what this file will look like is below: >ENSG00000035141 ENST00000037869 MAELQOLRVQEAVESMVKSLERENIRKMQGLMFRCSASCCEDSQASMKOVHOCIERCHVP LAQAQALVTSELEKFODRLARCTMHCNDKAKDSIDAGSKELQVKOQLDSCVTKCVDDHMH LIPTMTKKMKEALLSIGK >ENSG00000003137ENST00000001146 MLFEGLDLVSALATLAACLVSVTLLLAVSQQLWOLRWAATRDKSCKLIPKGSMGFPLIG ETGHWLLOGSGFOSSRREKYGNVEKTHLLGRPLIRVTGAENVRKILMGEHHLVSTEWPRS TRMLLGPNTVSNSIGDIHRNKRKVFSKIFSHEALESYLPKIQLVIQDTLRAWSSHPEAIN VYQEAQKLTFRMAIR VLLGFSIPEEDLGHLFEVYQOFVDNVFSLPVDLPFSGYRRGIQAR QILOKGLEKAIREKLOCTOGKDYLDALDLLIESSKEHGKEMTMQELKDGTLELIFAAYAT TASASTSLIMQLLKHPTVLEKLRDELRAHGILHSGGCPCEGTLRLDTLSGLRYLDCVIKE VMRLFTPISGGYRTVLOTFELDGFQIPKGWSVMYSIRDTHDTAPVFKDVNVFDPDRESOA RSED DGRFHYLPFOOOVRTCLGKHLAKLFLKVLAVELASTSRFELATRTEPRITLVPVL HPVDGLSVKFFGLDSNONEILPETEAMLSATV These lines: ENSGO000003514 HENSTOOO00037869 >ENSGO0000003137ENSTODO00001146 Are the sequence names. They start with what follows is the protein sequence itsell You are given two files to read motifs x and human as chr2 partial.xl. The first file contains a list of motifs that you are to search for. The length of the motif is variable. The second file contains the protein sequences

in Python

Answer 1

# Open the Motifs file - Give the correct file name for Motifs  here.
motiffile=open("C:\Tmp\Motifs.txt","r")

#list to store the motifs file pointers
motiflist=[]

#list to store the motifs names
motifnames=[]

#list to store counts of each motif
motifcounts=[]

#read motifs file
for motif in motiffile:
    motif=motif.rstrip("\n")
    if (motif and motif.strip()):
        ## change path as you wish
        fname="C:\Tmp\motif"+motif.rstrip("\n")+".txt"
        motiflist.append(open(fname,"w+"))
        motifnames.append(motif)

# close the motiflist file now
motiffile.close()
motifcounts=[0]*len(motifnames)


# Read the sequence file
seqfile = open("/nfshome/raltobasei/public_html/1170/public/human_aa_chr2_partial.txt","r")

# for each line check if the pattern matches the motif
for line in seqfile:
    line=line.rstrip("\n")
    if line.startswith(">"):
       seqline=line
       continue
    else:
        i=0
        for motif in motifnames:
                pos=line.find(motif)
                # if motif is found then write sequences and the line
                j=motifcounts[i]
                if (pos!=-1):
                    nline = line[0:pos - 1] + " " + motif + " " + line[pos + len(motif):]
                    fname = motiflist[i];
                    fname.write(seqline + "\n")
                    fname.write(nline+"\n")
                    j=j+1
                motifcounts[i] = j    # update counts
                i=i+1


## write counts to files
k=0
for motiffile in motiflist:
    motiffile.write("# of motifs for " + motifnames[k] +" :" + str(motifcounts[k]))
    k=k+1
    motiffile.close()

## close the sequential file 
seqfile.close()