Programming Language

[Desai]

Dear Friends,

I am newbie in Biology field, I dont know how to use progrmming language. My query is I have one file which I want to convert in simple file which should be without white space, line breaker and without any space, e.g I have attached my file with this query. I need some script or some command.

Thank you for viewing replying in advance,
Have great day ahead

[omerfaruk]

you can use string replace in python

[Desai]

Originally Posted by omerfaruk

you can use string replace in python

Hey, thanks for your help but as I said I dont know how to use python. Could you do it for me? Thank you for giving your time?

[SNPsaurus]

at a unix command line:
awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < test.txt

[Desai]

Originally Posted by SNPsaurus

at a unix command line:
awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < test.txt

Hey friend Thank you for reply. However still it dosent working for me, the script which you had send that was just for the that test.txt file not working with my original problem file . I am here attaching second file which is exact format that I want. Please help me, Its very urgent. I have to analysis thousands files so I can not waste time behind erasing every space.

Thanks again for your help.

[omerfaruk]

make eol_format.py executable with chmod a+x eol_format.py

run as:

python eol_format.py test.txt (put a space after .py and write file path/name)

this will write you a file with test.txt.edit.txt.

Code is pretty straightforward, you can read what it does and change by checking syntax by googling.

[wolma]

omerfaruk's script works though it doesn't really show the beauty of the python language, so here is a more elegant version of it:

import sys

with open(sys.argv[1], 'r') as infile:
with open(sys.argv[2], 'w') as outfile:
for line in infile:
if line[0] != '>':
line = line.strip()
outfile.write(line)

copy this exactly as it is formatted to a text editor, save it under whatevername.py, then from the command line run it like this:

python nameofscript input_file output_file

Recommendation: if you consider learning one programming language, choose python.

Cheers,
Wolfgang

[wolma]

great, this forum removes significant whitespace

so here's the script again as an attachment with correct formatting.

[Desai]

Tons of thank you omerfaruk and wolma. It really helped me. I did know about python much but now I would like to learn because of beauty of python, thanks again wolma and omerfaruk.

Have great time ahead,

[dpryan]

@wolma: You need to just use the "code" tags:

import sys

with open(sys.argv[1], 'r') as infile:
with open(sys.argv[2], 'w') as outfile:
for line in infile:
    if line[0] != '>':
        line = line.strip()
    outfile.write(line)

[Brian Bushnell]

Originally Posted by dpryan

@wolma: You need to just use the "code" tags:

Or a language where indent level is not syntactically relevant *cough*

Just kidding, I think Python is a good choice in this case.

[wolma]

@dpryan: Thanks for the hint (should have read the FAQ before complaining) !

I'll give it a try with a slightly enhanced version of my previous suggestion. This one will work correctly with multisequence fasta files (my first version would not put a line break between the end of the previous sequence and a new title line):

import sys

record_sep = ''
with open(sys.argv[1], 'r') as infile:
    with open(sys.argv[2], 'w') as outfile:
        for line in infile:
            if line[0] == '>':
                outfile.write(record_sep)
                record_sep = '\n'
            else:
                line = line.strip()
            outfile.write(line)

[westerman]

Originally Posted by wolma

great, this forum removes significant whitespace

Only if you consider whitespace to be significant. :-)