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basic problem on loop python

Hello everyone I have a problem with my code on python. The goal is to write a text file of the name of organisms which has cdna file. The problem is that I have a file that looks like this:

./anas_platyrhynchos/pep:
-rwxrwxr-x    1 ftp      ftp      10561439 May 07 11:02 Anas_platyrhynchos.BGI_duck_1.0.pep.abinitio.fa.gz
-rwxrwxr-x    1 ftp      ftp       5762174 May 07 10:34 Anas_platyrhynchos.BGI_duck_1.0.pep.all.fa.gz
-rwxrwxr-x    1 ftp      ftp           140 May 09 16:17 CHECKSUMS
-rwxrwxr-x    1 ftp      ftp          3065 May 07 11:02 README

./ancestral_alleles:
-rwxrwxr-x    1 ftp      ftp      590904827 May 16 09:58 callithrix_jacchus_ancestor_C_jacchus3.2.1_e86.tar.gz
-rwxrwxr-x    1 ftp      ftp      848229938 May 16 09:59 chlorocebus_sabaeus_ancestor_ChlSab1.1_e86.tar.gz
-rwxrwxr-x    1 ftp      ftp      767402743 May 16 09:59 gorilla_gorilla_ancestor_gorGor3.1_e86.tar.gz
-rwxrwxr-x    1 ftp      ftp      845762805 May 16 09:58 homo_sapiens_ancestor_GRCh38_e86.tar.gz
-rwxrwxr-x    1 ftp      ftp      791833177 May 16 09:59 macaca_mulatta_ancestor_Mmul_8.0.1_e86.tar.gz
-rwxrwxr-x    1 ftp      ftp      812588425 May 16 09:59 pan_troglodytes_ancestor_CHIMP2.1.4_e86.tar.gz
-rwxrwxr-x    1 ftp      ftp      804459736 May 16 09:59 papio_anubis_ancestor_PapAnu2.0_e86.tar.gz
-rwxrwxr-x    1 ftp      ftp      799305351 May 16 09:59 pongo_abelii_ancestor_PPYG2_e86.tar.gz

./anolis_carolinensis:
drwxrwxr-x    2 ftp      ftp          4096 May 09 16:17 cdna
drwxrwxr-x    2 ftp      ftp          4096 May 09 16:17 cds
drwxrwxr-x    2 ftp      ftp          8192 May 09 16:17 dna
drwxrwxr-x    2 ftp      ftp          4096 May 09 16:17 dna_index
drwxrwxr-x    2 ftp      ftp          4096 May 09 16:17 ncrna
drwxrwxr-x    2 ftp      ftp          4096 May 09 16:17 pep

./anolis_carolinensis/cdna:
-rwxrwxr-x    1 ftp      ftp      43505585 May 07 22:42 Anolis_carolinensis.AnoCar2.0.cdna.abinitio.fa.gz
-rwxrwxr-x    1 ftp      ftp      16313984 May 07 22:21 Anolis_carolinensis.AnoCar2.0.cdna.all.fa.gz
-rwxrwxr-x    1 ftp      ftp           138 May 09 16:17 CHECKSUMS
-rwxrwxr-x    1 ftp      ftp          3153 May 07 22:42 README

./anolis_carolinensis/cds:
-rwxrwxr-x    1 ftp      ftp      10413036 May 07 22:21 Anolis_carolinensis.AnoCar2.0.cds.all.fa.gz
-rwxrwxr-x    1 ftp      ftp            75 May 09 16:17 CHECKSUMS
-rwxrwxr-x    1 ftp      ftp          2501 May 07 22:42 README

So for this example I have to write only anolis_carolinensis.
Here is my code so far:

def separate(s):
    """This function gets a text file withe some data and "sifts" only the
        require information"""

    index = 0 #Initialize the index of the text.
    while(True):        
        if not s: #If the file is over.
            break
        current =  s.find("cdna.all.fa.gz",index) #The "location of that particular string"
        if current > -1: #If indeed the "cdna..." was found           
            root = s.rfind("./",0,current) #Goes back to find the organism.
            organ.write(s[root+2: s.find(":",root)]+"/\n") #Writes the organisms into a text file.
            index = current #Updates the index to the current position.
            s = s[index:] #Promotes the text
        else: #If there is no more "cdna...".
            break

data =  open('Content.txt','r') #The file of all the data.
organ = open ('ftp.txt','w') #A file for the "ftp"
s = data.read() 
separate(s)
data.close()
organ.close()

The problem is that it doesn't write all the organisms - it skips some of them...
I guess it's because of the index, I'v tried to change it but not successfully.

Thanks!!

python
• 359 views • link
updated by lakhujanivijay lakhujanivijay • written by elisheva elisheva

What are you expecting as output? Can you provide an example?

• 0 views • link
written by lakhujanivijay lakhujanivijay

for the file I had upload The output should be "anolis_carolinensis" cause it's has the "Anolis_carolinensis.AnoCar2.0.cdna.all.fa.gz" file.

• 0 views • link
written by elisheva elisheva

data.read() just read string one by one, you should use data.readlines() to read all the data. of course, you did not provide the example that you hope to get. Maybe what I said was worry.

• 0 views • link
written by Ben Ben

But readlines() returns a list - I don't think it will be helpfull.... The problem is in the function....

• 0 views • link
written by elisheva elisheva

I really do not understand what you want to get.

• 0 views • link
written by Ben Ben

root , organ , current! such variable names, seriously ?

• 0 views • link
written by lakhujanivijay lakhujanivijay

2 answers

Code:

fh = open('Content.txt')
oh = open('ftp.txt', 'w')
for line in fh:
    if line.startswith('./'):
        organism = line.split('/')[1].rstrip(':')
    if 'cdna.all.fa' in line:
        oh.write(organism + '\n')
fh.close()
oh.close()

ftp.txt:

anolis_carolinensis
• 0 views • link
written by Andrzej Zielezinski Andrzej Zielezinski

fh = open('Content.txt')

oh = open('ftp.txt', 'w')

for line in fh:

if line.startswith('./') and 'cdna' in line:

    oh.write(line.split('/')[1].rstrip(':') + '\n')

fh.close()

oh.close()

• 0 views • link
written by Ben Ben

But what if cdna directory is empty or it has only *.cdna.abinitio.fa.gz file (not cdna.all.fa as @elisheva requested) :P

• 0 views • link
written by Andrzej Zielezinski Andrzej Zielezinski

Perhaps I missed something, but can't we fully ignore the directory structure and just search for files ending in cdna.all.fa.gz, then getting the species name out of that filename Anolis_carolinensis.AnoCar2.0.cdna.all.fa.gz?

• 0 views • link
written by WouterDeCoster WouterDeCoster

Yes. you'r right. It just that I thought about it as a path...

• 0 views • link
written by elisheva elisheva

Just in case if Python is not really required, you can just

grep "cdna.all.fa" <your_file> | awk '{print $9}' | cut -d "." -f1
• 0 views • link
written by lakhujanivijay lakhujanivijay

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