How to link two python scripts

[Larz60+]

Actually a few more hours, forgot I had a doctor's preventative maintenance appointment, and just got back.

[Larz60+]

Here is the final program. It Sorts and Selects in one module.

It is written so that you can run it from the command line using:

1	python SelsectAndSortFasta infilename outfilename min_seq_size

Or, you can import it into another program and call from within similar to:

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# Add following import at top of your program import SelectAndSortFasta   # In your initialization routine, add: # If a class:     self.sasf = SelectAndSortFasta.SelectAndSortFasta() # If just a function:     sasf = SelectAndSortFasta.SelectAndSortFasta()   # Then when you want to run a file     sasf.sort_fasta_file(infile, outfile, minlen)

Here's the code:

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from operator import itemgetter import sys     class SelectAndSortFasta:     """     Sort in decreasing size order     """     def __init__(self):         self.headers = []         self.infile = None         self.outfile = None         self.minlen = 0       def ExtractHeader(self):         """         Reads all headers, saves starting file position, header, and size in self.headers         :return: None         """         seqlen = 0         this_header = []         firstseq = True           f = open(self.infile, 'r')         f.seek(0, 2)         file_size = f.tell()         f.seek(0)         while True:             fptr = f.tell()             if fptr == file_size:                 break             line = None             line = f.readline()             line = line.strip()               # skip empty lines             if len(line) > 0:                 # print(f'line len: {len(line)}')                 if line.startswith('>'):                     if firstseq:                         firstseq = False                     else:                         this_header.append(seqlen)                         self.headers.append(this_header)                       seqlen = 0                     this_header = []                     this_header.append(fptr)                     this_header.append(line)                 else:                     seqlen += len(line)         this_header.append(seqlen)         self.headers.append(this_header)         f.close()         # This is the sort routine, sorts on column 2 (size) of self.headers, in reverse order         self.headers.sort(key=itemgetter(2), reverse=True)         self.show_header()       def show_header(self):         """         display self.headers list         :return: None         """         for item in self.headers:             print(f'File ptr: {item[0]}, Size: {item[2]}, Header: {item[1]}')       def write_outfile(self):         """         Reads self.headers (which is sorted in reverse size order,         seeks to that record in the inout file (from file pointer which i in column 0 of self.headers)         and writes the output file         :return:         """         with open(self.infile) as f, open(self.outfile, 'w') as fo:             for item in self.headers:                 # Ignore entry if too small                 if item[2] < minlen:                     continue                 f.seek(item[0], 0)                 fo.write(f.readline())                 while True:                     buf = f.readline()                     if buf.startswith('>'):                         break                     fo.write(buf)       def sort_fasta_file(self, infile, outfile, minlen):         """         Launch pad for sort and select program         :param infile: Name of input fasta file         :param outfile: Name of output fasta file         :param minlen: Minimun size of output record. (smaller inut records are ignored)         :return: None         """         self.infile = infile         self.outfile = outfile         self.minlen = minlen         self.ExtractHeader()         self.write_outfile()     if __name__ == '__main__':     # Test routine     srtf = SelectAndSortFasta()     numargs = len(sys.argv)     if numargs > 1:         infile = sys.argv[1]         outfile = sys.argv[2]         minlen = sys.argv[3]     else:         infile = 'data/fasta/AINZ01/AINZ01.1.fsa_nt'         outfile = 'data/fasta/AINZ01/AINZ01sorted.1.fsa_nt'         minlen = 1000       srtf.sort_fasta_file(infile, outfile, minlen)

You may want to supress the printout on line 57 (self.show_header())

[berthenet]

Thanks !

I get a similar error than before:

Error:
 File "SelectAndSortFasta.py", line 65
    print(f'File ptr: {item[0]}, Size: {item[2]}, Header: {item[1]}')
                                                                   ^
SyntaxError: invalid syntax

I am assuming it's again because of my version of python. I'll ask the admin from the cluster I work on if they can install python 3 instead of the 2.6 I am working with at the moment, because it looks like I am going to get lots of these errors.

In the meantime, can you help me correcting the print syntax so that I can check if the script is doing what I wanted?

Thanks again!

[Larz60+]

I'm sorry, I've got in the habit of using f-string because I really like it.
It was introduced in python 3.6
change to:

1	print('File ptr: {}, Size: {}, Header: {}'.format(item[0], item[2], item[1]))

or install python 3.6.4

Python 2.6 is so old!
maintenance for 2.7 and below is scheduled to stop in less than 2 years.
F-string won't work with anything less than 3.6, but 3.7 is coming out soon, maybe the admin can wait for that,
It's going to have some fantastic async additions.

[berthenet]

I contacter the admin, to see if I can get access to a more recent version of python, but I don't know how fast they are to respond.

I fixed this line now, so it's running.

However my output file is created, but is completely empty. I have this on the screen:

Output:
$ python SelectAndSortFasta.py 2013_1056H.contigs.fa 2013_1056HTestOutput 1000
File ptr: 0, Size: 550068, Header: >NODE_1_length_550068_cov_488.448
File ptr: 559270, Size: 190085, Header: >NODE_2_length_190085_cov_532.242
File ptr: 752558, Size: 153922, Header: >NODE_3_length_153922_cov_529.57
File ptr: 909079, Size: 114954, Header: >NODE_4_length_114954_cov_494.41
File ptr: 1025982, Size: 106564, Header: >NODE_5_length_106564_cov_477.255
File ptr: 1134357, Size: 103116, Header: >NODE_6_length_103116_cov_541.733
File ptr: 1239226, Size: 102698, Header: >NODE_7_length_102698_cov_564.458

I didn't copy and paste the whole thing, but it goes till the end of my original fasta, all the contigs including those less than 1000bp.

I am not sure what goes wrong, as I don't have an error showing.

[Larz60+]

How are you running it?
I just ran it and it worked fine

Try to modify the input and output in the else part
of the code at the bottom:

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if __name__ == '__main__':     sf = SplitFasta()     numargs = len(sys.argv)     if numargs > 1:         infile = sys.argv[1]         outfile = sys.argv[2]         minlen = sys.argv[3]     else:         infile = '2013_1056H.contigs.fa'         outfile = '2013_1056HTestOutput.fa'         minlen = 1000     sf.split_file(infile, outfile, int(minlen))     sf.show_seq_out()

[Larz60+]

And run like:

1	python SelectAndSortFasta.py

without arguments. Perhaps there's an issue with command line arguments

[Larz60+]

I'm going to have to call it quits soon. Getting pretty sleepy.
I'll wait a few minutes to see if you have success.

[berthenet]

Okay I've done the modifications in the infile and outfile part, and run it without arguments. It does work now.

So I think it is safe to assume the issue comes from the command line arguments.

[Larz60+]

It worked like a charm with new file